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+anno_start	anno_end	anno_text	entity_type	sentence	section
+29	45	Escherichia coli	species	Structural insights into the Escherichia coli lysine decarboxylases and molecular determinants of interaction with the AAA+ ATPase RavA	TITLE
+46	67	lysine decarboxylases	protein_type	Structural insights into the Escherichia coli lysine decarboxylases and molecular determinants of interaction with the AAA+ ATPase RavA	TITLE
+119	130	AAA+ ATPase	protein_type	Structural insights into the Escherichia coli lysine decarboxylases and molecular determinants of interaction with the AAA+ ATPase RavA	TITLE
+131	135	RavA	protein	Structural insights into the Escherichia coli lysine decarboxylases and molecular determinants of interaction with the AAA+ ATPase RavA	TITLE
+4	13	inducible	protein_state	The inducible lysine decarboxylase LdcI is an important enterobacterial acid stress response enzyme whereas LdcC is its close paralogue thought to play mainly a metabolic role.	ABSTRACT
+14	34	lysine decarboxylase	protein_type	The inducible lysine decarboxylase LdcI is an important enterobacterial acid stress response enzyme whereas LdcC is its close paralogue thought to play mainly a metabolic role.	ABSTRACT
+35	39	LdcI	protein	The inducible lysine decarboxylase LdcI is an important enterobacterial acid stress response enzyme whereas LdcC is its close paralogue thought to play mainly a metabolic role.	ABSTRACT
+56	71	enterobacterial	taxonomy_domain	The inducible lysine decarboxylase LdcI is an important enterobacterial acid stress response enzyme whereas LdcC is its close paralogue thought to play mainly a metabolic role.	ABSTRACT
+72	99	acid stress response enzyme	protein_type	The inducible lysine decarboxylase LdcI is an important enterobacterial acid stress response enzyme whereas LdcC is its close paralogue thought to play mainly a metabolic role.	ABSTRACT
+108	112	LdcC	protein	The inducible lysine decarboxylase LdcI is an important enterobacterial acid stress response enzyme whereas LdcC is its close paralogue thought to play mainly a metabolic role.	ABSTRACT
+43	51	decamers	oligomeric_state	A unique macromolecular cage formed by two decamers of the Escherichia coli LdcI and five hexamers of the AAA+ ATPase RavA was shown to counteract acid stress under starvation.	ABSTRACT
+59	75	Escherichia coli	species	A unique macromolecular cage formed by two decamers of the Escherichia coli LdcI and five hexamers of the AAA+ ATPase RavA was shown to counteract acid stress under starvation.	ABSTRACT
+76	80	LdcI	protein	A unique macromolecular cage formed by two decamers of the Escherichia coli LdcI and five hexamers of the AAA+ ATPase RavA was shown to counteract acid stress under starvation.	ABSTRACT
+90	98	hexamers	oligomeric_state	A unique macromolecular cage formed by two decamers of the Escherichia coli LdcI and five hexamers of the AAA+ ATPase RavA was shown to counteract acid stress under starvation.	ABSTRACT
+106	117	AAA+ ATPase	protein_type	A unique macromolecular cage formed by two decamers of the Escherichia coli LdcI and five hexamers of the AAA+ ATPase RavA was shown to counteract acid stress under starvation.	ABSTRACT
+118	122	RavA	protein	A unique macromolecular cage formed by two decamers of the Escherichia coli LdcI and five hexamers of the AAA+ ATPase RavA was shown to counteract acid stress under starvation.	ABSTRACT
+26	44	pseudoatomic model	evidence	Previously, we proposed a pseudoatomic model of the LdcI-RavA cage based on its cryo-electron microscopy map and crystal structures of an inactive LdcI decamer and a RavA monomer.	ABSTRACT
+52	61	LdcI-RavA	complex_assembly	Previously, we proposed a pseudoatomic model of the LdcI-RavA cage based on its cryo-electron microscopy map and crystal structures of an inactive LdcI decamer and a RavA monomer.	ABSTRACT
+80	104	cryo-electron microscopy	experimental_method	Previously, we proposed a pseudoatomic model of the LdcI-RavA cage based on its cryo-electron microscopy map and crystal structures of an inactive LdcI decamer and a RavA monomer.	ABSTRACT
+105	108	map	evidence	Previously, we proposed a pseudoatomic model of the LdcI-RavA cage based on its cryo-electron microscopy map and crystal structures of an inactive LdcI decamer and a RavA monomer.	ABSTRACT
+113	131	crystal structures	evidence	Previously, we proposed a pseudoatomic model of the LdcI-RavA cage based on its cryo-electron microscopy map and crystal structures of an inactive LdcI decamer and a RavA monomer.	ABSTRACT
+138	146	inactive	protein_state	Previously, we proposed a pseudoatomic model of the LdcI-RavA cage based on its cryo-electron microscopy map and crystal structures of an inactive LdcI decamer and a RavA monomer.	ABSTRACT
+147	151	LdcI	protein	Previously, we proposed a pseudoatomic model of the LdcI-RavA cage based on its cryo-electron microscopy map and crystal structures of an inactive LdcI decamer and a RavA monomer.	ABSTRACT
+152	159	decamer	oligomeric_state	Previously, we proposed a pseudoatomic model of the LdcI-RavA cage based on its cryo-electron microscopy map and crystal structures of an inactive LdcI decamer and a RavA monomer.	ABSTRACT
+166	170	RavA	protein	Previously, we proposed a pseudoatomic model of the LdcI-RavA cage based on its cryo-electron microscopy map and crystal structures of an inactive LdcI decamer and a RavA monomer.	ABSTRACT
+171	178	monomer	oligomeric_state	Previously, we proposed a pseudoatomic model of the LdcI-RavA cage based on its cryo-electron microscopy map and crystal structures of an inactive LdcI decamer and a RavA monomer.	ABSTRACT
+15	39	cryo-electron microscopy	experimental_method	We now present cryo-electron microscopy 3D reconstructions of the E. coli LdcI and LdcC, and an improved map of the LdcI bound to the LARA domain of RavA, at pH optimal for their enzymatic activity.	ABSTRACT
+40	58	3D reconstructions	evidence	We now present cryo-electron microscopy 3D reconstructions of the E. coli LdcI and LdcC, and an improved map of the LdcI bound to the LARA domain of RavA, at pH optimal for their enzymatic activity.	ABSTRACT
+66	73	E. coli	species	We now present cryo-electron microscopy 3D reconstructions of the E. coli LdcI and LdcC, and an improved map of the LdcI bound to the LARA domain of RavA, at pH optimal for their enzymatic activity.	ABSTRACT
+74	78	LdcI	protein	We now present cryo-electron microscopy 3D reconstructions of the E. coli LdcI and LdcC, and an improved map of the LdcI bound to the LARA domain of RavA, at pH optimal for their enzymatic activity.	ABSTRACT
+83	87	LdcC	protein	We now present cryo-electron microscopy 3D reconstructions of the E. coli LdcI and LdcC, and an improved map of the LdcI bound to the LARA domain of RavA, at pH optimal for their enzymatic activity.	ABSTRACT
+96	108	improved map	evidence	We now present cryo-electron microscopy 3D reconstructions of the E. coli LdcI and LdcC, and an improved map of the LdcI bound to the LARA domain of RavA, at pH optimal for their enzymatic activity.	ABSTRACT
+116	120	LdcI	protein	We now present cryo-electron microscopy 3D reconstructions of the E. coli LdcI and LdcC, and an improved map of the LdcI bound to the LARA domain of RavA, at pH optimal for their enzymatic activity.	ABSTRACT
+121	129	bound to	protein_state	We now present cryo-electron microscopy 3D reconstructions of the E. coli LdcI and LdcC, and an improved map of the LdcI bound to the LARA domain of RavA, at pH optimal for their enzymatic activity.	ABSTRACT
+134	145	LARA domain	structure_element	We now present cryo-electron microscopy 3D reconstructions of the E. coli LdcI and LdcC, and an improved map of the LdcI bound to the LARA domain of RavA, at pH optimal for their enzymatic activity.	ABSTRACT
+149	153	RavA	protein	We now present cryo-electron microscopy 3D reconstructions of the E. coli LdcI and LdcC, and an improved map of the LdcI bound to the LARA domain of RavA, at pH optimal for their enzymatic activity.	ABSTRACT
+158	168	pH optimal	protein_state	We now present cryo-electron microscopy 3D reconstructions of the E. coli LdcI and LdcC, and an improved map of the LdcI bound to the LARA domain of RavA, at pH optimal for their enzymatic activity.	ABSTRACT
+0	10	Comparison	experimental_method	Comparison with each other and with available structures uncovers differences between LdcI and LdcC explaining why only the acid stress response enzyme is capable of binding RavA. We identify interdomain movements associated with the pH-dependent enzyme activation and with the RavA binding.	ABSTRACT
+46	56	structures	evidence	Comparison with each other and with available structures uncovers differences between LdcI and LdcC explaining why only the acid stress response enzyme is capable of binding RavA. We identify interdomain movements associated with the pH-dependent enzyme activation and with the RavA binding.	ABSTRACT
+86	90	LdcI	protein	Comparison with each other and with available structures uncovers differences between LdcI and LdcC explaining why only the acid stress response enzyme is capable of binding RavA. We identify interdomain movements associated with the pH-dependent enzyme activation and with the RavA binding.	ABSTRACT
+95	99	LdcC	protein	Comparison with each other and with available structures uncovers differences between LdcI and LdcC explaining why only the acid stress response enzyme is capable of binding RavA. We identify interdomain movements associated with the pH-dependent enzyme activation and with the RavA binding.	ABSTRACT
+124	151	acid stress response enzyme	protein_type	Comparison with each other and with available structures uncovers differences between LdcI and LdcC explaining why only the acid stress response enzyme is capable of binding RavA. We identify interdomain movements associated with the pH-dependent enzyme activation and with the RavA binding.	ABSTRACT
+174	178	RavA	protein	Comparison with each other and with available structures uncovers differences between LdcI and LdcC explaining why only the acid stress response enzyme is capable of binding RavA. We identify interdomain movements associated with the pH-dependent enzyme activation and with the RavA binding.	ABSTRACT
+234	246	pH-dependent	protein_state	Comparison with each other and with available structures uncovers differences between LdcI and LdcC explaining why only the acid stress response enzyme is capable of binding RavA. We identify interdomain movements associated with the pH-dependent enzyme activation and with the RavA binding.	ABSTRACT
+278	282	RavA	protein	Comparison with each other and with available structures uncovers differences between LdcI and LdcC explaining why only the acid stress response enzyme is capable of binding RavA. We identify interdomain movements associated with the pH-dependent enzyme activation and with the RavA binding.	ABSTRACT
+0	27	Multiple sequence alignment	experimental_method	Multiple sequence alignment coupled to a phylogenetic analysis reveals that certain enterobacteria exert evolutionary pressure on the lysine decarboxylase towards the cage-like assembly with RavA, implying that this complex may have an important function under particular stress conditions.	ABSTRACT
+41	62	phylogenetic analysis	experimental_method	Multiple sequence alignment coupled to a phylogenetic analysis reveals that certain enterobacteria exert evolutionary pressure on the lysine decarboxylase towards the cage-like assembly with RavA, implying that this complex may have an important function under particular stress conditions.	ABSTRACT
+84	98	enterobacteria	taxonomy_domain	Multiple sequence alignment coupled to a phylogenetic analysis reveals that certain enterobacteria exert evolutionary pressure on the lysine decarboxylase towards the cage-like assembly with RavA, implying that this complex may have an important function under particular stress conditions.	ABSTRACT
+134	154	lysine decarboxylase	protein_type	Multiple sequence alignment coupled to a phylogenetic analysis reveals that certain enterobacteria exert evolutionary pressure on the lysine decarboxylase towards the cage-like assembly with RavA, implying that this complex may have an important function under particular stress conditions.	ABSTRACT
+191	195	RavA	protein	Multiple sequence alignment coupled to a phylogenetic analysis reveals that certain enterobacteria exert evolutionary pressure on the lysine decarboxylase towards the cage-like assembly with RavA, implying that this complex may have an important function under particular stress conditions.	ABSTRACT
+0	15	Enterobacterial	taxonomy_domain	Enterobacterial inducible decarboxylases of basic amino acids lysine, arginine and ornithine have a common evolutionary origin and belong to the α-family of pyridoxal-5′-phosphate (PLP)-dependent enzymes.	INTRO
+16	25	inducible	protein_state	Enterobacterial inducible decarboxylases of basic amino acids lysine, arginine and ornithine have a common evolutionary origin and belong to the α-family of pyridoxal-5′-phosphate (PLP)-dependent enzymes.	INTRO
+26	40	decarboxylases	protein_type	Enterobacterial inducible decarboxylases of basic amino acids lysine, arginine and ornithine have a common evolutionary origin and belong to the α-family of pyridoxal-5′-phosphate (PLP)-dependent enzymes.	INTRO
+44	49	basic	protein_state	Enterobacterial inducible decarboxylases of basic amino acids lysine, arginine and ornithine have a common evolutionary origin and belong to the α-family of pyridoxal-5′-phosphate (PLP)-dependent enzymes.	INTRO
+50	61	amino acids	chemical	Enterobacterial inducible decarboxylases of basic amino acids lysine, arginine and ornithine have a common evolutionary origin and belong to the α-family of pyridoxal-5′-phosphate (PLP)-dependent enzymes.	INTRO
+62	68	lysine	residue_name	Enterobacterial inducible decarboxylases of basic amino acids lysine, arginine and ornithine have a common evolutionary origin and belong to the α-family of pyridoxal-5′-phosphate (PLP)-dependent enzymes.	INTRO
+70	78	arginine	residue_name	Enterobacterial inducible decarboxylases of basic amino acids lysine, arginine and ornithine have a common evolutionary origin and belong to the α-family of pyridoxal-5′-phosphate (PLP)-dependent enzymes.	INTRO
+83	92	ornithine	residue_name	Enterobacterial inducible decarboxylases of basic amino acids lysine, arginine and ornithine have a common evolutionary origin and belong to the α-family of pyridoxal-5′-phosphate (PLP)-dependent enzymes.	INTRO
+145	153	α-family	protein_type	Enterobacterial inducible decarboxylases of basic amino acids lysine, arginine and ornithine have a common evolutionary origin and belong to the α-family of pyridoxal-5′-phosphate (PLP)-dependent enzymes.	INTRO
+157	179	pyridoxal-5′-phosphate	chemical	Enterobacterial inducible decarboxylases of basic amino acids lysine, arginine and ornithine have a common evolutionary origin and belong to the α-family of pyridoxal-5′-phosphate (PLP)-dependent enzymes.	INTRO
+181	184	PLP	chemical	Enterobacterial inducible decarboxylases of basic amino acids lysine, arginine and ornithine have a common evolutionary origin and belong to the α-family of pyridoxal-5′-phosphate (PLP)-dependent enzymes.	INTRO
+47	56	bacterium	taxonomy_domain	They counteract acid stress experienced by the bacterium in the host digestive and urinary tract, and in particular in the extremely acidic stomach.	INTRO
+5	18	decarboxylase	protein_type	Each decarboxylase is induced by an excess of the target amino acid and a specific range of extracellular pH, and works in conjunction with a cognate inner membrane antiporter.	INTRO
+57	67	amino acid	chemical	Each decarboxylase is induced by an excess of the target amino acid and a specific range of extracellular pH, and works in conjunction with a cognate inner membrane antiporter.	INTRO
+150	175	inner membrane antiporter	protein_type	Each decarboxylase is induced by an excess of the target amino acid and a specific range of extracellular pH, and works in conjunction with a cognate inner membrane antiporter.	INTRO
+23	33	amino acid	chemical	Decarboxylation of the amino acid into a polyamine is catalysed by a PLP cofactor in a multistep reaction that consumes a cytoplasmic proton and produces a CO2 molecule passively diffusing out of the cell, while the polyamine is excreted by the antiporter in exchange for a new amino acid substrate.	INTRO
+41	50	polyamine	chemical	Decarboxylation of the amino acid into a polyamine is catalysed by a PLP cofactor in a multistep reaction that consumes a cytoplasmic proton and produces a CO2 molecule passively diffusing out of the cell, while the polyamine is excreted by the antiporter in exchange for a new amino acid substrate.	INTRO
+69	72	PLP	chemical	Decarboxylation of the amino acid into a polyamine is catalysed by a PLP cofactor in a multistep reaction that consumes a cytoplasmic proton and produces a CO2 molecule passively diffusing out of the cell, while the polyamine is excreted by the antiporter in exchange for a new amino acid substrate.	INTRO
+134	140	proton	chemical	Decarboxylation of the amino acid into a polyamine is catalysed by a PLP cofactor in a multistep reaction that consumes a cytoplasmic proton and produces a CO2 molecule passively diffusing out of the cell, while the polyamine is excreted by the antiporter in exchange for a new amino acid substrate.	INTRO
+156	159	CO2	chemical	Decarboxylation of the amino acid into a polyamine is catalysed by a PLP cofactor in a multistep reaction that consumes a cytoplasmic proton and produces a CO2 molecule passively diffusing out of the cell, while the polyamine is excreted by the antiporter in exchange for a new amino acid substrate.	INTRO
+216	225	polyamine	chemical	Decarboxylation of the amino acid into a polyamine is catalysed by a PLP cofactor in a multistep reaction that consumes a cytoplasmic proton and produces a CO2 molecule passively diffusing out of the cell, while the polyamine is excreted by the antiporter in exchange for a new amino acid substrate.	INTRO
+245	255	antiporter	protein_type	Decarboxylation of the amino acid into a polyamine is catalysed by a PLP cofactor in a multistep reaction that consumes a cytoplasmic proton and produces a CO2 molecule passively diffusing out of the cell, while the polyamine is excreted by the antiporter in exchange for a new amino acid substrate.	INTRO
+278	288	amino acid	chemical	Decarboxylation of the amino acid into a polyamine is catalysed by a PLP cofactor in a multistep reaction that consumes a cytoplasmic proton and produces a CO2 molecule passively diffusing out of the cell, while the polyamine is excreted by the antiporter in exchange for a new amino acid substrate.	INTRO
+44	53	bacterial	taxonomy_domain	Consequently, these enzymes buffer both the bacterial cytoplasm and the local extracellular environment.	INTRO
+6	31	amino acid decarboxylases	protein_type	These amino acid decarboxylases are therefore called acid stress inducible or biodegradative to distinguish them from their biosynthetic lysine and ornithine decarboxylase paralogs catalysing the same reaction but responsible for the polyamine production at neutral pH.	INTRO
+65	74	inducible	protein_state	These amino acid decarboxylases are therefore called acid stress inducible or biodegradative to distinguish them from their biosynthetic lysine and ornithine decarboxylase paralogs catalysing the same reaction but responsible for the polyamine production at neutral pH.	INTRO
+78	92	biodegradative	protein_state	These amino acid decarboxylases are therefore called acid stress inducible or biodegradative to distinguish them from their biosynthetic lysine and ornithine decarboxylase paralogs catalysing the same reaction but responsible for the polyamine production at neutral pH.	INTRO
+124	136	biosynthetic	protein_state	These amino acid decarboxylases are therefore called acid stress inducible or biodegradative to distinguish them from their biosynthetic lysine and ornithine decarboxylase paralogs catalysing the same reaction but responsible for the polyamine production at neutral pH.	INTRO
+137	171	lysine and ornithine decarboxylase	protein_type	These amino acid decarboxylases are therefore called acid stress inducible or biodegradative to distinguish them from their biosynthetic lysine and ornithine decarboxylase paralogs catalysing the same reaction but responsible for the polyamine production at neutral pH.	INTRO
+234	243	polyamine	chemical	These amino acid decarboxylases are therefore called acid stress inducible or biodegradative to distinguish them from their biosynthetic lysine and ornithine decarboxylase paralogs catalysing the same reaction but responsible for the polyamine production at neutral pH.	INTRO
+258	268	neutral pH	protein_state	These amino acid decarboxylases are therefore called acid stress inducible or biodegradative to distinguish them from their biosynthetic lysine and ornithine decarboxylase paralogs catalysing the same reaction but responsible for the polyamine production at neutral pH.	INTRO
+0	9	Inducible	protein_state	Inducible enterobacterial amino acid decarboxylases have been intensively studied since the early 1940 because the ability of bacteria to withstand acid stress can be linked to their pathogenicity in humans.	INTRO
+10	25	enterobacterial	taxonomy_domain	Inducible enterobacterial amino acid decarboxylases have been intensively studied since the early 1940 because the ability of bacteria to withstand acid stress can be linked to their pathogenicity in humans.	INTRO
+26	51	amino acid decarboxylases	protein_type	Inducible enterobacterial amino acid decarboxylases have been intensively studied since the early 1940 because the ability of bacteria to withstand acid stress can be linked to their pathogenicity in humans.	INTRO
+126	134	bacteria	taxonomy_domain	Inducible enterobacterial amino acid decarboxylases have been intensively studied since the early 1940 because the ability of bacteria to withstand acid stress can be linked to their pathogenicity in humans.	INTRO
+200	206	humans	species	Inducible enterobacterial amino acid decarboxylases have been intensively studied since the early 1940 because the ability of bacteria to withstand acid stress can be linked to their pathogenicity in humans.	INTRO
+19	28	inducible	protein_state	In particular, the inducible lysine decarboxylase LdcI (or CadA) attracts attention due to its broad pH range of activity and its capacity to promote survival and growth of pathogenic enterobacteria such as Salmonella enterica serovar Typhimurium, Vibrio cholerae and Vibrio vulnificus under acidic conditions.	INTRO
+29	49	lysine decarboxylase	protein_type	In particular, the inducible lysine decarboxylase LdcI (or CadA) attracts attention due to its broad pH range of activity and its capacity to promote survival and growth of pathogenic enterobacteria such as Salmonella enterica serovar Typhimurium, Vibrio cholerae and Vibrio vulnificus under acidic conditions.	INTRO
+50	54	LdcI	protein	In particular, the inducible lysine decarboxylase LdcI (or CadA) attracts attention due to its broad pH range of activity and its capacity to promote survival and growth of pathogenic enterobacteria such as Salmonella enterica serovar Typhimurium, Vibrio cholerae and Vibrio vulnificus under acidic conditions.	INTRO
+59	63	CadA	protein	In particular, the inducible lysine decarboxylase LdcI (or CadA) attracts attention due to its broad pH range of activity and its capacity to promote survival and growth of pathogenic enterobacteria such as Salmonella enterica serovar Typhimurium, Vibrio cholerae and Vibrio vulnificus under acidic conditions.	INTRO
+95	109	broad pH range	protein_state	In particular, the inducible lysine decarboxylase LdcI (or CadA) attracts attention due to its broad pH range of activity and its capacity to promote survival and growth of pathogenic enterobacteria such as Salmonella enterica serovar Typhimurium, Vibrio cholerae and Vibrio vulnificus under acidic conditions.	INTRO
+184	198	enterobacteria	taxonomy_domain	In particular, the inducible lysine decarboxylase LdcI (or CadA) attracts attention due to its broad pH range of activity and its capacity to promote survival and growth of pathogenic enterobacteria such as Salmonella enterica serovar Typhimurium, Vibrio cholerae and Vibrio vulnificus under acidic conditions.	INTRO
+207	246	Salmonella enterica serovar Typhimurium	species	In particular, the inducible lysine decarboxylase LdcI (or CadA) attracts attention due to its broad pH range of activity and its capacity to promote survival and growth of pathogenic enterobacteria such as Salmonella enterica serovar Typhimurium, Vibrio cholerae and Vibrio vulnificus under acidic conditions.	INTRO
+248	263	Vibrio cholerae	species	In particular, the inducible lysine decarboxylase LdcI (or CadA) attracts attention due to its broad pH range of activity and its capacity to promote survival and growth of pathogenic enterobacteria such as Salmonella enterica serovar Typhimurium, Vibrio cholerae and Vibrio vulnificus under acidic conditions.	INTRO
+268	285	Vibrio vulnificus	species	In particular, the inducible lysine decarboxylase LdcI (or CadA) attracts attention due to its broad pH range of activity and its capacity to promote survival and growth of pathogenic enterobacteria such as Salmonella enterica serovar Typhimurium, Vibrio cholerae and Vibrio vulnificus under acidic conditions.	INTRO
+18	22	LdcI	protein	Furthermore, both LdcI and the biosynthetic lysine decarboxylase LdcC of uropathogenic Escherichia coli (UPEC) appear to play an important role in increased resistance of this pathogen to nitrosative stress produced by nitric oxide and other damaging reactive nitrogen intermediates accumulating during the course of urinary tract infections (UTI).	INTRO
+31	43	biosynthetic	protein_state	Furthermore, both LdcI and the biosynthetic lysine decarboxylase LdcC of uropathogenic Escherichia coli (UPEC) appear to play an important role in increased resistance of this pathogen to nitrosative stress produced by nitric oxide and other damaging reactive nitrogen intermediates accumulating during the course of urinary tract infections (UTI).	INTRO
+44	64	lysine decarboxylase	protein_type	Furthermore, both LdcI and the biosynthetic lysine decarboxylase LdcC of uropathogenic Escherichia coli (UPEC) appear to play an important role in increased resistance of this pathogen to nitrosative stress produced by nitric oxide and other damaging reactive nitrogen intermediates accumulating during the course of urinary tract infections (UTI).	INTRO
+65	69	LdcC	protein	Furthermore, both LdcI and the biosynthetic lysine decarboxylase LdcC of uropathogenic Escherichia coli (UPEC) appear to play an important role in increased resistance of this pathogen to nitrosative stress produced by nitric oxide and other damaging reactive nitrogen intermediates accumulating during the course of urinary tract infections (UTI).	INTRO
+73	103	uropathogenic Escherichia coli	species	Furthermore, both LdcI and the biosynthetic lysine decarboxylase LdcC of uropathogenic Escherichia coli (UPEC) appear to play an important role in increased resistance of this pathogen to nitrosative stress produced by nitric oxide and other damaging reactive nitrogen intermediates accumulating during the course of urinary tract infections (UTI).	INTRO
+105	109	UPEC	species	Furthermore, both LdcI and the biosynthetic lysine decarboxylase LdcC of uropathogenic Escherichia coli (UPEC) appear to play an important role in increased resistance of this pathogen to nitrosative stress produced by nitric oxide and other damaging reactive nitrogen intermediates accumulating during the course of urinary tract infections (UTI).	INTRO
+219	231	nitric oxide	chemical	Furthermore, both LdcI and the biosynthetic lysine decarboxylase LdcC of uropathogenic Escherichia coli (UPEC) appear to play an important role in increased resistance of this pathogen to nitrosative stress produced by nitric oxide and other damaging reactive nitrogen intermediates accumulating during the course of urinary tract infections (UTI).	INTRO
+29	39	cadaverine	chemical	This effect is attributed to cadaverine, the diamine produced by decarboxylation of lysine by LdcI and LdcC, that was shown to enhance UPEC colonisation of the bladder.	INTRO
+84	90	lysine	residue_name	This effect is attributed to cadaverine, the diamine produced by decarboxylation of lysine by LdcI and LdcC, that was shown to enhance UPEC colonisation of the bladder.	INTRO
+94	98	LdcI	protein	This effect is attributed to cadaverine, the diamine produced by decarboxylation of lysine by LdcI and LdcC, that was shown to enhance UPEC colonisation of the bladder.	INTRO
+103	107	LdcC	protein	This effect is attributed to cadaverine, the diamine produced by decarboxylation of lysine by LdcI and LdcC, that was shown to enhance UPEC colonisation of the bladder.	INTRO
+135	139	UPEC	species	This effect is attributed to cadaverine, the diamine produced by decarboxylation of lysine by LdcI and LdcC, that was shown to enhance UPEC colonisation of the bladder.	INTRO
+17	29	biosynthetic	protein_state	In addition, the biosynthetic E. coli lysine decarboxylase LdcC, long thought to be constitutively expressed in low amounts, was demonstrated to be strongly upregulated by fluoroquinolones via their induction of RpoS. A direct correlation between the level of cadaverine and the resistance of E. coli to these antibiotics commonly used as a first-line treatment of UTI could be established.	INTRO
+30	37	E. coli	species	In addition, the biosynthetic E. coli lysine decarboxylase LdcC, long thought to be constitutively expressed in low amounts, was demonstrated to be strongly upregulated by fluoroquinolones via their induction of RpoS. A direct correlation between the level of cadaverine and the resistance of E. coli to these antibiotics commonly used as a first-line treatment of UTI could be established.	INTRO
+38	58	lysine decarboxylase	protein_type	In addition, the biosynthetic E. coli lysine decarboxylase LdcC, long thought to be constitutively expressed in low amounts, was demonstrated to be strongly upregulated by fluoroquinolones via their induction of RpoS. A direct correlation between the level of cadaverine and the resistance of E. coli to these antibiotics commonly used as a first-line treatment of UTI could be established.	INTRO
+59	63	LdcC	protein	In addition, the biosynthetic E. coli lysine decarboxylase LdcC, long thought to be constitutively expressed in low amounts, was demonstrated to be strongly upregulated by fluoroquinolones via their induction of RpoS. A direct correlation between the level of cadaverine and the resistance of E. coli to these antibiotics commonly used as a first-line treatment of UTI could be established.	INTRO
+172	188	fluoroquinolones	chemical	In addition, the biosynthetic E. coli lysine decarboxylase LdcC, long thought to be constitutively expressed in low amounts, was demonstrated to be strongly upregulated by fluoroquinolones via their induction of RpoS. A direct correlation between the level of cadaverine and the resistance of E. coli to these antibiotics commonly used as a first-line treatment of UTI could be established.	INTRO
+212	216	RpoS	protein	In addition, the biosynthetic E. coli lysine decarboxylase LdcC, long thought to be constitutively expressed in low amounts, was demonstrated to be strongly upregulated by fluoroquinolones via their induction of RpoS. A direct correlation between the level of cadaverine and the resistance of E. coli to these antibiotics commonly used as a first-line treatment of UTI could be established.	INTRO
+260	270	cadaverine	chemical	In addition, the biosynthetic E. coli lysine decarboxylase LdcC, long thought to be constitutively expressed in low amounts, was demonstrated to be strongly upregulated by fluoroquinolones via their induction of RpoS. A direct correlation between the level of cadaverine and the resistance of E. coli to these antibiotics commonly used as a first-line treatment of UTI could be established.	INTRO
+293	300	E. coli	species	In addition, the biosynthetic E. coli lysine decarboxylase LdcC, long thought to be constitutively expressed in low amounts, was demonstrated to be strongly upregulated by fluoroquinolones via their induction of RpoS. A direct correlation between the level of cadaverine and the resistance of E. coli to these antibiotics commonly used as a first-line treatment of UTI could be established.	INTRO
+5	12	acid pH	protein_state	Both acid pH and cadaverine induce closure of outer membrane porins thereby contributing to bacterial protection from acid stress, but also from certain antibiotics, by reduction in membrane permeability.	INTRO
+17	27	cadaverine	chemical	Both acid pH and cadaverine induce closure of outer membrane porins thereby contributing to bacterial protection from acid stress, but also from certain antibiotics, by reduction in membrane permeability.	INTRO
+61	67	porins	protein_type	Both acid pH and cadaverine induce closure of outer membrane porins thereby contributing to bacterial protection from acid stress, but also from certain antibiotics, by reduction in membrane permeability.	INTRO
+92	101	bacterial	taxonomy_domain	Both acid pH and cadaverine induce closure of outer membrane porins thereby contributing to bacterial protection from acid stress, but also from certain antibiotics, by reduction in membrane permeability.	INTRO
+4	21	crystal structure	evidence	The crystal structure of the E. coli LdcI as well as its low resolution characterisation by electron microscopy (EM) showed that it is a decamer made of two pentameric rings.	INTRO
+29	36	E. coli	species	The crystal structure of the E. coli LdcI as well as its low resolution characterisation by electron microscopy (EM) showed that it is a decamer made of two pentameric rings.	INTRO
+37	41	LdcI	protein	The crystal structure of the E. coli LdcI as well as its low resolution characterisation by electron microscopy (EM) showed that it is a decamer made of two pentameric rings.	INTRO
+92	111	electron microscopy	experimental_method	The crystal structure of the E. coli LdcI as well as its low resolution characterisation by electron microscopy (EM) showed that it is a decamer made of two pentameric rings.	INTRO
+113	115	EM	experimental_method	The crystal structure of the E. coli LdcI as well as its low resolution characterisation by electron microscopy (EM) showed that it is a decamer made of two pentameric rings.	INTRO
+137	144	decamer	oligomeric_state	The crystal structure of the E. coli LdcI as well as its low resolution characterisation by electron microscopy (EM) showed that it is a decamer made of two pentameric rings.	INTRO
+157	167	pentameric	oligomeric_state	The crystal structure of the E. coli LdcI as well as its low resolution characterisation by electron microscopy (EM) showed that it is a decamer made of two pentameric rings.	INTRO
+168	173	rings	structure_element	The crystal structure of the E. coli LdcI as well as its low resolution characterisation by electron microscopy (EM) showed that it is a decamer made of two pentameric rings.	INTRO
+5	12	monomer	oligomeric_state	Each monomer is composed of three domains – an N-terminal wing domain (residues 1–129), a PLP-binding core domain (residues 130–563), and a C-terminal domain (CTD, residues 564–715).	INTRO
+58	69	wing domain	structure_element	Each monomer is composed of three domains – an N-terminal wing domain (residues 1–129), a PLP-binding core domain (residues 130–563), and a C-terminal domain (CTD, residues 564–715).	INTRO
+80	85	1–129	residue_range	Each monomer is composed of three domains – an N-terminal wing domain (residues 1–129), a PLP-binding core domain (residues 130–563), and a C-terminal domain (CTD, residues 564–715).	INTRO
+90	113	PLP-binding core domain	structure_element	Each monomer is composed of three domains – an N-terminal wing domain (residues 1–129), a PLP-binding core domain (residues 130–563), and a C-terminal domain (CTD, residues 564–715).	INTRO
+124	131	130–563	residue_range	Each monomer is composed of three domains – an N-terminal wing domain (residues 1–129), a PLP-binding core domain (residues 130–563), and a C-terminal domain (CTD, residues 564–715).	INTRO
+140	157	C-terminal domain	structure_element	Each monomer is composed of three domains – an N-terminal wing domain (residues 1–129), a PLP-binding core domain (residues 130–563), and a C-terminal domain (CTD, residues 564–715).	INTRO
+159	162	CTD	structure_element	Each monomer is composed of three domains – an N-terminal wing domain (residues 1–129), a PLP-binding core domain (residues 130–563), and a C-terminal domain (CTD, residues 564–715).	INTRO
+173	180	564–715	residue_range	Each monomer is composed of three domains – an N-terminal wing domain (residues 1–129), a PLP-binding core domain (residues 130–563), and a C-terminal domain (CTD, residues 564–715).	INTRO
+0	8	Monomers	oligomeric_state	Monomers tightly associate via their core domains into 2-fold symmetrical dimers with two complete active sites, and further build a toroidal D5-symmetrical structure held by the wing and core domain interactions around the central pore, with the CTDs at the periphery.	INTRO
+37	49	core domains	structure_element	Monomers tightly associate via their core domains into 2-fold symmetrical dimers with two complete active sites, and further build a toroidal D5-symmetrical structure held by the wing and core domain interactions around the central pore, with the CTDs at the periphery.	INTRO
+55	73	2-fold symmetrical	protein_state	Monomers tightly associate via their core domains into 2-fold symmetrical dimers with two complete active sites, and further build a toroidal D5-symmetrical structure held by the wing and core domain interactions around the central pore, with the CTDs at the periphery.	INTRO
+74	80	dimers	oligomeric_state	Monomers tightly associate via their core domains into 2-fold symmetrical dimers with two complete active sites, and further build a toroidal D5-symmetrical structure held by the wing and core domain interactions around the central pore, with the CTDs at the periphery.	INTRO
+99	111	active sites	site	Monomers tightly associate via their core domains into 2-fold symmetrical dimers with two complete active sites, and further build a toroidal D5-symmetrical structure held by the wing and core domain interactions around the central pore, with the CTDs at the periphery.	INTRO
+133	166	toroidal D5-symmetrical structure	structure_element	Monomers tightly associate via their core domains into 2-fold symmetrical dimers with two complete active sites, and further build a toroidal D5-symmetrical structure held by the wing and core domain interactions around the central pore, with the CTDs at the periphery.	INTRO
+179	183	wing	structure_element	Monomers tightly associate via their core domains into 2-fold symmetrical dimers with two complete active sites, and further build a toroidal D5-symmetrical structure held by the wing and core domain interactions around the central pore, with the CTDs at the periphery.	INTRO
+188	199	core domain	structure_element	Monomers tightly associate via their core domains into 2-fold symmetrical dimers with two complete active sites, and further build a toroidal D5-symmetrical structure held by the wing and core domain interactions around the central pore, with the CTDs at the periphery.	INTRO
+224	236	central pore	structure_element	Monomers tightly associate via their core domains into 2-fold symmetrical dimers with two complete active sites, and further build a toroidal D5-symmetrical structure held by the wing and core domain interactions around the central pore, with the CTDs at the periphery.	INTRO
+247	251	CTDs	structure_element	Monomers tightly associate via their core domains into 2-fold symmetrical dimers with two complete active sites, and further build a toroidal D5-symmetrical structure held by the wing and core domain interactions around the central pore, with the CTDs at the periphery.	INTRO
+33	40	E. coli	species	Ten years ago we showed that the E. coli AAA+ ATPase RavA, involved in multiple stress response pathways, tightly interacted with LdcI but was not capable of binding to LdcC. We described how two double pentameric rings of the LdcI tightly associate with five hexameric rings of RavA to form a unique cage-like architecture that enables the bacterium to withstand acid stress even under conditions of nutrient deprivation eliciting stringent response.	INTRO
+41	52	AAA+ ATPase	protein_type	Ten years ago we showed that the E. coli AAA+ ATPase RavA, involved in multiple stress response pathways, tightly interacted with LdcI but was not capable of binding to LdcC. We described how two double pentameric rings of the LdcI tightly associate with five hexameric rings of RavA to form a unique cage-like architecture that enables the bacterium to withstand acid stress even under conditions of nutrient deprivation eliciting stringent response.	INTRO
+53	57	RavA	protein	Ten years ago we showed that the E. coli AAA+ ATPase RavA, involved in multiple stress response pathways, tightly interacted with LdcI but was not capable of binding to LdcC. We described how two double pentameric rings of the LdcI tightly associate with five hexameric rings of RavA to form a unique cage-like architecture that enables the bacterium to withstand acid stress even under conditions of nutrient deprivation eliciting stringent response.	INTRO
+130	134	LdcI	protein	Ten years ago we showed that the E. coli AAA+ ATPase RavA, involved in multiple stress response pathways, tightly interacted with LdcI but was not capable of binding to LdcC. We described how two double pentameric rings of the LdcI tightly associate with five hexameric rings of RavA to form a unique cage-like architecture that enables the bacterium to withstand acid stress even under conditions of nutrient deprivation eliciting stringent response.	INTRO
+169	173	LdcC	protein	Ten years ago we showed that the E. coli AAA+ ATPase RavA, involved in multiple stress response pathways, tightly interacted with LdcI but was not capable of binding to LdcC. We described how two double pentameric rings of the LdcI tightly associate with five hexameric rings of RavA to form a unique cage-like architecture that enables the bacterium to withstand acid stress even under conditions of nutrient deprivation eliciting stringent response.	INTRO
+203	213	pentameric	oligomeric_state	Ten years ago we showed that the E. coli AAA+ ATPase RavA, involved in multiple stress response pathways, tightly interacted with LdcI but was not capable of binding to LdcC. We described how two double pentameric rings of the LdcI tightly associate with five hexameric rings of RavA to form a unique cage-like architecture that enables the bacterium to withstand acid stress even under conditions of nutrient deprivation eliciting stringent response.	INTRO
+214	219	rings	structure_element	Ten years ago we showed that the E. coli AAA+ ATPase RavA, involved in multiple stress response pathways, tightly interacted with LdcI but was not capable of binding to LdcC. We described how two double pentameric rings of the LdcI tightly associate with five hexameric rings of RavA to form a unique cage-like architecture that enables the bacterium to withstand acid stress even under conditions of nutrient deprivation eliciting stringent response.	INTRO
+227	231	LdcI	protein	Ten years ago we showed that the E. coli AAA+ ATPase RavA, involved in multiple stress response pathways, tightly interacted with LdcI but was not capable of binding to LdcC. We described how two double pentameric rings of the LdcI tightly associate with five hexameric rings of RavA to form a unique cage-like architecture that enables the bacterium to withstand acid stress even under conditions of nutrient deprivation eliciting stringent response.	INTRO
+260	269	hexameric	oligomeric_state	Ten years ago we showed that the E. coli AAA+ ATPase RavA, involved in multiple stress response pathways, tightly interacted with LdcI but was not capable of binding to LdcC. We described how two double pentameric rings of the LdcI tightly associate with five hexameric rings of RavA to form a unique cage-like architecture that enables the bacterium to withstand acid stress even under conditions of nutrient deprivation eliciting stringent response.	INTRO
+270	275	rings	structure_element	Ten years ago we showed that the E. coli AAA+ ATPase RavA, involved in multiple stress response pathways, tightly interacted with LdcI but was not capable of binding to LdcC. We described how two double pentameric rings of the LdcI tightly associate with five hexameric rings of RavA to form a unique cage-like architecture that enables the bacterium to withstand acid stress even under conditions of nutrient deprivation eliciting stringent response.	INTRO
+279	283	RavA	protein	Ten years ago we showed that the E. coli AAA+ ATPase RavA, involved in multiple stress response pathways, tightly interacted with LdcI but was not capable of binding to LdcC. We described how two double pentameric rings of the LdcI tightly associate with five hexameric rings of RavA to form a unique cage-like architecture that enables the bacterium to withstand acid stress even under conditions of nutrient deprivation eliciting stringent response.	INTRO
+341	350	bacterium	taxonomy_domain	Ten years ago we showed that the E. coli AAA+ ATPase RavA, involved in multiple stress response pathways, tightly interacted with LdcI but was not capable of binding to LdcC. We described how two double pentameric rings of the LdcI tightly associate with five hexameric rings of RavA to form a unique cage-like architecture that enables the bacterium to withstand acid stress even under conditions of nutrient deprivation eliciting stringent response.	INTRO
+25	45	solved the structure	experimental_method	Furthermore, we recently solved the structure of the E. coli LdcI-RavA complex by cryo-electron microscopy (cryoEM) and combined it with the crystal structures of the individual proteins.	INTRO
+53	60	E. coli	species	Furthermore, we recently solved the structure of the E. coli LdcI-RavA complex by cryo-electron microscopy (cryoEM) and combined it with the crystal structures of the individual proteins.	INTRO
+61	70	LdcI-RavA	complex_assembly	Furthermore, we recently solved the structure of the E. coli LdcI-RavA complex by cryo-electron microscopy (cryoEM) and combined it with the crystal structures of the individual proteins.	INTRO
+82	106	cryo-electron microscopy	experimental_method	Furthermore, we recently solved the structure of the E. coli LdcI-RavA complex by cryo-electron microscopy (cryoEM) and combined it with the crystal structures of the individual proteins.	INTRO
+108	114	cryoEM	experimental_method	Furthermore, we recently solved the structure of the E. coli LdcI-RavA complex by cryo-electron microscopy (cryoEM) and combined it with the crystal structures of the individual proteins.	INTRO
+141	159	crystal structures	evidence	Furthermore, we recently solved the structure of the E. coli LdcI-RavA complex by cryo-electron microscopy (cryoEM) and combined it with the crystal structures of the individual proteins.	INTRO
+26	44	pseudoatomic model	evidence	This allowed us to make a pseudoatomic model of the whole assembly, underpinned by a cryoEM map of the LdcI-LARA complex (with LARA standing for LdcI associating domain of RavA), and to identify conformational rearrangements and specific elements essential for complex formation.	INTRO
+85	91	cryoEM	experimental_method	This allowed us to make a pseudoatomic model of the whole assembly, underpinned by a cryoEM map of the LdcI-LARA complex (with LARA standing for LdcI associating domain of RavA), and to identify conformational rearrangements and specific elements essential for complex formation.	INTRO
+92	95	map	evidence	This allowed us to make a pseudoatomic model of the whole assembly, underpinned by a cryoEM map of the LdcI-LARA complex (with LARA standing for LdcI associating domain of RavA), and to identify conformational rearrangements and specific elements essential for complex formation.	INTRO
+103	112	LdcI-LARA	complex_assembly	This allowed us to make a pseudoatomic model of the whole assembly, underpinned by a cryoEM map of the LdcI-LARA complex (with LARA standing for LdcI associating domain of RavA), and to identify conformational rearrangements and specific elements essential for complex formation.	INTRO
+127	131	LARA	structure_element	This allowed us to make a pseudoatomic model of the whole assembly, underpinned by a cryoEM map of the LdcI-LARA complex (with LARA standing for LdcI associating domain of RavA), and to identify conformational rearrangements and specific elements essential for complex formation.	INTRO
+145	176	LdcI associating domain of RavA	structure_element	This allowed us to make a pseudoatomic model of the whole assembly, underpinned by a cryoEM map of the LdcI-LARA complex (with LARA standing for LdcI associating domain of RavA), and to identify conformational rearrangements and specific elements essential for complex formation.	INTRO
+29	38	LdcI-RavA	complex_assembly	The main determinants of the LdcI-RavA cage assembly appeared to be the N-terminal loop of the LARA domain of RavA and the C-terminal β-sheet of LdcI.	INTRO
+83	87	loop	structure_element	The main determinants of the LdcI-RavA cage assembly appeared to be the N-terminal loop of the LARA domain of RavA and the C-terminal β-sheet of LdcI.	INTRO
+95	106	LARA domain	structure_element	The main determinants of the LdcI-RavA cage assembly appeared to be the N-terminal loop of the LARA domain of RavA and the C-terminal β-sheet of LdcI.	INTRO
+110	114	RavA	protein	The main determinants of the LdcI-RavA cage assembly appeared to be the N-terminal loop of the LARA domain of RavA and the C-terminal β-sheet of LdcI.	INTRO
+134	141	β-sheet	structure_element	The main determinants of the LdcI-RavA cage assembly appeared to be the N-terminal loop of the LARA domain of RavA and the C-terminal β-sheet of LdcI.	INTRO
+145	149	LdcI	protein	The main determinants of the LdcI-RavA cage assembly appeared to be the N-terminal loop of the LARA domain of RavA and the C-terminal β-sheet of LdcI.	INTRO
+27	49	structural information	evidence	In spite of this wealth of structural information, the fact that LdcC does not interact with RavA, although the two lysine decarboxylases are 69% identical and 84% similar, and the physiological significance of the absence of this interaction remained unexplored.	INTRO
+65	69	LdcC	protein	In spite of this wealth of structural information, the fact that LdcC does not interact with RavA, although the two lysine decarboxylases are 69% identical and 84% similar, and the physiological significance of the absence of this interaction remained unexplored.	INTRO
+93	97	RavA	protein	In spite of this wealth of structural information, the fact that LdcC does not interact with RavA, although the two lysine decarboxylases are 69% identical and 84% similar, and the physiological significance of the absence of this interaction remained unexplored.	INTRO
+116	137	lysine decarboxylases	protein_type	In spite of this wealth of structural information, the fact that LdcC does not interact with RavA, although the two lysine decarboxylases are 69% identical and 84% similar, and the physiological significance of the absence of this interaction remained unexplored.	INTRO
+84	90	cryoEM	experimental_method	To solve this discrepancy, in the present work we provided a three-dimensional (3D) cryoEM reconstruction of LdcC and compared it with the available LdcI and LdcI-RavA structures.	INTRO
+91	105	reconstruction	evidence	To solve this discrepancy, in the present work we provided a three-dimensional (3D) cryoEM reconstruction of LdcC and compared it with the available LdcI and LdcI-RavA structures.	INTRO
+109	113	LdcC	protein	To solve this discrepancy, in the present work we provided a three-dimensional (3D) cryoEM reconstruction of LdcC and compared it with the available LdcI and LdcI-RavA structures.	INTRO
+149	153	LdcI	protein	To solve this discrepancy, in the present work we provided a three-dimensional (3D) cryoEM reconstruction of LdcC and compared it with the available LdcI and LdcI-RavA structures.	INTRO
+158	167	LdcI-RavA	complex_assembly	To solve this discrepancy, in the present work we provided a three-dimensional (3D) cryoEM reconstruction of LdcC and compared it with the available LdcI and LdcI-RavA structures.	INTRO
+168	178	structures	evidence	To solve this discrepancy, in the present work we provided a three-dimensional (3D) cryoEM reconstruction of LdcC and compared it with the available LdcI and LdcI-RavA structures.	INTRO
+15	19	LdcI	protein	Given that the LdcI crystal structures were obtained at high pH where the enzyme is inactive (LdcIi, pH 8.5), whereas the cryoEM reconstructions of LdcI-RavA and LdcI-LARA were done at acidic pH optimal for the enzymatic activity, for a meaningful comparison, we also produced a 3D reconstruction of the LdcI at active pH (LdcIa, pH 6.2).	INTRO
+20	38	crystal structures	evidence	Given that the LdcI crystal structures were obtained at high pH where the enzyme is inactive (LdcIi, pH 8.5), whereas the cryoEM reconstructions of LdcI-RavA and LdcI-LARA were done at acidic pH optimal for the enzymatic activity, for a meaningful comparison, we also produced a 3D reconstruction of the LdcI at active pH (LdcIa, pH 6.2).	INTRO
+56	63	high pH	protein_state	Given that the LdcI crystal structures were obtained at high pH where the enzyme is inactive (LdcIi, pH 8.5), whereas the cryoEM reconstructions of LdcI-RavA and LdcI-LARA were done at acidic pH optimal for the enzymatic activity, for a meaningful comparison, we also produced a 3D reconstruction of the LdcI at active pH (LdcIa, pH 6.2).	INTRO
+84	92	inactive	protein_state	Given that the LdcI crystal structures were obtained at high pH where the enzyme is inactive (LdcIi, pH 8.5), whereas the cryoEM reconstructions of LdcI-RavA and LdcI-LARA were done at acidic pH optimal for the enzymatic activity, for a meaningful comparison, we also produced a 3D reconstruction of the LdcI at active pH (LdcIa, pH 6.2).	INTRO
+94	99	LdcIi	protein	Given that the LdcI crystal structures were obtained at high pH where the enzyme is inactive (LdcIi, pH 8.5), whereas the cryoEM reconstructions of LdcI-RavA and LdcI-LARA were done at acidic pH optimal for the enzymatic activity, for a meaningful comparison, we also produced a 3D reconstruction of the LdcI at active pH (LdcIa, pH 6.2).	INTRO
+101	107	pH 8.5	protein_state	Given that the LdcI crystal structures were obtained at high pH where the enzyme is inactive (LdcIi, pH 8.5), whereas the cryoEM reconstructions of LdcI-RavA and LdcI-LARA were done at acidic pH optimal for the enzymatic activity, for a meaningful comparison, we also produced a 3D reconstruction of the LdcI at active pH (LdcIa, pH 6.2).	INTRO
+122	128	cryoEM	experimental_method	Given that the LdcI crystal structures were obtained at high pH where the enzyme is inactive (LdcIi, pH 8.5), whereas the cryoEM reconstructions of LdcI-RavA and LdcI-LARA were done at acidic pH optimal for the enzymatic activity, for a meaningful comparison, we also produced a 3D reconstruction of the LdcI at active pH (LdcIa, pH 6.2).	INTRO
+129	144	reconstructions	evidence	Given that the LdcI crystal structures were obtained at high pH where the enzyme is inactive (LdcIi, pH 8.5), whereas the cryoEM reconstructions of LdcI-RavA and LdcI-LARA were done at acidic pH optimal for the enzymatic activity, for a meaningful comparison, we also produced a 3D reconstruction of the LdcI at active pH (LdcIa, pH 6.2).	INTRO
+148	157	LdcI-RavA	complex_assembly	Given that the LdcI crystal structures were obtained at high pH where the enzyme is inactive (LdcIi, pH 8.5), whereas the cryoEM reconstructions of LdcI-RavA and LdcI-LARA were done at acidic pH optimal for the enzymatic activity, for a meaningful comparison, we also produced a 3D reconstruction of the LdcI at active pH (LdcIa, pH 6.2).	INTRO
+162	171	LdcI-LARA	complex_assembly	Given that the LdcI crystal structures were obtained at high pH where the enzyme is inactive (LdcIi, pH 8.5), whereas the cryoEM reconstructions of LdcI-RavA and LdcI-LARA were done at acidic pH optimal for the enzymatic activity, for a meaningful comparison, we also produced a 3D reconstruction of the LdcI at active pH (LdcIa, pH 6.2).	INTRO
+185	202	acidic pH optimal	protein_state	Given that the LdcI crystal structures were obtained at high pH where the enzyme is inactive (LdcIi, pH 8.5), whereas the cryoEM reconstructions of LdcI-RavA and LdcI-LARA were done at acidic pH optimal for the enzymatic activity, for a meaningful comparison, we also produced a 3D reconstruction of the LdcI at active pH (LdcIa, pH 6.2).	INTRO
+279	296	3D reconstruction	evidence	Given that the LdcI crystal structures were obtained at high pH where the enzyme is inactive (LdcIi, pH 8.5), whereas the cryoEM reconstructions of LdcI-RavA and LdcI-LARA were done at acidic pH optimal for the enzymatic activity, for a meaningful comparison, we also produced a 3D reconstruction of the LdcI at active pH (LdcIa, pH 6.2).	INTRO
+304	308	LdcI	protein	Given that the LdcI crystal structures were obtained at high pH where the enzyme is inactive (LdcIi, pH 8.5), whereas the cryoEM reconstructions of LdcI-RavA and LdcI-LARA were done at acidic pH optimal for the enzymatic activity, for a meaningful comparison, we also produced a 3D reconstruction of the LdcI at active pH (LdcIa, pH 6.2).	INTRO
+312	321	active pH	protein_state	Given that the LdcI crystal structures were obtained at high pH where the enzyme is inactive (LdcIi, pH 8.5), whereas the cryoEM reconstructions of LdcI-RavA and LdcI-LARA were done at acidic pH optimal for the enzymatic activity, for a meaningful comparison, we also produced a 3D reconstruction of the LdcI at active pH (LdcIa, pH 6.2).	INTRO
+323	328	LdcIa	protein	Given that the LdcI crystal structures were obtained at high pH where the enzyme is inactive (LdcIi, pH 8.5), whereas the cryoEM reconstructions of LdcI-RavA and LdcI-LARA were done at acidic pH optimal for the enzymatic activity, for a meaningful comparison, we also produced a 3D reconstruction of the LdcI at active pH (LdcIa, pH 6.2).	INTRO
+330	336	pH 6.2	protein_state	Given that the LdcI crystal structures were obtained at high pH where the enzyme is inactive (LdcIi, pH 8.5), whereas the cryoEM reconstructions of LdcI-RavA and LdcI-LARA were done at acidic pH optimal for the enzymatic activity, for a meaningful comparison, we also produced a 3D reconstruction of the LdcI at active pH (LdcIa, pH 6.2).	INTRO
+51	65	biodegradative	protein_state	This comparison pinpointed differences between the biodegradative and the biosynthetic lysine decarboxylases and brought to light interdomain movements associated to pH-dependent enzyme activation and RavA binding, notably at the predicted RavA binding site at the level of the C-terminal β-sheet of LdcI. Consequently, we tested the capacity of cage formation by LdcI-LdcC chimeras where we interchanged the C-terminal β-sheets in question.	INTRO
+74	86	biosynthetic	protein_state	This comparison pinpointed differences between the biodegradative and the biosynthetic lysine decarboxylases and brought to light interdomain movements associated to pH-dependent enzyme activation and RavA binding, notably at the predicted RavA binding site at the level of the C-terminal β-sheet of LdcI. Consequently, we tested the capacity of cage formation by LdcI-LdcC chimeras where we interchanged the C-terminal β-sheets in question.	INTRO
+87	108	lysine decarboxylases	protein_type	This comparison pinpointed differences between the biodegradative and the biosynthetic lysine decarboxylases and brought to light interdomain movements associated to pH-dependent enzyme activation and RavA binding, notably at the predicted RavA binding site at the level of the C-terminal β-sheet of LdcI. Consequently, we tested the capacity of cage formation by LdcI-LdcC chimeras where we interchanged the C-terminal β-sheets in question.	INTRO
+166	178	pH-dependent	protein_state	This comparison pinpointed differences between the biodegradative and the biosynthetic lysine decarboxylases and brought to light interdomain movements associated to pH-dependent enzyme activation and RavA binding, notably at the predicted RavA binding site at the level of the C-terminal β-sheet of LdcI. Consequently, we tested the capacity of cage formation by LdcI-LdcC chimeras where we interchanged the C-terminal β-sheets in question.	INTRO
+201	205	RavA	protein	This comparison pinpointed differences between the biodegradative and the biosynthetic lysine decarboxylases and brought to light interdomain movements associated to pH-dependent enzyme activation and RavA binding, notably at the predicted RavA binding site at the level of the C-terminal β-sheet of LdcI. Consequently, we tested the capacity of cage formation by LdcI-LdcC chimeras where we interchanged the C-terminal β-sheets in question.	INTRO
+240	257	RavA binding site	site	This comparison pinpointed differences between the biodegradative and the biosynthetic lysine decarboxylases and brought to light interdomain movements associated to pH-dependent enzyme activation and RavA binding, notably at the predicted RavA binding site at the level of the C-terminal β-sheet of LdcI. Consequently, we tested the capacity of cage formation by LdcI-LdcC chimeras where we interchanged the C-terminal β-sheets in question.	INTRO
+289	296	β-sheet	structure_element	This comparison pinpointed differences between the biodegradative and the biosynthetic lysine decarboxylases and brought to light interdomain movements associated to pH-dependent enzyme activation and RavA binding, notably at the predicted RavA binding site at the level of the C-terminal β-sheet of LdcI. Consequently, we tested the capacity of cage formation by LdcI-LdcC chimeras where we interchanged the C-terminal β-sheets in question.	INTRO
+300	304	LdcI	protein	This comparison pinpointed differences between the biodegradative and the biosynthetic lysine decarboxylases and brought to light interdomain movements associated to pH-dependent enzyme activation and RavA binding, notably at the predicted RavA binding site at the level of the C-terminal β-sheet of LdcI. Consequently, we tested the capacity of cage formation by LdcI-LdcC chimeras where we interchanged the C-terminal β-sheets in question.	INTRO
+364	382	LdcI-LdcC chimeras	mutant	This comparison pinpointed differences between the biodegradative and the biosynthetic lysine decarboxylases and brought to light interdomain movements associated to pH-dependent enzyme activation and RavA binding, notably at the predicted RavA binding site at the level of the C-terminal β-sheet of LdcI. Consequently, we tested the capacity of cage formation by LdcI-LdcC chimeras where we interchanged the C-terminal β-sheets in question.	INTRO
+392	404	interchanged	experimental_method	This comparison pinpointed differences between the biodegradative and the biosynthetic lysine decarboxylases and brought to light interdomain movements associated to pH-dependent enzyme activation and RavA binding, notably at the predicted RavA binding site at the level of the C-terminal β-sheet of LdcI. Consequently, we tested the capacity of cage formation by LdcI-LdcC chimeras where we interchanged the C-terminal β-sheets in question.	INTRO
+420	428	β-sheets	structure_element	This comparison pinpointed differences between the biodegradative and the biosynthetic lysine decarboxylases and brought to light interdomain movements associated to pH-dependent enzyme activation and RavA binding, notably at the predicted RavA binding site at the level of the C-terminal β-sheet of LdcI. Consequently, we tested the capacity of cage formation by LdcI-LdcC chimeras where we interchanged the C-terminal β-sheets in question.	INTRO
+22	49	multiple sequence alignment	experimental_method	Finally, we performed multiple sequence alignment of 22 lysine decarboxylases from Enterobacteriaceae containing the ravA-viaA operon in their genome.	INTRO
+56	77	lysine decarboxylases	protein_type	Finally, we performed multiple sequence alignment of 22 lysine decarboxylases from Enterobacteriaceae containing the ravA-viaA operon in their genome.	INTRO
+83	101	Enterobacteriaceae	taxonomy_domain	Finally, we performed multiple sequence alignment of 22 lysine decarboxylases from Enterobacteriaceae containing the ravA-viaA operon in their genome.	INTRO
+117	133	ravA-viaA operon	gene	Finally, we performed multiple sequence alignment of 22 lysine decarboxylases from Enterobacteriaceae containing the ravA-viaA operon in their genome.	INTRO
+48	65	specific residues	structure_element	Remarkably, this analysis revealed that several specific residues in the above-mentioned β-sheet, independently of the rest of the protein sequence, are sufficient to define if a particular lysine decarboxylase should be classified as an “LdcC-like” or an “LdcI-like”.	INTRO
+89	96	β-sheet	structure_element	Remarkably, this analysis revealed that several specific residues in the above-mentioned β-sheet, independently of the rest of the protein sequence, are sufficient to define if a particular lysine decarboxylase should be classified as an “LdcC-like” or an “LdcI-like”.	INTRO
+190	210	lysine decarboxylase	protein_type	Remarkably, this analysis revealed that several specific residues in the above-mentioned β-sheet, independently of the rest of the protein sequence, are sufficient to define if a particular lysine decarboxylase should be classified as an “LdcC-like” or an “LdcI-like”.	INTRO
+239	248	LdcC-like	protein_type	Remarkably, this analysis revealed that several specific residues in the above-mentioned β-sheet, independently of the rest of the protein sequence, are sufficient to define if a particular lysine decarboxylase should be classified as an “LdcC-like” or an “LdcI-like”.	INTRO
+257	266	LdcI-like	protein_type	Remarkably, this analysis revealed that several specific residues in the above-mentioned β-sheet, independently of the rest of the protein sequence, are sufficient to define if a particular lysine decarboxylase should be classified as an “LdcC-like” or an “LdcI-like”.	INTRO
+56	60	RavA	protein	This fascinating parallelism between the propensity for RavA binding and the genetic environment of an enterobacterial lysine decarboxylase, as well as the high degree of conservation of this small structural motif, emphasize the functional importance of the interaction between biodegradative enterobacterial lysine decarboxylases and the AAA+ ATPase RavA.	INTRO
+103	118	enterobacterial	taxonomy_domain	This fascinating parallelism between the propensity for RavA binding and the genetic environment of an enterobacterial lysine decarboxylase, as well as the high degree of conservation of this small structural motif, emphasize the functional importance of the interaction between biodegradative enterobacterial lysine decarboxylases and the AAA+ ATPase RavA.	INTRO
+119	139	lysine decarboxylase	protein_type	This fascinating parallelism between the propensity for RavA binding and the genetic environment of an enterobacterial lysine decarboxylase, as well as the high degree of conservation of this small structural motif, emphasize the functional importance of the interaction between biodegradative enterobacterial lysine decarboxylases and the AAA+ ATPase RavA.	INTRO
+156	183	high degree of conservation	protein_state	This fascinating parallelism between the propensity for RavA binding and the genetic environment of an enterobacterial lysine decarboxylase, as well as the high degree of conservation of this small structural motif, emphasize the functional importance of the interaction between biodegradative enterobacterial lysine decarboxylases and the AAA+ ATPase RavA.	INTRO
+192	214	small structural motif	structure_element	This fascinating parallelism between the propensity for RavA binding and the genetic environment of an enterobacterial lysine decarboxylase, as well as the high degree of conservation of this small structural motif, emphasize the functional importance of the interaction between biodegradative enterobacterial lysine decarboxylases and the AAA+ ATPase RavA.	INTRO
+279	293	biodegradative	protein_state	This fascinating parallelism between the propensity for RavA binding and the genetic environment of an enterobacterial lysine decarboxylase, as well as the high degree of conservation of this small structural motif, emphasize the functional importance of the interaction between biodegradative enterobacterial lysine decarboxylases and the AAA+ ATPase RavA.	INTRO
+294	309	enterobacterial	taxonomy_domain	This fascinating parallelism between the propensity for RavA binding and the genetic environment of an enterobacterial lysine decarboxylase, as well as the high degree of conservation of this small structural motif, emphasize the functional importance of the interaction between biodegradative enterobacterial lysine decarboxylases and the AAA+ ATPase RavA.	INTRO
+310	331	lysine decarboxylases	protein_type	This fascinating parallelism between the propensity for RavA binding and the genetic environment of an enterobacterial lysine decarboxylase, as well as the high degree of conservation of this small structural motif, emphasize the functional importance of the interaction between biodegradative enterobacterial lysine decarboxylases and the AAA+ ATPase RavA.	INTRO
+340	351	AAA+ ATPase	protein_type	This fascinating parallelism between the propensity for RavA binding and the genetic environment of an enterobacterial lysine decarboxylase, as well as the high degree of conservation of this small structural motif, emphasize the functional importance of the interaction between biodegradative enterobacterial lysine decarboxylases and the AAA+ ATPase RavA.	INTRO
+352	356	RavA	protein	This fascinating parallelism between the propensity for RavA binding and the genetic environment of an enterobacterial lysine decarboxylase, as well as the high degree of conservation of this small structural motif, emphasize the functional importance of the interaction between biodegradative enterobacterial lysine decarboxylases and the AAA+ ATPase RavA.	INTRO
+0	6	CryoEM	experimental_method	CryoEM 3D reconstructions of LdcC, LdcIa and LdcI-LARA	RESULTS
+7	25	3D reconstructions	evidence	CryoEM 3D reconstructions of LdcC, LdcIa and LdcI-LARA	RESULTS
+29	33	LdcC	protein	CryoEM 3D reconstructions of LdcC, LdcIa and LdcI-LARA	RESULTS
+35	40	LdcIa	protein	CryoEM 3D reconstructions of LdcC, LdcIa and LdcI-LARA	RESULTS
+45	54	LdcI-LARA	complex_assembly	CryoEM 3D reconstructions of LdcC, LdcIa and LdcI-LARA	RESULTS
+73	79	cryoEM	experimental_method	In the frame of this work, we produced two novel subnanometer resolution cryoEM reconstructions of the E. coli lysine decarboxylases at pH optimal for their enzymatic activity – a 5.5 Å resolution cryoEM map of the LdcC (pH 7.5) for which no 3D structural information has been previously available (Figs 1A,B and S1), and a 6.1 Å resolution cryoEM map of the LdcIa, (pH 6.2) (Figs 1C,D and S2).	RESULTS
+80	95	reconstructions	evidence	In the frame of this work, we produced two novel subnanometer resolution cryoEM reconstructions of the E. coli lysine decarboxylases at pH optimal for their enzymatic activity – a 5.5 Å resolution cryoEM map of the LdcC (pH 7.5) for which no 3D structural information has been previously available (Figs 1A,B and S1), and a 6.1 Å resolution cryoEM map of the LdcIa, (pH 6.2) (Figs 1C,D and S2).	RESULTS
+103	110	E. coli	species	In the frame of this work, we produced two novel subnanometer resolution cryoEM reconstructions of the E. coli lysine decarboxylases at pH optimal for their enzymatic activity – a 5.5 Å resolution cryoEM map of the LdcC (pH 7.5) for which no 3D structural information has been previously available (Figs 1A,B and S1), and a 6.1 Å resolution cryoEM map of the LdcIa, (pH 6.2) (Figs 1C,D and S2).	RESULTS
+111	132	lysine decarboxylases	protein_type	In the frame of this work, we produced two novel subnanometer resolution cryoEM reconstructions of the E. coli lysine decarboxylases at pH optimal for their enzymatic activity – a 5.5 Å resolution cryoEM map of the LdcC (pH 7.5) for which no 3D structural information has been previously available (Figs 1A,B and S1), and a 6.1 Å resolution cryoEM map of the LdcIa, (pH 6.2) (Figs 1C,D and S2).	RESULTS
+136	146	pH optimal	protein_state	In the frame of this work, we produced two novel subnanometer resolution cryoEM reconstructions of the E. coli lysine decarboxylases at pH optimal for their enzymatic activity – a 5.5 Å resolution cryoEM map of the LdcC (pH 7.5) for which no 3D structural information has been previously available (Figs 1A,B and S1), and a 6.1 Å resolution cryoEM map of the LdcIa, (pH 6.2) (Figs 1C,D and S2).	RESULTS
+197	203	cryoEM	experimental_method	In the frame of this work, we produced two novel subnanometer resolution cryoEM reconstructions of the E. coli lysine decarboxylases at pH optimal for their enzymatic activity – a 5.5 Å resolution cryoEM map of the LdcC (pH 7.5) for which no 3D structural information has been previously available (Figs 1A,B and S1), and a 6.1 Å resolution cryoEM map of the LdcIa, (pH 6.2) (Figs 1C,D and S2).	RESULTS
+204	207	map	evidence	In the frame of this work, we produced two novel subnanometer resolution cryoEM reconstructions of the E. coli lysine decarboxylases at pH optimal for their enzymatic activity – a 5.5 Å resolution cryoEM map of the LdcC (pH 7.5) for which no 3D structural information has been previously available (Figs 1A,B and S1), and a 6.1 Å resolution cryoEM map of the LdcIa, (pH 6.2) (Figs 1C,D and S2).	RESULTS
+215	219	LdcC	protein	In the frame of this work, we produced two novel subnanometer resolution cryoEM reconstructions of the E. coli lysine decarboxylases at pH optimal for their enzymatic activity – a 5.5 Å resolution cryoEM map of the LdcC (pH 7.5) for which no 3D structural information has been previously available (Figs 1A,B and S1), and a 6.1 Å resolution cryoEM map of the LdcIa, (pH 6.2) (Figs 1C,D and S2).	RESULTS
+221	227	pH 7.5	protein_state	In the frame of this work, we produced two novel subnanometer resolution cryoEM reconstructions of the E. coli lysine decarboxylases at pH optimal for their enzymatic activity – a 5.5 Å resolution cryoEM map of the LdcC (pH 7.5) for which no 3D structural information has been previously available (Figs 1A,B and S1), and a 6.1 Å resolution cryoEM map of the LdcIa, (pH 6.2) (Figs 1C,D and S2).	RESULTS
+341	347	cryoEM	experimental_method	In the frame of this work, we produced two novel subnanometer resolution cryoEM reconstructions of the E. coli lysine decarboxylases at pH optimal for their enzymatic activity – a 5.5 Å resolution cryoEM map of the LdcC (pH 7.5) for which no 3D structural information has been previously available (Figs 1A,B and S1), and a 6.1 Å resolution cryoEM map of the LdcIa, (pH 6.2) (Figs 1C,D and S2).	RESULTS
+348	351	map	evidence	In the frame of this work, we produced two novel subnanometer resolution cryoEM reconstructions of the E. coli lysine decarboxylases at pH optimal for their enzymatic activity – a 5.5 Å resolution cryoEM map of the LdcC (pH 7.5) for which no 3D structural information has been previously available (Figs 1A,B and S1), and a 6.1 Å resolution cryoEM map of the LdcIa, (pH 6.2) (Figs 1C,D and S2).	RESULTS
+359	364	LdcIa	protein	In the frame of this work, we produced two novel subnanometer resolution cryoEM reconstructions of the E. coli lysine decarboxylases at pH optimal for their enzymatic activity – a 5.5 Å resolution cryoEM map of the LdcC (pH 7.5) for which no 3D structural information has been previously available (Figs 1A,B and S1), and a 6.1 Å resolution cryoEM map of the LdcIa, (pH 6.2) (Figs 1C,D and S2).	RESULTS
+367	373	pH 6.2	protein_state	In the frame of this work, we produced two novel subnanometer resolution cryoEM reconstructions of the E. coli lysine decarboxylases at pH optimal for their enzymatic activity – a 5.5 Å resolution cryoEM map of the LdcC (pH 7.5) for which no 3D structural information has been previously available (Figs 1A,B and S1), and a 6.1 Å resolution cryoEM map of the LdcIa, (pH 6.2) (Figs 1C,D and S2).	RESULTS
+37	43	cryoEM	experimental_method	In addition, we improved our earlier cryoEM map of the LdcI-LARA complex from 7.5 Å to 6.2 Å resolution (Figs 1E,F and S3).	RESULTS
+44	47	map	evidence	In addition, we improved our earlier cryoEM map of the LdcI-LARA complex from 7.5 Å to 6.2 Å resolution (Figs 1E,F and S3).	RESULTS
+55	64	LdcI-LARA	complex_assembly	In addition, we improved our earlier cryoEM map of the LdcI-LARA complex from 7.5 Å to 6.2 Å resolution (Figs 1E,F and S3).	RESULTS
+15	30	reconstructions	evidence	Based on these reconstructions, reliable pseudoatomic models of the three assemblies were obtained by flexible fitting of either the crystal structure of LdcIi or a derived structural homology model of LdcC (Table S1).	RESULTS
+41	60	pseudoatomic models	evidence	Based on these reconstructions, reliable pseudoatomic models of the three assemblies were obtained by flexible fitting of either the crystal structure of LdcIi or a derived structural homology model of LdcC (Table S1).	RESULTS
+102	121	flexible fitting of	experimental_method	Based on these reconstructions, reliable pseudoatomic models of the three assemblies were obtained by flexible fitting of either the crystal structure of LdcIi or a derived structural homology model of LdcC (Table S1).	RESULTS
+133	150	crystal structure	evidence	Based on these reconstructions, reliable pseudoatomic models of the three assemblies were obtained by flexible fitting of either the crystal structure of LdcIi or a derived structural homology model of LdcC (Table S1).	RESULTS
+154	159	LdcIi	protein	Based on these reconstructions, reliable pseudoatomic models of the three assemblies were obtained by flexible fitting of either the crystal structure of LdcIi or a derived structural homology model of LdcC (Table S1).	RESULTS
+173	198	structural homology model	experimental_method	Based on these reconstructions, reliable pseudoatomic models of the three assemblies were obtained by flexible fitting of either the crystal structure of LdcIi or a derived structural homology model of LdcC (Table S1).	RESULTS
+202	206	LdcC	protein	Based on these reconstructions, reliable pseudoatomic models of the three assemblies were obtained by flexible fitting of either the crystal structure of LdcIi or a derived structural homology model of LdcC (Table S1).	RESULTS
+38	57	pseudoatomic models	evidence	Significant differences between these pseudoatomic models can be interpreted as movements between specific biological states of the proteins as described below.	RESULTS
+4	16	wing domains	structure_element	The wing domains as a stable anchor at the center of the double-ring	RESULTS
+57	68	double-ring	structure_element	The wing domains as a stable anchor at the center of the double-ring	RESULTS
+46	58	superimposed	experimental_method	As a first step of a comparative analysis, we superimposed the three cryoEM reconstructions (LdcIa, LdcI-LARA and LdcC) and the crystal structure of the LdcIi decamer (Fig. 2 and Movie S1).	RESULTS
+69	75	cryoEM	experimental_method	As a first step of a comparative analysis, we superimposed the three cryoEM reconstructions (LdcIa, LdcI-LARA and LdcC) and the crystal structure of the LdcIi decamer (Fig. 2 and Movie S1).	RESULTS
+76	91	reconstructions	evidence	As a first step of a comparative analysis, we superimposed the three cryoEM reconstructions (LdcIa, LdcI-LARA and LdcC) and the crystal structure of the LdcIi decamer (Fig. 2 and Movie S1).	RESULTS
+93	98	LdcIa	protein	As a first step of a comparative analysis, we superimposed the three cryoEM reconstructions (LdcIa, LdcI-LARA and LdcC) and the crystal structure of the LdcIi decamer (Fig. 2 and Movie S1).	RESULTS
+100	109	LdcI-LARA	complex_assembly	As a first step of a comparative analysis, we superimposed the three cryoEM reconstructions (LdcIa, LdcI-LARA and LdcC) and the crystal structure of the LdcIi decamer (Fig. 2 and Movie S1).	RESULTS
+114	118	LdcC	protein	As a first step of a comparative analysis, we superimposed the three cryoEM reconstructions (LdcIa, LdcI-LARA and LdcC) and the crystal structure of the LdcIi decamer (Fig. 2 and Movie S1).	RESULTS
+128	145	crystal structure	evidence	As a first step of a comparative analysis, we superimposed the three cryoEM reconstructions (LdcIa, LdcI-LARA and LdcC) and the crystal structure of the LdcIi decamer (Fig. 2 and Movie S1).	RESULTS
+153	158	LdcIi	protein	As a first step of a comparative analysis, we superimposed the three cryoEM reconstructions (LdcIa, LdcI-LARA and LdcC) and the crystal structure of the LdcIi decamer (Fig. 2 and Movie S1).	RESULTS
+159	166	decamer	oligomeric_state	As a first step of a comparative analysis, we superimposed the three cryoEM reconstructions (LdcIa, LdcI-LARA and LdcC) and the crystal structure of the LdcIi decamer (Fig. 2 and Movie S1).	RESULTS
+5	18	superposition	experimental_method	This superposition reveals that the densities lining the central hole of the toroid are roughly at the same location, while the rest of the structure exhibits noticeable changes.	RESULTS
+36	45	densities	evidence	This superposition reveals that the densities lining the central hole of the toroid are roughly at the same location, while the rest of the structure exhibits noticeable changes.	RESULTS
+57	69	central hole	structure_element	This superposition reveals that the densities lining the central hole of the toroid are roughly at the same location, while the rest of the structure exhibits noticeable changes.	RESULTS
+77	83	toroid	structure_element	This superposition reveals that the densities lining the central hole of the toroid are roughly at the same location, while the rest of the structure exhibits noticeable changes.	RESULTS
+140	149	structure	evidence	This superposition reveals that the densities lining the central hole of the toroid are roughly at the same location, while the rest of the structure exhibits noticeable changes.	RESULTS
+35	46	double-ring	structure_element	Specifically, at the center of the double-ring the wing domains of the subunits provide the conserved basis for the assembly with the lowest root mean square deviation (RMSD) (between 1.4 and 2 Å for the Cα atoms only), whereas the peripheral CTDs containing the RavA binding interface manifest the highest RMSD (up to 4.2 Å) (Table S2).	RESULTS
+51	63	wing domains	structure_element	Specifically, at the center of the double-ring the wing domains of the subunits provide the conserved basis for the assembly with the lowest root mean square deviation (RMSD) (between 1.4 and 2 Å for the Cα atoms only), whereas the peripheral CTDs containing the RavA binding interface manifest the highest RMSD (up to 4.2 Å) (Table S2).	RESULTS
+92	101	conserved	protein_state	Specifically, at the center of the double-ring the wing domains of the subunits provide the conserved basis for the assembly with the lowest root mean square deviation (RMSD) (between 1.4 and 2 Å for the Cα atoms only), whereas the peripheral CTDs containing the RavA binding interface manifest the highest RMSD (up to 4.2 Å) (Table S2).	RESULTS
+134	167	lowest root mean square deviation	evidence	Specifically, at the center of the double-ring the wing domains of the subunits provide the conserved basis for the assembly with the lowest root mean square deviation (RMSD) (between 1.4 and 2 Å for the Cα atoms only), whereas the peripheral CTDs containing the RavA binding interface manifest the highest RMSD (up to 4.2 Å) (Table S2).	RESULTS
+169	173	RMSD	evidence	Specifically, at the center of the double-ring the wing domains of the subunits provide the conserved basis for the assembly with the lowest root mean square deviation (RMSD) (between 1.4 and 2 Å for the Cα atoms only), whereas the peripheral CTDs containing the RavA binding interface manifest the highest RMSD (up to 4.2 Å) (Table S2).	RESULTS
+243	247	CTDs	structure_element	Specifically, at the center of the double-ring the wing domains of the subunits provide the conserved basis for the assembly with the lowest root mean square deviation (RMSD) (between 1.4 and 2 Å for the Cα atoms only), whereas the peripheral CTDs containing the RavA binding interface manifest the highest RMSD (up to 4.2 Å) (Table S2).	RESULTS
+263	285	RavA binding interface	site	Specifically, at the center of the double-ring the wing domains of the subunits provide the conserved basis for the assembly with the lowest root mean square deviation (RMSD) (between 1.4 and 2 Å for the Cα atoms only), whereas the peripheral CTDs containing the RavA binding interface manifest the highest RMSD (up to 4.2 Å) (Table S2).	RESULTS
+307	311	RMSD	evidence	Specifically, at the center of the double-ring the wing domains of the subunits provide the conserved basis for the assembly with the lowest root mean square deviation (RMSD) (between 1.4 and 2 Å for the Cα atoms only), whereas the peripheral CTDs containing the RavA binding interface manifest the highest RMSD (up to 4.2 Å) (Table S2).	RESULTS
+17	29	wing domains	structure_element	In addition, the wing domains of all structures are very similar, with the RMSD after optimal rigid body alignment (RMSDmin) less than 1.1 Å. Thus, taking the limited resolution of the cryoEM maps into account, we consider that the wing domains of all the four structures are essentially identical and that in the present study the RMSD of less than 2 Å can serve as a baseline below which differences may be assumed as insignificant.	RESULTS
+37	47	structures	evidence	In addition, the wing domains of all structures are very similar, with the RMSD after optimal rigid body alignment (RMSDmin) less than 1.1 Å. Thus, taking the limited resolution of the cryoEM maps into account, we consider that the wing domains of all the four structures are essentially identical and that in the present study the RMSD of less than 2 Å can serve as a baseline below which differences may be assumed as insignificant.	RESULTS
+75	79	RMSD	evidence	In addition, the wing domains of all structures are very similar, with the RMSD after optimal rigid body alignment (RMSDmin) less than 1.1 Å. Thus, taking the limited resolution of the cryoEM maps into account, we consider that the wing domains of all the four structures are essentially identical and that in the present study the RMSD of less than 2 Å can serve as a baseline below which differences may be assumed as insignificant.	RESULTS
+116	123	RMSDmin	evidence	In addition, the wing domains of all structures are very similar, with the RMSD after optimal rigid body alignment (RMSDmin) less than 1.1 Å. Thus, taking the limited resolution of the cryoEM maps into account, we consider that the wing domains of all the four structures are essentially identical and that in the present study the RMSD of less than 2 Å can serve as a baseline below which differences may be assumed as insignificant.	RESULTS
+185	191	cryoEM	experimental_method	In addition, the wing domains of all structures are very similar, with the RMSD after optimal rigid body alignment (RMSDmin) less than 1.1 Å. Thus, taking the limited resolution of the cryoEM maps into account, we consider that the wing domains of all the four structures are essentially identical and that in the present study the RMSD of less than 2 Å can serve as a baseline below which differences may be assumed as insignificant.	RESULTS
+192	196	maps	evidence	In addition, the wing domains of all structures are very similar, with the RMSD after optimal rigid body alignment (RMSDmin) less than 1.1 Å. Thus, taking the limited resolution of the cryoEM maps into account, we consider that the wing domains of all the four structures are essentially identical and that in the present study the RMSD of less than 2 Å can serve as a baseline below which differences may be assumed as insignificant.	RESULTS
+232	244	wing domains	structure_element	In addition, the wing domains of all structures are very similar, with the RMSD after optimal rigid body alignment (RMSDmin) less than 1.1 Å. Thus, taking the limited resolution of the cryoEM maps into account, we consider that the wing domains of all the four structures are essentially identical and that in the present study the RMSD of less than 2 Å can serve as a baseline below which differences may be assumed as insignificant.	RESULTS
+261	271	structures	evidence	In addition, the wing domains of all structures are very similar, with the RMSD after optimal rigid body alignment (RMSDmin) less than 1.1 Å. Thus, taking the limited resolution of the cryoEM maps into account, we consider that the wing domains of all the four structures are essentially identical and that in the present study the RMSD of less than 2 Å can serve as a baseline below which differences may be assumed as insignificant.	RESULTS
+332	336	RMSD	evidence	In addition, the wing domains of all structures are very similar, with the RMSD after optimal rigid body alignment (RMSDmin) less than 1.1 Å. Thus, taking the limited resolution of the cryoEM maps into account, we consider that the wing domains of all the four structures are essentially identical and that in the present study the RMSD of less than 2 Å can serve as a baseline below which differences may be assumed as insignificant.	RESULTS
+25	37	central part	structure_element	This preservation of the central part of the double-ring assembly may help the enzymes to maintain their decameric state upon activation and incorporation into the LdcI-RavA cage.	RESULTS
+105	114	decameric	oligomeric_state	This preservation of the central part of the double-ring assembly may help the enzymes to maintain their decameric state upon activation and incorporation into the LdcI-RavA cage.	RESULTS
+164	173	LdcI-RavA	complex_assembly	This preservation of the central part of the double-ring assembly may help the enzymes to maintain their decameric state upon activation and incorporation into the LdcI-RavA cage.	RESULTS
+4	15	core domain	structure_element	The core domain and the active site rearrangements upon pH-dependent enzyme activation and LARA binding	RESULTS
+24	35	active site	site	The core domain and the active site rearrangements upon pH-dependent enzyme activation and LARA binding	RESULTS
+56	68	pH-dependent	protein_state	The core domain and the active site rearrangements upon pH-dependent enzyme activation and LARA binding	RESULTS
+5	22	visual inspection	experimental_method	Both visual inspection (Fig. 2) and RMSD calculations (Table S2) show that globally the three structures at active pH (LdcIa, LdcI-LARA and LdcC) are more similar to each other than to the structure determined at high pH conditions (LdcIi).	RESULTS
+36	53	RMSD calculations	experimental_method	Both visual inspection (Fig. 2) and RMSD calculations (Table S2) show that globally the three structures at active pH (LdcIa, LdcI-LARA and LdcC) are more similar to each other than to the structure determined at high pH conditions (LdcIi).	RESULTS
+94	104	structures	evidence	Both visual inspection (Fig. 2) and RMSD calculations (Table S2) show that globally the three structures at active pH (LdcIa, LdcI-LARA and LdcC) are more similar to each other than to the structure determined at high pH conditions (LdcIi).	RESULTS
+108	117	active pH	protein_state	Both visual inspection (Fig. 2) and RMSD calculations (Table S2) show that globally the three structures at active pH (LdcIa, LdcI-LARA and LdcC) are more similar to each other than to the structure determined at high pH conditions (LdcIi).	RESULTS
+119	124	LdcIa	protein	Both visual inspection (Fig. 2) and RMSD calculations (Table S2) show that globally the three structures at active pH (LdcIa, LdcI-LARA and LdcC) are more similar to each other than to the structure determined at high pH conditions (LdcIi).	RESULTS
+126	135	LdcI-LARA	complex_assembly	Both visual inspection (Fig. 2) and RMSD calculations (Table S2) show that globally the three structures at active pH (LdcIa, LdcI-LARA and LdcC) are more similar to each other than to the structure determined at high pH conditions (LdcIi).	RESULTS
+140	144	LdcC	protein	Both visual inspection (Fig. 2) and RMSD calculations (Table S2) show that globally the three structures at active pH (LdcIa, LdcI-LARA and LdcC) are more similar to each other than to the structure determined at high pH conditions (LdcIi).	RESULTS
+213	220	high pH	protein_state	Both visual inspection (Fig. 2) and RMSD calculations (Table S2) show that globally the three structures at active pH (LdcIa, LdcI-LARA and LdcC) are more similar to each other than to the structure determined at high pH conditions (LdcIi).	RESULTS
+233	238	LdcIi	protein	Both visual inspection (Fig. 2) and RMSD calculations (Table S2) show that globally the three structures at active pH (LdcIa, LdcI-LARA and LdcC) are more similar to each other than to the structure determined at high pH conditions (LdcIi).	RESULTS
+4	13	decameric	oligomeric_state	The decameric enzyme is built of five dimers associating into a 5-fold symmetrical double-ring (two monomers making a dimer are delineated in Fig. 1).	RESULTS
+38	44	dimers	oligomeric_state	The decameric enzyme is built of five dimers associating into a 5-fold symmetrical double-ring (two monomers making a dimer are delineated in Fig. 1).	RESULTS
+64	94	5-fold symmetrical double-ring	structure_element	The decameric enzyme is built of five dimers associating into a 5-fold symmetrical double-ring (two monomers making a dimer are delineated in Fig. 1).	RESULTS
+100	108	monomers	oligomeric_state	The decameric enzyme is built of five dimers associating into a 5-fold symmetrical double-ring (two monomers making a dimer are delineated in Fig. 1).	RESULTS
+118	123	dimer	oligomeric_state	The decameric enzyme is built of five dimers associating into a 5-fold symmetrical double-ring (two monomers making a dimer are delineated in Fig. 1).	RESULTS
+18	26	α family	protein_type	As common for the α family of the PLP-dependent decarboxylases, dimerization is required for the enzymatic activity because the active site is buried in the dimer interface (Fig. 3A,B).	RESULTS
+34	62	PLP-dependent decarboxylases	protein_type	As common for the α family of the PLP-dependent decarboxylases, dimerization is required for the enzymatic activity because the active site is buried in the dimer interface (Fig. 3A,B).	RESULTS
+128	139	active site	site	As common for the α family of the PLP-dependent decarboxylases, dimerization is required for the enzymatic activity because the active site is buried in the dimer interface (Fig. 3A,B).	RESULTS
+157	172	dimer interface	site	As common for the α family of the PLP-dependent decarboxylases, dimerization is required for the enzymatic activity because the active site is buried in the dimer interface (Fig. 3A,B).	RESULTS
+5	14	interface	site	This interface is formed essentially by the core domains with some contribution of the CTDs.	RESULTS
+44	56	core domains	structure_element	This interface is formed essentially by the core domains with some contribution of the CTDs.	RESULTS
+87	91	CTDs	structure_element	This interface is formed essentially by the core domains with some contribution of the CTDs.	RESULTS
+4	15	core domain	structure_element	The core domain is built by the PLP-binding subdomain (PLP-SD, residues 184–417) flanked by two smaller subdomains rich in partly disordered loops – the linker region (residues 130–183) and the subdomain 4 (residues 418–563).	RESULTS
+32	53	PLP-binding subdomain	structure_element	The core domain is built by the PLP-binding subdomain (PLP-SD, residues 184–417) flanked by two smaller subdomains rich in partly disordered loops – the linker region (residues 130–183) and the subdomain 4 (residues 418–563).	RESULTS
+55	61	PLP-SD	structure_element	The core domain is built by the PLP-binding subdomain (PLP-SD, residues 184–417) flanked by two smaller subdomains rich in partly disordered loops – the linker region (residues 130–183) and the subdomain 4 (residues 418–563).	RESULTS
+72	79	184–417	residue_range	The core domain is built by the PLP-binding subdomain (PLP-SD, residues 184–417) flanked by two smaller subdomains rich in partly disordered loops – the linker region (residues 130–183) and the subdomain 4 (residues 418–563).	RESULTS
+104	114	subdomains	structure_element	The core domain is built by the PLP-binding subdomain (PLP-SD, residues 184–417) flanked by two smaller subdomains rich in partly disordered loops – the linker region (residues 130–183) and the subdomain 4 (residues 418–563).	RESULTS
+123	140	partly disordered	protein_state	The core domain is built by the PLP-binding subdomain (PLP-SD, residues 184–417) flanked by two smaller subdomains rich in partly disordered loops – the linker region (residues 130–183) and the subdomain 4 (residues 418–563).	RESULTS
+141	146	loops	structure_element	The core domain is built by the PLP-binding subdomain (PLP-SD, residues 184–417) flanked by two smaller subdomains rich in partly disordered loops – the linker region (residues 130–183) and the subdomain 4 (residues 418–563).	RESULTS
+153	166	linker region	structure_element	The core domain is built by the PLP-binding subdomain (PLP-SD, residues 184–417) flanked by two smaller subdomains rich in partly disordered loops – the linker region (residues 130–183) and the subdomain 4 (residues 418–563).	RESULTS
+177	184	130–183	residue_range	The core domain is built by the PLP-binding subdomain (PLP-SD, residues 184–417) flanked by two smaller subdomains rich in partly disordered loops – the linker region (residues 130–183) and the subdomain 4 (residues 418–563).	RESULTS
+194	205	subdomain 4	structure_element	The core domain is built by the PLP-binding subdomain (PLP-SD, residues 184–417) flanked by two smaller subdomains rich in partly disordered loops – the linker region (residues 130–183) and the subdomain 4 (residues 418–563).	RESULTS
+216	223	418–563	residue_range	The core domain is built by the PLP-binding subdomain (PLP-SD, residues 184–417) flanked by two smaller subdomains rich in partly disordered loops – the linker region (residues 130–183) and the subdomain 4 (residues 418–563).	RESULTS
+33	39	PLP-SD	structure_element	Zooming in the variations in the PLP-SD shows that most of the structural changes concern displacements in the active site (Fig. 3C–F).	RESULTS
+111	122	active site	site	Zooming in the variations in the PLP-SD shows that most of the structural changes concern displacements in the active site (Fig. 3C–F).	RESULTS
+45	52	PLP-SDs	structure_element	The most conspicuous differences between the PLP-SDs can be linked to the pH-dependent activation of the enzymes.	RESULTS
+74	86	pH-dependent	protein_state	The most conspicuous differences between the PLP-SDs can be linked to the pH-dependent activation of the enzymes.	RESULTS
+22	28	cryoEM	experimental_method	The resolution of the cryoEM maps does not allow modeling the position of the PLP moiety and calls for caution in detailed mechanistic interpretations in terms of individual amino acids.	RESULTS
+29	33	maps	evidence	The resolution of the cryoEM maps does not allow modeling the position of the PLP moiety and calls for caution in detailed mechanistic interpretations in terms of individual amino acids.	RESULTS
+78	81	PLP	chemical	The resolution of the cryoEM maps does not allow modeling the position of the PLP moiety and calls for caution in detailed mechanistic interpretations in terms of individual amino acids.	RESULTS
+174	185	amino acids	chemical	The resolution of the cryoEM maps does not allow modeling the position of the PLP moiety and calls for caution in detailed mechanistic interpretations in terms of individual amino acids.	RESULTS
+31	36	LdcIi	protein	In particular, transition from LdcIi to LdcI-LARA involves ~3.5 Å and ~4.5 Å shifts away from the 5-fold axis in the active site α-helices spanning residues 218–232 and 246–254 respectively (Fig. 3C–E).	RESULTS
+40	49	LdcI-LARA	complex_assembly	In particular, transition from LdcIi to LdcI-LARA involves ~3.5 Å and ~4.5 Å shifts away from the 5-fold axis in the active site α-helices spanning residues 218–232 and 246–254 respectively (Fig. 3C–E).	RESULTS
+117	128	active site	site	In particular, transition from LdcIi to LdcI-LARA involves ~3.5 Å and ~4.5 Å shifts away from the 5-fold axis in the active site α-helices spanning residues 218–232 and 246–254 respectively (Fig. 3C–E).	RESULTS
+129	138	α-helices	structure_element	In particular, transition from LdcIi to LdcI-LARA involves ~3.5 Å and ~4.5 Å shifts away from the 5-fold axis in the active site α-helices spanning residues 218–232 and 246–254 respectively (Fig. 3C–E).	RESULTS
+157	164	218–232	residue_range	In particular, transition from LdcIi to LdcI-LARA involves ~3.5 Å and ~4.5 Å shifts away from the 5-fold axis in the active site α-helices spanning residues 218–232 and 246–254 respectively (Fig. 3C–E).	RESULTS
+169	176	246–254	residue_range	In particular, transition from LdcIi to LdcI-LARA involves ~3.5 Å and ~4.5 Å shifts away from the 5-fold axis in the active site α-helices spanning residues 218–232 and 246–254 respectively (Fig. 3C–E).	RESULTS
+32	39	PLP-SDs	structure_element	Between these two extremes, the PLP-SDs of LdcIa and LdcC are similar both in the context of the decamer (Fig. 3F) and in terms of RMSDmin = 0.9 Å, which probably reflects the fact that, at the optimal pH, these lysine decarboxylases have a similar enzymatic activity.	RESULTS
+43	48	LdcIa	protein	Between these two extremes, the PLP-SDs of LdcIa and LdcC are similar both in the context of the decamer (Fig. 3F) and in terms of RMSDmin = 0.9 Å, which probably reflects the fact that, at the optimal pH, these lysine decarboxylases have a similar enzymatic activity.	RESULTS
+53	57	LdcC	protein	Between these two extremes, the PLP-SDs of LdcIa and LdcC are similar both in the context of the decamer (Fig. 3F) and in terms of RMSDmin = 0.9 Å, which probably reflects the fact that, at the optimal pH, these lysine decarboxylases have a similar enzymatic activity.	RESULTS
+97	104	decamer	oligomeric_state	Between these two extremes, the PLP-SDs of LdcIa and LdcC are similar both in the context of the decamer (Fig. 3F) and in terms of RMSDmin = 0.9 Å, which probably reflects the fact that, at the optimal pH, these lysine decarboxylases have a similar enzymatic activity.	RESULTS
+131	138	RMSDmin	evidence	Between these two extremes, the PLP-SDs of LdcIa and LdcC are similar both in the context of the decamer (Fig. 3F) and in terms of RMSDmin = 0.9 Å, which probably reflects the fact that, at the optimal pH, these lysine decarboxylases have a similar enzymatic activity.	RESULTS
+194	204	optimal pH	protein_state	Between these two extremes, the PLP-SDs of LdcIa and LdcC are similar both in the context of the decamer (Fig. 3F) and in terms of RMSDmin = 0.9 Å, which probably reflects the fact that, at the optimal pH, these lysine decarboxylases have a similar enzymatic activity.	RESULTS
+212	233	lysine decarboxylases	protein_type	Between these two extremes, the PLP-SDs of LdcIa and LdcC are similar both in the context of the decamer (Fig. 3F) and in terms of RMSDmin = 0.9 Å, which probably reflects the fact that, at the optimal pH, these lysine decarboxylases have a similar enzymatic activity.	RESULTS
+25	48	biochemical observation	experimental_method	In addition, our earlier biochemical observation that the enzymatic activity of LdcIa is unaffected by RavA binding is consistent with the relatively small changes undergone by the active site upon transition from LdcIa to LdcI-LARA.	RESULTS
+80	85	LdcIa	protein	In addition, our earlier biochemical observation that the enzymatic activity of LdcIa is unaffected by RavA binding is consistent with the relatively small changes undergone by the active site upon transition from LdcIa to LdcI-LARA.	RESULTS
+103	107	RavA	protein	In addition, our earlier biochemical observation that the enzymatic activity of LdcIa is unaffected by RavA binding is consistent with the relatively small changes undergone by the active site upon transition from LdcIa to LdcI-LARA.	RESULTS
+181	192	active site	site	In addition, our earlier biochemical observation that the enzymatic activity of LdcIa is unaffected by RavA binding is consistent with the relatively small changes undergone by the active site upon transition from LdcIa to LdcI-LARA.	RESULTS
+214	219	LdcIa	protein	In addition, our earlier biochemical observation that the enzymatic activity of LdcIa is unaffected by RavA binding is consistent with the relatively small changes undergone by the active site upon transition from LdcIa to LdcI-LARA.	RESULTS
+223	232	LdcI-LARA	complex_assembly	In addition, our earlier biochemical observation that the enzymatic activity of LdcIa is unaffected by RavA binding is consistent with the relatively small changes undergone by the active site upon transition from LdcIa to LdcI-LARA.	RESULTS
+47	64	crystal structure	evidence	Worthy of note, our previous comparison of the crystal structure of LdcIi with that of the inducible arginine decarboxylase AdiA revealed high conservation of the PLP-coordinating residues and identified a patch of negatively charged residues lining the active site channel as a potential binding site for the target amino acid substrate (Figs S3 and S4 in ref.).	RESULTS
+68	73	LdcIi	protein	Worthy of note, our previous comparison of the crystal structure of LdcIi with that of the inducible arginine decarboxylase AdiA revealed high conservation of the PLP-coordinating residues and identified a patch of negatively charged residues lining the active site channel as a potential binding site for the target amino acid substrate (Figs S3 and S4 in ref.).	RESULTS
+91	100	inducible	protein_state	Worthy of note, our previous comparison of the crystal structure of LdcIi with that of the inducible arginine decarboxylase AdiA revealed high conservation of the PLP-coordinating residues and identified a patch of negatively charged residues lining the active site channel as a potential binding site for the target amino acid substrate (Figs S3 and S4 in ref.).	RESULTS
+101	123	arginine decarboxylase	protein_type	Worthy of note, our previous comparison of the crystal structure of LdcIi with that of the inducible arginine decarboxylase AdiA revealed high conservation of the PLP-coordinating residues and identified a patch of negatively charged residues lining the active site channel as a potential binding site for the target amino acid substrate (Figs S3 and S4 in ref.).	RESULTS
+124	128	AdiA	protein	Worthy of note, our previous comparison of the crystal structure of LdcIi with that of the inducible arginine decarboxylase AdiA revealed high conservation of the PLP-coordinating residues and identified a patch of negatively charged residues lining the active site channel as a potential binding site for the target amino acid substrate (Figs S3 and S4 in ref.).	RESULTS
+138	155	high conservation	protein_state	Worthy of note, our previous comparison of the crystal structure of LdcIi with that of the inducible arginine decarboxylase AdiA revealed high conservation of the PLP-coordinating residues and identified a patch of negatively charged residues lining the active site channel as a potential binding site for the target amino acid substrate (Figs S3 and S4 in ref.).	RESULTS
+163	188	PLP-coordinating residues	site	Worthy of note, our previous comparison of the crystal structure of LdcIi with that of the inducible arginine decarboxylase AdiA revealed high conservation of the PLP-coordinating residues and identified a patch of negatively charged residues lining the active site channel as a potential binding site for the target amino acid substrate (Figs S3 and S4 in ref.).	RESULTS
+206	242	patch of negatively charged residues	site	Worthy of note, our previous comparison of the crystal structure of LdcIi with that of the inducible arginine decarboxylase AdiA revealed high conservation of the PLP-coordinating residues and identified a patch of negatively charged residues lining the active site channel as a potential binding site for the target amino acid substrate (Figs S3 and S4 in ref.).	RESULTS
+254	273	active site channel	site	Worthy of note, our previous comparison of the crystal structure of LdcIi with that of the inducible arginine decarboxylase AdiA revealed high conservation of the PLP-coordinating residues and identified a patch of negatively charged residues lining the active site channel as a potential binding site for the target amino acid substrate (Figs S3 and S4 in ref.).	RESULTS
+289	301	binding site	site	Worthy of note, our previous comparison of the crystal structure of LdcIi with that of the inducible arginine decarboxylase AdiA revealed high conservation of the PLP-coordinating residues and identified a patch of negatively charged residues lining the active site channel as a potential binding site for the target amino acid substrate (Figs S3 and S4 in ref.).	RESULTS
+317	327	amino acid	chemical	Worthy of note, our previous comparison of the crystal structure of LdcIi with that of the inducible arginine decarboxylase AdiA revealed high conservation of the PLP-coordinating residues and identified a patch of negatively charged residues lining the active site channel as a potential binding site for the target amino acid substrate (Figs S3 and S4 in ref.).	RESULTS
+22	42	ppGpp binding pocket	site	Rearrangements of the ppGpp binding pocket upon pH-dependent enzyme activation and LARA binding	RESULTS
+48	60	pH-dependent	protein_state	Rearrangements of the ppGpp binding pocket upon pH-dependent enzyme activation and LARA binding	RESULTS
+83	87	LARA	structure_element	Rearrangements of the ppGpp binding pocket upon pH-dependent enzyme activation and LARA binding	RESULTS
+20	24	LdcI	protein	An inhibitor of the LdcI and LdcC activity, the stringent response alarmone ppGpp, is known to bind at the interface between neighboring monomers within each ring (Fig. S4).	RESULTS
+29	33	LdcC	protein	An inhibitor of the LdcI and LdcC activity, the stringent response alarmone ppGpp, is known to bind at the interface between neighboring monomers within each ring (Fig. S4).	RESULTS
+48	75	stringent response alarmone	chemical	An inhibitor of the LdcI and LdcC activity, the stringent response alarmone ppGpp, is known to bind at the interface between neighboring monomers within each ring (Fig. S4).	RESULTS
+76	81	ppGpp	chemical	An inhibitor of the LdcI and LdcC activity, the stringent response alarmone ppGpp, is known to bind at the interface between neighboring monomers within each ring (Fig. S4).	RESULTS
+107	116	interface	site	An inhibitor of the LdcI and LdcC activity, the stringent response alarmone ppGpp, is known to bind at the interface between neighboring monomers within each ring (Fig. S4).	RESULTS
+137	145	monomers	oligomeric_state	An inhibitor of the LdcI and LdcC activity, the stringent response alarmone ppGpp, is known to bind at the interface between neighboring monomers within each ring (Fig. S4).	RESULTS
+158	162	ring	structure_element	An inhibitor of the LdcI and LdcC activity, the stringent response alarmone ppGpp, is known to bind at the interface between neighboring monomers within each ring (Fig. S4).	RESULTS
+4	24	ppGpp binding pocket	site	The ppGpp binding pocket is made up by residues from all domains and is located approximately 30 Å away from the PLP moiety.	RESULTS
+113	116	PLP	chemical	The ppGpp binding pocket is made up by residues from all domains and is located approximately 30 Å away from the PLP moiety.	RESULTS
+12	29	crystal structure	evidence	Whereas the crystal structure of the ppGpp-LdcIi was solved to 2 Å resolution, only a 4.1 Å resolution structure of the ppGpp-free LdcIi could be obtained.	RESULTS
+37	48	ppGpp-LdcIi	complex_assembly	Whereas the crystal structure of the ppGpp-LdcIi was solved to 2 Å resolution, only a 4.1 Å resolution structure of the ppGpp-free LdcIi could be obtained.	RESULTS
+53	59	solved	experimental_method	Whereas the crystal structure of the ppGpp-LdcIi was solved to 2 Å resolution, only a 4.1 Å resolution structure of the ppGpp-free LdcIi could be obtained.	RESULTS
+103	112	structure	evidence	Whereas the crystal structure of the ppGpp-LdcIi was solved to 2 Å resolution, only a 4.1 Å resolution structure of the ppGpp-free LdcIi could be obtained.	RESULTS
+120	130	ppGpp-free	protein_state	Whereas the crystal structure of the ppGpp-LdcIi was solved to 2 Å resolution, only a 4.1 Å resolution structure of the ppGpp-free LdcIi could be obtained.	RESULTS
+131	136	LdcIi	protein	Whereas the crystal structure of the ppGpp-LdcIi was solved to 2 Å resolution, only a 4.1 Å resolution structure of the ppGpp-free LdcIi could be obtained.	RESULTS
+24	27	apo	protein_state	At this resolution, the apo-LdcIi and ppGpp-LdcIi structures (both solved at pH 8.5) appeared indistinguishable except for the presence of ppGpp (Fig. S11 in ref. ).	RESULTS
+28	33	LdcIi	protein	At this resolution, the apo-LdcIi and ppGpp-LdcIi structures (both solved at pH 8.5) appeared indistinguishable except for the presence of ppGpp (Fig. S11 in ref. ).	RESULTS
+38	49	ppGpp-LdcIi	complex_assembly	At this resolution, the apo-LdcIi and ppGpp-LdcIi structures (both solved at pH 8.5) appeared indistinguishable except for the presence of ppGpp (Fig. S11 in ref. ).	RESULTS
+50	60	structures	evidence	At this resolution, the apo-LdcIi and ppGpp-LdcIi structures (both solved at pH 8.5) appeared indistinguishable except for the presence of ppGpp (Fig. S11 in ref. ).	RESULTS
+77	83	pH 8.5	protein_state	At this resolution, the apo-LdcIi and ppGpp-LdcIi structures (both solved at pH 8.5) appeared indistinguishable except for the presence of ppGpp (Fig. S11 in ref. ).	RESULTS
+139	144	ppGpp	chemical	At this resolution, the apo-LdcIi and ppGpp-LdcIi structures (both solved at pH 8.5) appeared indistinguishable except for the presence of ppGpp (Fig. S11 in ref. ).	RESULTS
+39	43	LdcI	protein	Thus, we speculated that inhibition of LdcI by ppGpp would be accompanied by a transduction of subtle structural changes at the level of individual amino acid side chains between the ppGpp binding pocket and the active site of the enzyme.	RESULTS
+47	52	ppGpp	chemical	Thus, we speculated that inhibition of LdcI by ppGpp would be accompanied by a transduction of subtle structural changes at the level of individual amino acid side chains between the ppGpp binding pocket and the active site of the enzyme.	RESULTS
+148	158	amino acid	chemical	Thus, we speculated that inhibition of LdcI by ppGpp would be accompanied by a transduction of subtle structural changes at the level of individual amino acid side chains between the ppGpp binding pocket and the active site of the enzyme.	RESULTS
+183	203	ppGpp binding pocket	site	Thus, we speculated that inhibition of LdcI by ppGpp would be accompanied by a transduction of subtle structural changes at the level of individual amino acid side chains between the ppGpp binding pocket and the active site of the enzyme.	RESULTS
+212	223	active site	site	Thus, we speculated that inhibition of LdcI by ppGpp would be accompanied by a transduction of subtle structural changes at the level of individual amino acid side chains between the ppGpp binding pocket and the active site of the enzyme.	RESULTS
+16	22	cryoEM	experimental_method	All our current cryoEM reconstructions of the lysine decarboxylases were obtained in the absence of ppGpp in order to be closer to the active state of the enzymes under study.	RESULTS
+23	38	reconstructions	evidence	All our current cryoEM reconstructions of the lysine decarboxylases were obtained in the absence of ppGpp in order to be closer to the active state of the enzymes under study.	RESULTS
+46	67	lysine decarboxylases	protein_type	All our current cryoEM reconstructions of the lysine decarboxylases were obtained in the absence of ppGpp in order to be closer to the active state of the enzymes under study.	RESULTS
+89	99	absence of	protein_state	All our current cryoEM reconstructions of the lysine decarboxylases were obtained in the absence of ppGpp in order to be closer to the active state of the enzymes under study.	RESULTS
+100	105	ppGpp	chemical	All our current cryoEM reconstructions of the lysine decarboxylases were obtained in the absence of ppGpp in order to be closer to the active state of the enzymes under study.	RESULTS
+135	141	active	protein_state	All our current cryoEM reconstructions of the lysine decarboxylases were obtained in the absence of ppGpp in order to be closer to the active state of the enzymes under study.	RESULTS
+25	43	ppGpp binding site	site	While differences in the ppGpp binding site could indeed be visualized (Fig. S4), the level of resolution warns against speculations about their significance.	RESULTS
+31	35	RavA	protein	The fact that interaction with RavA reduces the ppGpp affinity for LdcI despite the long distance of ~30 Å between the LARA domain binding site and the closest ppGpp binding pocket (Fig. S5) seems to favor an allosteric regulation mechanism.	RESULTS
+48	53	ppGpp	chemical	The fact that interaction with RavA reduces the ppGpp affinity for LdcI despite the long distance of ~30 Å between the LARA domain binding site and the closest ppGpp binding pocket (Fig. S5) seems to favor an allosteric regulation mechanism.	RESULTS
+67	71	LdcI	protein	The fact that interaction with RavA reduces the ppGpp affinity for LdcI despite the long distance of ~30 Å between the LARA domain binding site and the closest ppGpp binding pocket (Fig. S5) seems to favor an allosteric regulation mechanism.	RESULTS
+119	143	LARA domain binding site	site	The fact that interaction with RavA reduces the ppGpp affinity for LdcI despite the long distance of ~30 Å between the LARA domain binding site and the closest ppGpp binding pocket (Fig. S5) seems to favor an allosteric regulation mechanism.	RESULTS
+160	180	ppGpp binding pocket	site	The fact that interaction with RavA reduces the ppGpp affinity for LdcI despite the long distance of ~30 Å between the LARA domain binding site and the closest ppGpp binding pocket (Fig. S5) seems to favor an allosteric regulation mechanism.	RESULTS
+36	58	ppGpp binding residues	site	Interestingly, although a number of ppGpp binding residues are strictly conserved between LdcI and AdiA that also forms decamers at low pH optimal for its arginine decarboxylase activity, no ppGpp regulation of AdiA could be demonstrated.	RESULTS
+63	81	strictly conserved	protein_state	Interestingly, although a number of ppGpp binding residues are strictly conserved between LdcI and AdiA that also forms decamers at low pH optimal for its arginine decarboxylase activity, no ppGpp regulation of AdiA could be demonstrated.	RESULTS
+90	94	LdcI	protein	Interestingly, although a number of ppGpp binding residues are strictly conserved between LdcI and AdiA that also forms decamers at low pH optimal for its arginine decarboxylase activity, no ppGpp regulation of AdiA could be demonstrated.	RESULTS
+99	103	AdiA	protein	Interestingly, although a number of ppGpp binding residues are strictly conserved between LdcI and AdiA that also forms decamers at low pH optimal for its arginine decarboxylase activity, no ppGpp regulation of AdiA could be demonstrated.	RESULTS
+120	128	decamers	oligomeric_state	Interestingly, although a number of ppGpp binding residues are strictly conserved between LdcI and AdiA that also forms decamers at low pH optimal for its arginine decarboxylase activity, no ppGpp regulation of AdiA could be demonstrated.	RESULTS
+132	146	low pH optimal	protein_state	Interestingly, although a number of ppGpp binding residues are strictly conserved between LdcI and AdiA that also forms decamers at low pH optimal for its arginine decarboxylase activity, no ppGpp regulation of AdiA could be demonstrated.	RESULTS
+155	177	arginine decarboxylase	protein_type	Interestingly, although a number of ppGpp binding residues are strictly conserved between LdcI and AdiA that also forms decamers at low pH optimal for its arginine decarboxylase activity, no ppGpp regulation of AdiA could be demonstrated.	RESULTS
+191	196	ppGpp	chemical	Interestingly, although a number of ppGpp binding residues are strictly conserved between LdcI and AdiA that also forms decamers at low pH optimal for its arginine decarboxylase activity, no ppGpp regulation of AdiA could be demonstrated.	RESULTS
+211	215	AdiA	protein	Interestingly, although a number of ppGpp binding residues are strictly conserved between LdcI and AdiA that also forms decamers at low pH optimal for its arginine decarboxylase activity, no ppGpp regulation of AdiA could be demonstrated.	RESULTS
+31	35	CTDs	structure_element	Swinging and stretching of the CTDs upon pH-dependent LdcI activation and LARA binding	RESULTS
+41	53	pH-dependent	protein_state	Swinging and stretching of the CTDs upon pH-dependent LdcI activation and LARA binding	RESULTS
+54	58	LdcI	protein	Swinging and stretching of the CTDs upon pH-dependent LdcI activation and LARA binding	RESULTS
+74	78	LARA	structure_element	Swinging and stretching of the CTDs upon pH-dependent LdcI activation and LARA binding	RESULTS
+18	30	superimposed	experimental_method	Inspection of the superimposed decameric structures (Figs 2 and S6) suggests a depiction of the wing domains as an anchor around which the peripheral CTDs swing.	RESULTS
+31	40	decameric	oligomeric_state	Inspection of the superimposed decameric structures (Figs 2 and S6) suggests a depiction of the wing domains as an anchor around which the peripheral CTDs swing.	RESULTS
+41	51	structures	evidence	Inspection of the superimposed decameric structures (Figs 2 and S6) suggests a depiction of the wing domains as an anchor around which the peripheral CTDs swing.	RESULTS
+96	108	wing domains	structure_element	Inspection of the superimposed decameric structures (Figs 2 and S6) suggests a depiction of the wing domains as an anchor around which the peripheral CTDs swing.	RESULTS
+150	154	CTDs	structure_element	Inspection of the superimposed decameric structures (Figs 2 and S6) suggests a depiction of the wing domains as an anchor around which the peripheral CTDs swing.	RESULTS
+51	63	core domains	structure_element	This swinging movement seems to be mediated by the core domains and is accompanied by a stretching of the whole LdcI subunits attracted by the RavA magnets.	RESULTS
+112	116	LdcI	protein	This swinging movement seems to be mediated by the core domains and is accompanied by a stretching of the whole LdcI subunits attracted by the RavA magnets.	RESULTS
+117	125	subunits	structure_element	This swinging movement seems to be mediated by the core domains and is accompanied by a stretching of the whole LdcI subunits attracted by the RavA magnets.	RESULTS
+143	147	RavA	protein	This swinging movement seems to be mediated by the core domains and is accompanied by a stretching of the whole LdcI subunits attracted by the RavA magnets.	RESULTS
+12	16	CTDs	structure_element	Indeed, all CTDs have very similar structures (RMSDmin <1 Å).	RESULTS
+47	54	RMSDmin	evidence	Indeed, all CTDs have very similar structures (RMSDmin <1 Å).	RESULTS
+8	21	superposition	experimental_method	Yet the superposition of the decamers lays bare a progressive movement of the CTD as a whole upon enzyme activation by pH and the binding of LARA.	RESULTS
+29	37	decamers	oligomeric_state	Yet the superposition of the decamers lays bare a progressive movement of the CTD as a whole upon enzyme activation by pH and the binding of LARA.	RESULTS
+78	81	CTD	structure_element	Yet the superposition of the decamers lays bare a progressive movement of the CTD as a whole upon enzyme activation by pH and the binding of LARA.	RESULTS
+141	145	LARA	structure_element	Yet the superposition of the decamers lays bare a progressive movement of the CTD as a whole upon enzyme activation by pH and the binding of LARA.	RESULTS
+4	9	LdcIi	protein	The LdcIi monomer is the most compact, whereas LdcIa and especially LdcI-LARA gradually extend their CTDs towards the LARA domain of RavA (Figs 2 and 4).	RESULTS
+10	17	monomer	oligomeric_state	The LdcIi monomer is the most compact, whereas LdcIa and especially LdcI-LARA gradually extend their CTDs towards the LARA domain of RavA (Figs 2 and 4).	RESULTS
+25	37	most compact	protein_state	The LdcIi monomer is the most compact, whereas LdcIa and especially LdcI-LARA gradually extend their CTDs towards the LARA domain of RavA (Figs 2 and 4).	RESULTS
+47	52	LdcIa	protein	The LdcIi monomer is the most compact, whereas LdcIa and especially LdcI-LARA gradually extend their CTDs towards the LARA domain of RavA (Figs 2 and 4).	RESULTS
+68	77	LdcI-LARA	complex_assembly	The LdcIi monomer is the most compact, whereas LdcIa and especially LdcI-LARA gradually extend their CTDs towards the LARA domain of RavA (Figs 2 and 4).	RESULTS
+78	94	gradually extend	protein_state	The LdcIi monomer is the most compact, whereas LdcIa and especially LdcI-LARA gradually extend their CTDs towards the LARA domain of RavA (Figs 2 and 4).	RESULTS
+101	105	CTDs	structure_element	The LdcIi monomer is the most compact, whereas LdcIa and especially LdcI-LARA gradually extend their CTDs towards the LARA domain of RavA (Figs 2 and 4).	RESULTS
+118	129	LARA domain	structure_element	The LdcIi monomer is the most compact, whereas LdcIa and especially LdcI-LARA gradually extend their CTDs towards the LARA domain of RavA (Figs 2 and 4).	RESULTS
+133	137	RavA	protein	The LdcIi monomer is the most compact, whereas LdcIa and especially LdcI-LARA gradually extend their CTDs towards the LARA domain of RavA (Figs 2 and 4).	RESULTS
+107	111	LdcI	protein	These small but noticeable swinging and stretching (up to ~4 Å) may be related to the incorporation of the LdcI decamer into the LdcI-RavA cage.	RESULTS
+112	119	decamer	oligomeric_state	These small but noticeable swinging and stretching (up to ~4 Å) may be related to the incorporation of the LdcI decamer into the LdcI-RavA cage.	RESULTS
+129	138	LdcI-RavA	complex_assembly	These small but noticeable swinging and stretching (up to ~4 Å) may be related to the incorporation of the LdcI decamer into the LdcI-RavA cage.	RESULTS
+15	22	β-sheet	structure_element	The C-terminal β-sheet of a lysine decarboxylase as a major determinant of the interaction with RavA	RESULTS
+28	48	lysine decarboxylase	protein_type	The C-terminal β-sheet of a lysine decarboxylase as a major determinant of the interaction with RavA	RESULTS
+96	100	RavA	protein	The C-terminal β-sheet of a lysine decarboxylase as a major determinant of the interaction with RavA	RESULTS
+54	59	LdcIi	protein	In our previous contribution, based on the fit of the LdcIi and the LARA crystal structures into the LdcI-LARA cryoEM density, we predicted that the LdcI-RavA interaction should involve the C-terminal two-stranded β-sheet of the LdcI. Our present cryoEM maps and pseudoatomic models provide first structure-based insights into the differences between the inducible and the constitutive lysine decarboxylases.	RESULTS
+68	72	LARA	structure_element	In our previous contribution, based on the fit of the LdcIi and the LARA crystal structures into the LdcI-LARA cryoEM density, we predicted that the LdcI-RavA interaction should involve the C-terminal two-stranded β-sheet of the LdcI. Our present cryoEM maps and pseudoatomic models provide first structure-based insights into the differences between the inducible and the constitutive lysine decarboxylases.	RESULTS
+73	91	crystal structures	evidence	In our previous contribution, based on the fit of the LdcIi and the LARA crystal structures into the LdcI-LARA cryoEM density, we predicted that the LdcI-RavA interaction should involve the C-terminal two-stranded β-sheet of the LdcI. Our present cryoEM maps and pseudoatomic models provide first structure-based insights into the differences between the inducible and the constitutive lysine decarboxylases.	RESULTS
+101	110	LdcI-LARA	complex_assembly	In our previous contribution, based on the fit of the LdcIi and the LARA crystal structures into the LdcI-LARA cryoEM density, we predicted that the LdcI-RavA interaction should involve the C-terminal two-stranded β-sheet of the LdcI. Our present cryoEM maps and pseudoatomic models provide first structure-based insights into the differences between the inducible and the constitutive lysine decarboxylases.	RESULTS
+111	117	cryoEM	experimental_method	In our previous contribution, based on the fit of the LdcIi and the LARA crystal structures into the LdcI-LARA cryoEM density, we predicted that the LdcI-RavA interaction should involve the C-terminal two-stranded β-sheet of the LdcI. Our present cryoEM maps and pseudoatomic models provide first structure-based insights into the differences between the inducible and the constitutive lysine decarboxylases.	RESULTS
+118	125	density	evidence	In our previous contribution, based on the fit of the LdcIi and the LARA crystal structures into the LdcI-LARA cryoEM density, we predicted that the LdcI-RavA interaction should involve the C-terminal two-stranded β-sheet of the LdcI. Our present cryoEM maps and pseudoatomic models provide first structure-based insights into the differences between the inducible and the constitutive lysine decarboxylases.	RESULTS
+149	158	LdcI-RavA	complex_assembly	In our previous contribution, based on the fit of the LdcIi and the LARA crystal structures into the LdcI-LARA cryoEM density, we predicted that the LdcI-RavA interaction should involve the C-terminal two-stranded β-sheet of the LdcI. Our present cryoEM maps and pseudoatomic models provide first structure-based insights into the differences between the inducible and the constitutive lysine decarboxylases.	RESULTS
+201	221	two-stranded β-sheet	structure_element	In our previous contribution, based on the fit of the LdcIi and the LARA crystal structures into the LdcI-LARA cryoEM density, we predicted that the LdcI-RavA interaction should involve the C-terminal two-stranded β-sheet of the LdcI. Our present cryoEM maps and pseudoatomic models provide first structure-based insights into the differences between the inducible and the constitutive lysine decarboxylases.	RESULTS
+229	233	LdcI	protein	In our previous contribution, based on the fit of the LdcIi and the LARA crystal structures into the LdcI-LARA cryoEM density, we predicted that the LdcI-RavA interaction should involve the C-terminal two-stranded β-sheet of the LdcI. Our present cryoEM maps and pseudoatomic models provide first structure-based insights into the differences between the inducible and the constitutive lysine decarboxylases.	RESULTS
+247	253	cryoEM	experimental_method	In our previous contribution, based on the fit of the LdcIi and the LARA crystal structures into the LdcI-LARA cryoEM density, we predicted that the LdcI-RavA interaction should involve the C-terminal two-stranded β-sheet of the LdcI. Our present cryoEM maps and pseudoatomic models provide first structure-based insights into the differences between the inducible and the constitutive lysine decarboxylases.	RESULTS
+254	258	maps	evidence	In our previous contribution, based on the fit of the LdcIi and the LARA crystal structures into the LdcI-LARA cryoEM density, we predicted that the LdcI-RavA interaction should involve the C-terminal two-stranded β-sheet of the LdcI. Our present cryoEM maps and pseudoatomic models provide first structure-based insights into the differences between the inducible and the constitutive lysine decarboxylases.	RESULTS
+263	282	pseudoatomic models	evidence	In our previous contribution, based on the fit of the LdcIi and the LARA crystal structures into the LdcI-LARA cryoEM density, we predicted that the LdcI-RavA interaction should involve the C-terminal two-stranded β-sheet of the LdcI. Our present cryoEM maps and pseudoatomic models provide first structure-based insights into the differences between the inducible and the constitutive lysine decarboxylases.	RESULTS
+355	364	inducible	protein_state	In our previous contribution, based on the fit of the LdcIi and the LARA crystal structures into the LdcI-LARA cryoEM density, we predicted that the LdcI-RavA interaction should involve the C-terminal two-stranded β-sheet of the LdcI. Our present cryoEM maps and pseudoatomic models provide first structure-based insights into the differences between the inducible and the constitutive lysine decarboxylases.	RESULTS
+373	385	constitutive	protein_state	In our previous contribution, based on the fit of the LdcIi and the LARA crystal structures into the LdcI-LARA cryoEM density, we predicted that the LdcI-RavA interaction should involve the C-terminal two-stranded β-sheet of the LdcI. Our present cryoEM maps and pseudoatomic models provide first structure-based insights into the differences between the inducible and the constitutive lysine decarboxylases.	RESULTS
+386	407	lysine decarboxylases	protein_type	In our previous contribution, based on the fit of the LdcIi and the LARA crystal structures into the LdcI-LARA cryoEM density, we predicted that the LdcI-RavA interaction should involve the C-terminal two-stranded β-sheet of the LdcI. Our present cryoEM maps and pseudoatomic models provide first structure-based insights into the differences between the inducible and the constitutive lysine decarboxylases.	RESULTS
+137	141	RavA	protein	Therefore, we wanted to check the influence of the primary sequence of the two proteins in this region on their ability to interact with RavA. To this end, we swapped the relevant β-sheets of the two proteins and produced their chimeras, namely LdcIC (i.e. LdcI with the C-terminal β-sheet of LdcC) and LdcCI (i.e. LdcC with the C-terminal β-sheet of LdcI) (Fig. 5A–C).	RESULTS
+159	166	swapped	experimental_method	Therefore, we wanted to check the influence of the primary sequence of the two proteins in this region on their ability to interact with RavA. To this end, we swapped the relevant β-sheets of the two proteins and produced their chimeras, namely LdcIC (i.e. LdcI with the C-terminal β-sheet of LdcC) and LdcCI (i.e. LdcC with the C-terminal β-sheet of LdcI) (Fig. 5A–C).	RESULTS
+180	188	β-sheets	structure_element	Therefore, we wanted to check the influence of the primary sequence of the two proteins in this region on their ability to interact with RavA. To this end, we swapped the relevant β-sheets of the two proteins and produced their chimeras, namely LdcIC (i.e. LdcI with the C-terminal β-sheet of LdcC) and LdcCI (i.e. LdcC with the C-terminal β-sheet of LdcI) (Fig. 5A–C).	RESULTS
+228	236	chimeras	mutant	Therefore, we wanted to check the influence of the primary sequence of the two proteins in this region on their ability to interact with RavA. To this end, we swapped the relevant β-sheets of the two proteins and produced their chimeras, namely LdcIC (i.e. LdcI with the C-terminal β-sheet of LdcC) and LdcCI (i.e. LdcC with the C-terminal β-sheet of LdcI) (Fig. 5A–C).	RESULTS
+245	250	LdcIC	mutant	Therefore, we wanted to check the influence of the primary sequence of the two proteins in this region on their ability to interact with RavA. To this end, we swapped the relevant β-sheets of the two proteins and produced their chimeras, namely LdcIC (i.e. LdcI with the C-terminal β-sheet of LdcC) and LdcCI (i.e. LdcC with the C-terminal β-sheet of LdcI) (Fig. 5A–C).	RESULTS
+257	261	LdcI	protein	Therefore, we wanted to check the influence of the primary sequence of the two proteins in this region on their ability to interact with RavA. To this end, we swapped the relevant β-sheets of the two proteins and produced their chimeras, namely LdcIC (i.e. LdcI with the C-terminal β-sheet of LdcC) and LdcCI (i.e. LdcC with the C-terminal β-sheet of LdcI) (Fig. 5A–C).	RESULTS
+282	289	β-sheet	structure_element	Therefore, we wanted to check the influence of the primary sequence of the two proteins in this region on their ability to interact with RavA. To this end, we swapped the relevant β-sheets of the two proteins and produced their chimeras, namely LdcIC (i.e. LdcI with the C-terminal β-sheet of LdcC) and LdcCI (i.e. LdcC with the C-terminal β-sheet of LdcI) (Fig. 5A–C).	RESULTS
+293	297	LdcC	protein	Therefore, we wanted to check the influence of the primary sequence of the two proteins in this region on their ability to interact with RavA. To this end, we swapped the relevant β-sheets of the two proteins and produced their chimeras, namely LdcIC (i.e. LdcI with the C-terminal β-sheet of LdcC) and LdcCI (i.e. LdcC with the C-terminal β-sheet of LdcI) (Fig. 5A–C).	RESULTS
+303	308	LdcCI	mutant	Therefore, we wanted to check the influence of the primary sequence of the two proteins in this region on their ability to interact with RavA. To this end, we swapped the relevant β-sheets of the two proteins and produced their chimeras, namely LdcIC (i.e. LdcI with the C-terminal β-sheet of LdcC) and LdcCI (i.e. LdcC with the C-terminal β-sheet of LdcI) (Fig. 5A–C).	RESULTS
+315	319	LdcC	protein	Therefore, we wanted to check the influence of the primary sequence of the two proteins in this region on their ability to interact with RavA. To this end, we swapped the relevant β-sheets of the two proteins and produced their chimeras, namely LdcIC (i.e. LdcI with the C-terminal β-sheet of LdcC) and LdcCI (i.e. LdcC with the C-terminal β-sheet of LdcI) (Fig. 5A–C).	RESULTS
+340	347	β-sheet	structure_element	Therefore, we wanted to check the influence of the primary sequence of the two proteins in this region on their ability to interact with RavA. To this end, we swapped the relevant β-sheets of the two proteins and produced their chimeras, namely LdcIC (i.e. LdcI with the C-terminal β-sheet of LdcC) and LdcCI (i.e. LdcC with the C-terminal β-sheet of LdcI) (Fig. 5A–C).	RESULTS
+351	355	LdcI	protein	Therefore, we wanted to check the influence of the primary sequence of the two proteins in this region on their ability to interact with RavA. To this end, we swapped the relevant β-sheets of the two proteins and produced their chimeras, namely LdcIC (i.e. LdcI with the C-terminal β-sheet of LdcC) and LdcCI (i.e. LdcC with the C-terminal β-sheet of LdcI) (Fig. 5A–C).	RESULTS
+0	15	Both constructs	mutant	Both constructs could be purified and could form decamers visually indistinguishable from the wild-type proteins.	RESULTS
+49	57	decamers	oligomeric_state	Both constructs could be purified and could form decamers visually indistinguishable from the wild-type proteins.	RESULTS
+94	103	wild-type	protein_state	Both constructs could be purified and could form decamers visually indistinguishable from the wild-type proteins.	RESULTS
+24	28	LdcI	protein	As expected, binding of LdcI to RavA was completely abolished by this procedure and no LdcIC-RavA complex could be detected.	RESULTS
+32	36	RavA	protein	As expected, binding of LdcI to RavA was completely abolished by this procedure and no LdcIC-RavA complex could be detected.	RESULTS
+87	97	LdcIC-RavA	complex_assembly	As expected, binding of LdcI to RavA was completely abolished by this procedure and no LdcIC-RavA complex could be detected.	RESULTS
+17	29	introduction	experimental_method	On the contrary, introduction of the C-terminal β-sheet of LdcI into LdcC led to an assembly of the LdcCI-RavA complex.	RESULTS
+48	55	β-sheet	structure_element	On the contrary, introduction of the C-terminal β-sheet of LdcI into LdcC led to an assembly of the LdcCI-RavA complex.	RESULTS
+59	63	LdcI	protein	On the contrary, introduction of the C-terminal β-sheet of LdcI into LdcC led to an assembly of the LdcCI-RavA complex.	RESULTS
+69	73	LdcC	protein	On the contrary, introduction of the C-terminal β-sheet of LdcI into LdcC led to an assembly of the LdcCI-RavA complex.	RESULTS
+100	110	LdcCI-RavA	complex_assembly	On the contrary, introduction of the C-terminal β-sheet of LdcI into LdcC led to an assembly of the LdcCI-RavA complex.	RESULTS
+7	29	negative stain EM grid	experimental_method	On the negative stain EM grid, the chimeric cages appeared less rigid than the native LdcI-RavA, which probably means that the environment of the β-sheet contributes to the efficiency of the interaction and the stability of the entire architecture (Fig. 5D–F).	RESULTS
+35	43	chimeric	protein_state	On the negative stain EM grid, the chimeric cages appeared less rigid than the native LdcI-RavA, which probably means that the environment of the β-sheet contributes to the efficiency of the interaction and the stability of the entire architecture (Fig. 5D–F).	RESULTS
+79	85	native	protein_state	On the negative stain EM grid, the chimeric cages appeared less rigid than the native LdcI-RavA, which probably means that the environment of the β-sheet contributes to the efficiency of the interaction and the stability of the entire architecture (Fig. 5D–F).	RESULTS
+86	95	LdcI-RavA	complex_assembly	On the negative stain EM grid, the chimeric cages appeared less rigid than the native LdcI-RavA, which probably means that the environment of the β-sheet contributes to the efficiency of the interaction and the stability of the entire architecture (Fig. 5D–F).	RESULTS
+146	153	β-sheet	structure_element	On the negative stain EM grid, the chimeric cages appeared less rigid than the native LdcI-RavA, which probably means that the environment of the β-sheet contributes to the efficiency of the interaction and the stability of the entire architecture (Fig. 5D–F).	RESULTS
+15	22	β-sheet	structure_element	The C-terminal β-sheet of a lysine decarboxylase is a highly conserved signature allowing to distinguish between LdcI and LdcC	RESULTS
+28	48	lysine decarboxylase	protein_type	The C-terminal β-sheet of a lysine decarboxylase is a highly conserved signature allowing to distinguish between LdcI and LdcC	RESULTS
+54	70	highly conserved	protein_state	The C-terminal β-sheet of a lysine decarboxylase is a highly conserved signature allowing to distinguish between LdcI and LdcC	RESULTS
+113	117	LdcI	protein	The C-terminal β-sheet of a lysine decarboxylase is a highly conserved signature allowing to distinguish between LdcI and LdcC	RESULTS
+122	126	LdcC	protein	The C-terminal β-sheet of a lysine decarboxylase is a highly conserved signature allowing to distinguish between LdcI and LdcC	RESULTS
+0	34	Alignment of the primary sequences	experimental_method	Alignment of the primary sequences of the E. coli LdcI and LdcC shows that some amino acid residues of the C-terminal β-sheet are the same in the two proteins, whereas others are notably different in chemical nature.	RESULTS
+42	49	E. coli	species	Alignment of the primary sequences of the E. coli LdcI and LdcC shows that some amino acid residues of the C-terminal β-sheet are the same in the two proteins, whereas others are notably different in chemical nature.	RESULTS
+50	54	LdcI	protein	Alignment of the primary sequences of the E. coli LdcI and LdcC shows that some amino acid residues of the C-terminal β-sheet are the same in the two proteins, whereas others are notably different in chemical nature.	RESULTS
+59	63	LdcC	protein	Alignment of the primary sequences of the E. coli LdcI and LdcC shows that some amino acid residues of the C-terminal β-sheet are the same in the two proteins, whereas others are notably different in chemical nature.	RESULTS
+118	125	β-sheet	structure_element	Alignment of the primary sequences of the E. coli LdcI and LdcC shows that some amino acid residues of the C-terminal β-sheet are the same in the two proteins, whereas others are notably different in chemical nature.	RESULTS
+92	103	very region	structure_element	Importantly, most of the amino acid differences between the two enzymes are located in this very region.	RESULTS
+72	79	β-sheet	structure_element	Thus, to advance beyond our experimental confirmation of the C-terminal β-sheet as a major determinant of the capacity of a particular lysine decarboxylase to form a cage with RavA, we set out to investigate whether certain residues in this β-sheet are conserved in lysine decarboxylases of different enterobacteria that have the ravA-viaA operon in their genome.	RESULTS
+135	155	lysine decarboxylase	protein_type	Thus, to advance beyond our experimental confirmation of the C-terminal β-sheet as a major determinant of the capacity of a particular lysine decarboxylase to form a cage with RavA, we set out to investigate whether certain residues in this β-sheet are conserved in lysine decarboxylases of different enterobacteria that have the ravA-viaA operon in their genome.	RESULTS
+176	180	RavA	protein	Thus, to advance beyond our experimental confirmation of the C-terminal β-sheet as a major determinant of the capacity of a particular lysine decarboxylase to form a cage with RavA, we set out to investigate whether certain residues in this β-sheet are conserved in lysine decarboxylases of different enterobacteria that have the ravA-viaA operon in their genome.	RESULTS
+216	232	certain residues	structure_element	Thus, to advance beyond our experimental confirmation of the C-terminal β-sheet as a major determinant of the capacity of a particular lysine decarboxylase to form a cage with RavA, we set out to investigate whether certain residues in this β-sheet are conserved in lysine decarboxylases of different enterobacteria that have the ravA-viaA operon in their genome.	RESULTS
+241	248	β-sheet	structure_element	Thus, to advance beyond our experimental confirmation of the C-terminal β-sheet as a major determinant of the capacity of a particular lysine decarboxylase to form a cage with RavA, we set out to investigate whether certain residues in this β-sheet are conserved in lysine decarboxylases of different enterobacteria that have the ravA-viaA operon in their genome.	RESULTS
+253	262	conserved	protein_state	Thus, to advance beyond our experimental confirmation of the C-terminal β-sheet as a major determinant of the capacity of a particular lysine decarboxylase to form a cage with RavA, we set out to investigate whether certain residues in this β-sheet are conserved in lysine decarboxylases of different enterobacteria that have the ravA-viaA operon in their genome.	RESULTS
+266	287	lysine decarboxylases	protein_type	Thus, to advance beyond our experimental confirmation of the C-terminal β-sheet as a major determinant of the capacity of a particular lysine decarboxylase to form a cage with RavA, we set out to investigate whether certain residues in this β-sheet are conserved in lysine decarboxylases of different enterobacteria that have the ravA-viaA operon in their genome.	RESULTS
+301	315	enterobacteria	taxonomy_domain	Thus, to advance beyond our experimental confirmation of the C-terminal β-sheet as a major determinant of the capacity of a particular lysine decarboxylase to form a cage with RavA, we set out to investigate whether certain residues in this β-sheet are conserved in lysine decarboxylases of different enterobacteria that have the ravA-viaA operon in their genome.	RESULTS
+330	346	ravA-viaA operon	gene	Thus, to advance beyond our experimental confirmation of the C-terminal β-sheet as a major determinant of the capacity of a particular lysine decarboxylase to form a cage with RavA, we set out to investigate whether certain residues in this β-sheet are conserved in lysine decarboxylases of different enterobacteria that have the ravA-viaA operon in their genome.	RESULTS
+3	36	inspected the genetic environment	experimental_method	We inspected the genetic environment of lysine decarboxylases from 22 enterobacterial species referenced in the NCBI database, corrected the gene annotation where necessary (Tables S3 and S4), and performed multiple sequence alignment coupled to a phylogenetic analysis (see Methods).	RESULTS
+40	61	lysine decarboxylases	protein_type	We inspected the genetic environment of lysine decarboxylases from 22 enterobacterial species referenced in the NCBI database, corrected the gene annotation where necessary (Tables S3 and S4), and performed multiple sequence alignment coupled to a phylogenetic analysis (see Methods).	RESULTS
+70	85	enterobacterial	taxonomy_domain	We inspected the genetic environment of lysine decarboxylases from 22 enterobacterial species referenced in the NCBI database, corrected the gene annotation where necessary (Tables S3 and S4), and performed multiple sequence alignment coupled to a phylogenetic analysis (see Methods).	RESULTS
+207	234	multiple sequence alignment	experimental_method	We inspected the genetic environment of lysine decarboxylases from 22 enterobacterial species referenced in the NCBI database, corrected the gene annotation where necessary (Tables S3 and S4), and performed multiple sequence alignment coupled to a phylogenetic analysis (see Methods).	RESULTS
+248	269	phylogenetic analysis	experimental_method	We inspected the genetic environment of lysine decarboxylases from 22 enterobacterial species referenced in the NCBI database, corrected the gene annotation where necessary (Tables S3 and S4), and performed multiple sequence alignment coupled to a phylogenetic analysis (see Methods).	RESULTS
+14	32	consensus sequence	evidence	First of all, consensus sequence for the entire lysine decarboxylase family was derived.	RESULTS
+48	68	lysine decarboxylase	protein_type	First of all, consensus sequence for the entire lysine decarboxylase family was derived.	RESULTS
+12	33	phylogenetic analysis	experimental_method	Second, the phylogenetic analysis clearly split the lysine decarboxylases into two groups (Fig. 6A).	RESULTS
+52	73	lysine decarboxylases	protein_type	Second, the phylogenetic analysis clearly split the lysine decarboxylases into two groups (Fig. 6A).	RESULTS
+4	25	lysine decarboxylases	protein_type	All lysine decarboxylases predicted to be “LdcI-like” or biodegradable based on their genetic environment, as for example their organization in an operon with a gene encoding the CadB antiporter (see Methods), were found in one group, whereas all enzymes predicted as “LdcC-like” or biosynthetic partitioned into another group.	RESULTS
+43	52	LdcI-like	protein_type	All lysine decarboxylases predicted to be “LdcI-like” or biodegradable based on their genetic environment, as for example their organization in an operon with a gene encoding the CadB antiporter (see Methods), were found in one group, whereas all enzymes predicted as “LdcC-like” or biosynthetic partitioned into another group.	RESULTS
+57	70	biodegradable	protein_state	All lysine decarboxylases predicted to be “LdcI-like” or biodegradable based on their genetic environment, as for example their organization in an operon with a gene encoding the CadB antiporter (see Methods), were found in one group, whereas all enzymes predicted as “LdcC-like” or biosynthetic partitioned into another group.	RESULTS
+179	183	CadB	protein	All lysine decarboxylases predicted to be “LdcI-like” or biodegradable based on their genetic environment, as for example their organization in an operon with a gene encoding the CadB antiporter (see Methods), were found in one group, whereas all enzymes predicted as “LdcC-like” or biosynthetic partitioned into another group.	RESULTS
+184	194	antiporter	protein_type	All lysine decarboxylases predicted to be “LdcI-like” or biodegradable based on their genetic environment, as for example their organization in an operon with a gene encoding the CadB antiporter (see Methods), were found in one group, whereas all enzymes predicted as “LdcC-like” or biosynthetic partitioned into another group.	RESULTS
+247	254	enzymes	protein_type	All lysine decarboxylases predicted to be “LdcI-like” or biodegradable based on their genetic environment, as for example their organization in an operon with a gene encoding the CadB antiporter (see Methods), were found in one group, whereas all enzymes predicted as “LdcC-like” or biosynthetic partitioned into another group.	RESULTS
+269	278	LdcC-like	protein_type	All lysine decarboxylases predicted to be “LdcI-like” or biodegradable based on their genetic environment, as for example their organization in an operon with a gene encoding the CadB antiporter (see Methods), were found in one group, whereas all enzymes predicted as “LdcC-like” or biosynthetic partitioned into another group.	RESULTS
+283	295	biosynthetic	protein_state	All lysine decarboxylases predicted to be “LdcI-like” or biodegradable based on their genetic environment, as for example their organization in an operon with a gene encoding the CadB antiporter (see Methods), were found in one group, whereas all enzymes predicted as “LdcC-like” or biosynthetic partitioned into another group.	RESULTS
+6	25	consensus sequences	evidence	Thus, consensus sequences could also be determined for each of the two groups (Figs 6B,C and S7).	RESULTS
+20	39	consensus sequences	evidence	Inspection of these consensus sequences revealed important differences between the groups regarding charge, size and hydrophobicity of several residues precisely at the level of the C-terminal β-sheet that is responsible for the interaction with RavA (Fig. 6B–D).	RESULTS
+193	200	β-sheet	structure_element	Inspection of these consensus sequences revealed important differences between the groups regarding charge, size and hydrophobicity of several residues precisely at the level of the C-terminal β-sheet that is responsible for the interaction with RavA (Fig. 6B–D).	RESULTS
+246	250	RavA	protein	Inspection of these consensus sequences revealed important differences between the groups regarding charge, size and hydrophobicity of several residues precisely at the level of the C-terminal β-sheet that is responsible for the interaction with RavA (Fig. 6B–D).	RESULTS
+36	59	site-directed mutations	experimental_method	For example, in our previous study, site-directed mutations identified Y697 as critically required for the RavA binding.	RESULTS
+71	75	Y697	residue_name_number	For example, in our previous study, site-directed mutations identified Y697 as critically required for the RavA binding.	RESULTS
+107	111	RavA	protein	For example, in our previous study, site-directed mutations identified Y697 as critically required for the RavA binding.	RESULTS
+32	36	Y697	residue_name_number	Our current analysis shows that Y697 is strictly conserved in the “LdcI-like” group whereas the “LdcC-like” enzymes always have a lysine in this position; it also uncovers several other residues potentially essential for the interaction with RavA which can now be addressed by site-directed mutagenesis.	RESULTS
+40	58	strictly conserved	protein_state	Our current analysis shows that Y697 is strictly conserved in the “LdcI-like” group whereas the “LdcC-like” enzymes always have a lysine in this position; it also uncovers several other residues potentially essential for the interaction with RavA which can now be addressed by site-directed mutagenesis.	RESULTS
+67	76	LdcI-like	protein_type	Our current analysis shows that Y697 is strictly conserved in the “LdcI-like” group whereas the “LdcC-like” enzymes always have a lysine in this position; it also uncovers several other residues potentially essential for the interaction with RavA which can now be addressed by site-directed mutagenesis.	RESULTS
+97	106	LdcC-like	protein_type	Our current analysis shows that Y697 is strictly conserved in the “LdcI-like” group whereas the “LdcC-like” enzymes always have a lysine in this position; it also uncovers several other residues potentially essential for the interaction with RavA which can now be addressed by site-directed mutagenesis.	RESULTS
+116	127	always have	protein_state	Our current analysis shows that Y697 is strictly conserved in the “LdcI-like” group whereas the “LdcC-like” enzymes always have a lysine in this position; it also uncovers several other residues potentially essential for the interaction with RavA which can now be addressed by site-directed mutagenesis.	RESULTS
+130	136	lysine	residue_name	Our current analysis shows that Y697 is strictly conserved in the “LdcI-like” group whereas the “LdcC-like” enzymes always have a lysine in this position; it also uncovers several other residues potentially essential for the interaction with RavA which can now be addressed by site-directed mutagenesis.	RESULTS
+242	246	RavA	protein	Our current analysis shows that Y697 is strictly conserved in the “LdcI-like” group whereas the “LdcC-like” enzymes always have a lysine in this position; it also uncovers several other residues potentially essential for the interaction with RavA which can now be addressed by site-directed mutagenesis.	RESULTS
+277	302	site-directed mutagenesis	experimental_method	Our current analysis shows that Y697 is strictly conserved in the “LdcI-like” group whereas the “LdcC-like” enzymes always have a lysine in this position; it also uncovers several other residues potentially essential for the interaction with RavA which can now be addressed by site-directed mutagenesis.	RESULTS
+81	90	LdcI-like	protein_type	The third and most remarkable finding was that exactly the same separation into “LdcI-like” and “LdcC”-like groups can be obtained based on a comparison of the C-terminal β-sheets only, without taking the rest of the primary sequence into account.	RESULTS
+97	107	LdcC”-like	protein_type	The third and most remarkable finding was that exactly the same separation into “LdcI-like” and “LdcC”-like groups can be obtained based on a comparison of the C-terminal β-sheets only, without taking the rest of the primary sequence into account.	RESULTS
+171	179	β-sheets	structure_element	The third and most remarkable finding was that exactly the same separation into “LdcI-like” and “LdcC”-like groups can be obtained based on a comparison of the C-terminal β-sheets only, without taking the rest of the primary sequence into account.	RESULTS
+25	32	β-sheet	structure_element	Therefore the C-terminal β-sheet emerges as being a highly conserved signature sequence, sufficient to unambiguously discriminate between the “LdcI-like” and “LdcC-like” enterobacterial lysine decarboxylases independently of any other information (Figs 6 and S7).	RESULTS
+52	68	highly conserved	protein_state	Therefore the C-terminal β-sheet emerges as being a highly conserved signature sequence, sufficient to unambiguously discriminate between the “LdcI-like” and “LdcC-like” enterobacterial lysine decarboxylases independently of any other information (Figs 6 and S7).	RESULTS
+69	87	signature sequence	structure_element	Therefore the C-terminal β-sheet emerges as being a highly conserved signature sequence, sufficient to unambiguously discriminate between the “LdcI-like” and “LdcC-like” enterobacterial lysine decarboxylases independently of any other information (Figs 6 and S7).	RESULTS
+143	152	LdcI-like	protein_type	Therefore the C-terminal β-sheet emerges as being a highly conserved signature sequence, sufficient to unambiguously discriminate between the “LdcI-like” and “LdcC-like” enterobacterial lysine decarboxylases independently of any other information (Figs 6 and S7).	RESULTS
+159	168	LdcC-like	protein_type	Therefore the C-terminal β-sheet emerges as being a highly conserved signature sequence, sufficient to unambiguously discriminate between the “LdcI-like” and “LdcC-like” enterobacterial lysine decarboxylases independently of any other information (Figs 6 and S7).	RESULTS
+170	185	enterobacterial	taxonomy_domain	Therefore the C-terminal β-sheet emerges as being a highly conserved signature sequence, sufficient to unambiguously discriminate between the “LdcI-like” and “LdcC-like” enterobacterial lysine decarboxylases independently of any other information (Figs 6 and S7).	RESULTS
+186	207	lysine decarboxylases	protein_type	Therefore the C-terminal β-sheet emerges as being a highly conserved signature sequence, sufficient to unambiguously discriminate between the “LdcI-like” and “LdcC-like” enterobacterial lysine decarboxylases independently of any other information (Figs 6 and S7).	RESULTS
+4	14	structures	evidence	Our structures show that this motif is not involved in the enzymatic activity or the oligomeric state of the proteins.	RESULTS
+25	35	this motif	structure_element	Our structures show that this motif is not involved in the enzymatic activity or the oligomeric state of the proteins.	RESULTS
+6	20	enterobacteria	taxonomy_domain	Thus, enterobacteria identified here (Fig. 6, Table S4) appear to exert evolutionary pressure on the biodegradative lysine decarboxylase towards the RavA binding.	RESULTS
+101	115	biodegradative	protein_state	Thus, enterobacteria identified here (Fig. 6, Table S4) appear to exert evolutionary pressure on the biodegradative lysine decarboxylase towards the RavA binding.	RESULTS
+116	136	lysine decarboxylase	protein_type	Thus, enterobacteria identified here (Fig. 6, Table S4) appear to exert evolutionary pressure on the biodegradative lysine decarboxylase towards the RavA binding.	RESULTS
+149	153	RavA	protein	Thus, enterobacteria identified here (Fig. 6, Table S4) appear to exert evolutionary pressure on the biodegradative lysine decarboxylase towards the RavA binding.	RESULTS
+35	44	LdcI-RavA	complex_assembly	One of the elucidated roles of the LdcI-RavA cage is to maintain LdcI activity under conditions of enterobacterial starvation by preventing LdcI inhibition by the stringent response alarmone ppGpp.	RESULTS
+65	69	LdcI	protein	One of the elucidated roles of the LdcI-RavA cage is to maintain LdcI activity under conditions of enterobacterial starvation by preventing LdcI inhibition by the stringent response alarmone ppGpp.	RESULTS
+99	114	enterobacterial	taxonomy_domain	One of the elucidated roles of the LdcI-RavA cage is to maintain LdcI activity under conditions of enterobacterial starvation by preventing LdcI inhibition by the stringent response alarmone ppGpp.	RESULTS
+140	144	LdcI	protein	One of the elucidated roles of the LdcI-RavA cage is to maintain LdcI activity under conditions of enterobacterial starvation by preventing LdcI inhibition by the stringent response alarmone ppGpp.	RESULTS
+163	190	stringent response alarmone	chemical	One of the elucidated roles of the LdcI-RavA cage is to maintain LdcI activity under conditions of enterobacterial starvation by preventing LdcI inhibition by the stringent response alarmone ppGpp.	RESULTS
+191	196	ppGpp	chemical	One of the elucidated roles of the LdcI-RavA cage is to maintain LdcI activity under conditions of enterobacterial starvation by preventing LdcI inhibition by the stringent response alarmone ppGpp.	RESULTS
+57	61	LdcI	protein	Furthermore, the recently documented interaction of both LdcI and RavA with specific subunits of the respiratory complex I, together with the unanticipated link between RavA and maturation of numerous iron-sulfur proteins, tend to suggest an additional intriguing function for this 3.5 MDa assembly.	RESULTS
+66	70	RavA	protein	Furthermore, the recently documented interaction of both LdcI and RavA with specific subunits of the respiratory complex I, together with the unanticipated link between RavA and maturation of numerous iron-sulfur proteins, tend to suggest an additional intriguing function for this 3.5 MDa assembly.	RESULTS
+85	93	subunits	structure_element	Furthermore, the recently documented interaction of both LdcI and RavA with specific subunits of the respiratory complex I, together with the unanticipated link between RavA and maturation of numerous iron-sulfur proteins, tend to suggest an additional intriguing function for this 3.5 MDa assembly.	RESULTS
+101	122	respiratory complex I	protein_type	Furthermore, the recently documented interaction of both LdcI and RavA with specific subunits of the respiratory complex I, together with the unanticipated link between RavA and maturation of numerous iron-sulfur proteins, tend to suggest an additional intriguing function for this 3.5 MDa assembly.	RESULTS
+169	173	RavA	protein	Furthermore, the recently documented interaction of both LdcI and RavA with specific subunits of the respiratory complex I, together with the unanticipated link between RavA and maturation of numerous iron-sulfur proteins, tend to suggest an additional intriguing function for this 3.5 MDa assembly.	RESULTS
+201	221	iron-sulfur proteins	protein_type	Furthermore, the recently documented interaction of both LdcI and RavA with specific subunits of the respiratory complex I, together with the unanticipated link between RavA and maturation of numerous iron-sulfur proteins, tend to suggest an additional intriguing function for this 3.5 MDa assembly.	RESULTS
+37	41	LdcI	protein	The conformational rearrangements of LdcI upon enzyme activation and RavA binding revealed in this work, and our amazing finding that the molecular determinant of the LdcI-RavA interaction is the one that straightforwardly determines if a particular enterobacterial lysine decarboxylase belongs to “LdcI-like” or “LdcC-like” proteins, should give a new impetus to functional studies of the unique LdcI-RavA cage.	RESULTS
+69	73	RavA	protein	The conformational rearrangements of LdcI upon enzyme activation and RavA binding revealed in this work, and our amazing finding that the molecular determinant of the LdcI-RavA interaction is the one that straightforwardly determines if a particular enterobacterial lysine decarboxylase belongs to “LdcI-like” or “LdcC-like” proteins, should give a new impetus to functional studies of the unique LdcI-RavA cage.	RESULTS
+167	176	LdcI-RavA	complex_assembly	The conformational rearrangements of LdcI upon enzyme activation and RavA binding revealed in this work, and our amazing finding that the molecular determinant of the LdcI-RavA interaction is the one that straightforwardly determines if a particular enterobacterial lysine decarboxylase belongs to “LdcI-like” or “LdcC-like” proteins, should give a new impetus to functional studies of the unique LdcI-RavA cage.	RESULTS
+250	265	enterobacterial	taxonomy_domain	The conformational rearrangements of LdcI upon enzyme activation and RavA binding revealed in this work, and our amazing finding that the molecular determinant of the LdcI-RavA interaction is the one that straightforwardly determines if a particular enterobacterial lysine decarboxylase belongs to “LdcI-like” or “LdcC-like” proteins, should give a new impetus to functional studies of the unique LdcI-RavA cage.	RESULTS
+266	286	lysine decarboxylase	protein_type	The conformational rearrangements of LdcI upon enzyme activation and RavA binding revealed in this work, and our amazing finding that the molecular determinant of the LdcI-RavA interaction is the one that straightforwardly determines if a particular enterobacterial lysine decarboxylase belongs to “LdcI-like” or “LdcC-like” proteins, should give a new impetus to functional studies of the unique LdcI-RavA cage.	RESULTS
+299	308	LdcI-like	protein_type	The conformational rearrangements of LdcI upon enzyme activation and RavA binding revealed in this work, and our amazing finding that the molecular determinant of the LdcI-RavA interaction is the one that straightforwardly determines if a particular enterobacterial lysine decarboxylase belongs to “LdcI-like” or “LdcC-like” proteins, should give a new impetus to functional studies of the unique LdcI-RavA cage.	RESULTS
+314	323	LdcC-like	protein_type	The conformational rearrangements of LdcI upon enzyme activation and RavA binding revealed in this work, and our amazing finding that the molecular determinant of the LdcI-RavA interaction is the one that straightforwardly determines if a particular enterobacterial lysine decarboxylase belongs to “LdcI-like” or “LdcC-like” proteins, should give a new impetus to functional studies of the unique LdcI-RavA cage.	RESULTS
+397	406	LdcI-RavA	complex_assembly	The conformational rearrangements of LdcI upon enzyme activation and RavA binding revealed in this work, and our amazing finding that the molecular determinant of the LdcI-RavA interaction is the one that straightforwardly determines if a particular enterobacterial lysine decarboxylase belongs to “LdcI-like” or “LdcC-like” proteins, should give a new impetus to functional studies of the unique LdcI-RavA cage.	RESULTS
+13	23	structures	evidence	Besides, the structures and the pseudoatomic models of the active ppGpp-free states of both the biodegradative and the biosynthetic E. coli lysine decarboxylases offer an additional tool for analysis of their role in UPEC infectivity.	RESULTS
+32	51	pseudoatomic models	evidence	Besides, the structures and the pseudoatomic models of the active ppGpp-free states of both the biodegradative and the biosynthetic E. coli lysine decarboxylases offer an additional tool for analysis of their role in UPEC infectivity.	RESULTS
+59	65	active	protein_state	Besides, the structures and the pseudoatomic models of the active ppGpp-free states of both the biodegradative and the biosynthetic E. coli lysine decarboxylases offer an additional tool for analysis of their role in UPEC infectivity.	RESULTS
+66	76	ppGpp-free	protein_state	Besides, the structures and the pseudoatomic models of the active ppGpp-free states of both the biodegradative and the biosynthetic E. coli lysine decarboxylases offer an additional tool for analysis of their role in UPEC infectivity.	RESULTS
+96	110	biodegradative	protein_state	Besides, the structures and the pseudoatomic models of the active ppGpp-free states of both the biodegradative and the biosynthetic E. coli lysine decarboxylases offer an additional tool for analysis of their role in UPEC infectivity.	RESULTS
+119	131	biosynthetic	protein_state	Besides, the structures and the pseudoatomic models of the active ppGpp-free states of both the biodegradative and the biosynthetic E. coli lysine decarboxylases offer an additional tool for analysis of their role in UPEC infectivity.	RESULTS
+132	139	E. coli	species	Besides, the structures and the pseudoatomic models of the active ppGpp-free states of both the biodegradative and the biosynthetic E. coli lysine decarboxylases offer an additional tool for analysis of their role in UPEC infectivity.	RESULTS
+140	161	lysine decarboxylases	protein_type	Besides, the structures and the pseudoatomic models of the active ppGpp-free states of both the biodegradative and the biosynthetic E. coli lysine decarboxylases offer an additional tool for analysis of their role in UPEC infectivity.	RESULTS
+217	221	UPEC	species	Besides, the structures and the pseudoatomic models of the active ppGpp-free states of both the biodegradative and the biosynthetic E. coli lysine decarboxylases offer an additional tool for analysis of their role in UPEC infectivity.	RESULTS
+18	21	apo	protein_state	Together with the apo-LdcI and ppGpp-LdcIi crystal structures, our cryoEM reconstructions provide a structural framework for future studies of structure-function relationships of lysine decarboxylases from other enterobacteria and even of their homologues outside Enterobacteriaceae. For example, the lysine decarboxylase of Eikenella corrodens is thought to play a major role in the periodontal disease and its inhibitors were shown to retard gingivitis development.	RESULTS
+22	26	LdcI	protein	Together with the apo-LdcI and ppGpp-LdcIi crystal structures, our cryoEM reconstructions provide a structural framework for future studies of structure-function relationships of lysine decarboxylases from other enterobacteria and even of their homologues outside Enterobacteriaceae. For example, the lysine decarboxylase of Eikenella corrodens is thought to play a major role in the periodontal disease and its inhibitors were shown to retard gingivitis development.	RESULTS
+31	42	ppGpp-LdcIi	complex_assembly	Together with the apo-LdcI and ppGpp-LdcIi crystal structures, our cryoEM reconstructions provide a structural framework for future studies of structure-function relationships of lysine decarboxylases from other enterobacteria and even of their homologues outside Enterobacteriaceae. For example, the lysine decarboxylase of Eikenella corrodens is thought to play a major role in the periodontal disease and its inhibitors were shown to retard gingivitis development.	RESULTS
+43	61	crystal structures	evidence	Together with the apo-LdcI and ppGpp-LdcIi crystal structures, our cryoEM reconstructions provide a structural framework for future studies of structure-function relationships of lysine decarboxylases from other enterobacteria and even of their homologues outside Enterobacteriaceae. For example, the lysine decarboxylase of Eikenella corrodens is thought to play a major role in the periodontal disease and its inhibitors were shown to retard gingivitis development.	RESULTS
+67	73	cryoEM	experimental_method	Together with the apo-LdcI and ppGpp-LdcIi crystal structures, our cryoEM reconstructions provide a structural framework for future studies of structure-function relationships of lysine decarboxylases from other enterobacteria and even of their homologues outside Enterobacteriaceae. For example, the lysine decarboxylase of Eikenella corrodens is thought to play a major role in the periodontal disease and its inhibitors were shown to retard gingivitis development.	RESULTS
+74	89	reconstructions	evidence	Together with the apo-LdcI and ppGpp-LdcIi crystal structures, our cryoEM reconstructions provide a structural framework for future studies of structure-function relationships of lysine decarboxylases from other enterobacteria and even of their homologues outside Enterobacteriaceae. For example, the lysine decarboxylase of Eikenella corrodens is thought to play a major role in the periodontal disease and its inhibitors were shown to retard gingivitis development.	RESULTS
+179	200	lysine decarboxylases	protein_type	Together with the apo-LdcI and ppGpp-LdcIi crystal structures, our cryoEM reconstructions provide a structural framework for future studies of structure-function relationships of lysine decarboxylases from other enterobacteria and even of their homologues outside Enterobacteriaceae. For example, the lysine decarboxylase of Eikenella corrodens is thought to play a major role in the periodontal disease and its inhibitors were shown to retard gingivitis development.	RESULTS
+212	226	enterobacteria	taxonomy_domain	Together with the apo-LdcI and ppGpp-LdcIi crystal structures, our cryoEM reconstructions provide a structural framework for future studies of structure-function relationships of lysine decarboxylases from other enterobacteria and even of their homologues outside Enterobacteriaceae. For example, the lysine decarboxylase of Eikenella corrodens is thought to play a major role in the periodontal disease and its inhibitors were shown to retard gingivitis development.	RESULTS
+264	282	Enterobacteriaceae	taxonomy_domain	Together with the apo-LdcI and ppGpp-LdcIi crystal structures, our cryoEM reconstructions provide a structural framework for future studies of structure-function relationships of lysine decarboxylases from other enterobacteria and even of their homologues outside Enterobacteriaceae. For example, the lysine decarboxylase of Eikenella corrodens is thought to play a major role in the periodontal disease and its inhibitors were shown to retard gingivitis development.	RESULTS
+301	321	lysine decarboxylase	protein_type	Together with the apo-LdcI and ppGpp-LdcIi crystal structures, our cryoEM reconstructions provide a structural framework for future studies of structure-function relationships of lysine decarboxylases from other enterobacteria and even of their homologues outside Enterobacteriaceae. For example, the lysine decarboxylase of Eikenella corrodens is thought to play a major role in the periodontal disease and its inhibitors were shown to retard gingivitis development.	RESULTS
+325	344	Eikenella corrodens	species	Together with the apo-LdcI and ppGpp-LdcIi crystal structures, our cryoEM reconstructions provide a structural framework for future studies of structure-function relationships of lysine decarboxylases from other enterobacteria and even of their homologues outside Enterobacteriaceae. For example, the lysine decarboxylase of Eikenella corrodens is thought to play a major role in the periodontal disease and its inhibitors were shown to retard gingivitis development.	RESULTS
+9	19	cadaverine	chemical	Finally, cadaverine being an important platform chemical for the production of industrial polymers such as nylon, structural information is valuable for optimisation of bacterial lysine decarboxylases used for its production in biotechnology.	RESULTS
+169	178	bacterial	taxonomy_domain	Finally, cadaverine being an important platform chemical for the production of industrial polymers such as nylon, structural information is valuable for optimisation of bacterial lysine decarboxylases used for its production in biotechnology.	RESULTS
+179	200	lysine decarboxylases	protein_type	Finally, cadaverine being an important platform chemical for the production of industrial polymers such as nylon, structural information is valuable for optimisation of bacterial lysine decarboxylases used for its production in biotechnology.	RESULTS
+3	9	cryoEM	experimental_method	3D cryoEM reconstructions of LdcC, LdcI-LARA and LdcIa.	FIG
+10	25	reconstructions	evidence	3D cryoEM reconstructions of LdcC, LdcI-LARA and LdcIa.	FIG
+29	33	LdcC	protein	3D cryoEM reconstructions of LdcC, LdcI-LARA and LdcIa.	FIG
+35	44	LdcI-LARA	complex_assembly	3D cryoEM reconstructions of LdcC, LdcI-LARA and LdcIa.	FIG
+49	54	LdcIa	protein	3D cryoEM reconstructions of LdcC, LdcI-LARA and LdcIa.	FIG
+8	14	cryoEM	experimental_method	(A,C,E) cryoEM map of the LdcC (A), LdcIa (C) and LdcI-LARA (E) decamers with one protomer in light grey.	FIG
+15	18	map	evidence	(A,C,E) cryoEM map of the LdcC (A), LdcIa (C) and LdcI-LARA (E) decamers with one protomer in light grey.	FIG
+26	30	LdcC	protein	(A,C,E) cryoEM map of the LdcC (A), LdcIa (C) and LdcI-LARA (E) decamers with one protomer in light grey.	FIG
+36	41	LdcIa	protein	(A,C,E) cryoEM map of the LdcC (A), LdcIa (C) and LdcI-LARA (E) decamers with one protomer in light grey.	FIG
+50	59	LdcI-LARA	complex_assembly	(A,C,E) cryoEM map of the LdcC (A), LdcIa (C) and LdcI-LARA (E) decamers with one protomer in light grey.	FIG
+64	72	decamers	oligomeric_state	(A,C,E) cryoEM map of the LdcC (A), LdcIa (C) and LdcI-LARA (E) decamers with one protomer in light grey.	FIG
+82	90	protomer	oligomeric_state	(A,C,E) cryoEM map of the LdcC (A), LdcIa (C) and LdcI-LARA (E) decamers with one protomer in light grey.	FIG
+19	28	protomers	oligomeric_state	In the rest of the protomers, the wing, core and C-terminal domains are colored from light to dark in shades of green for LdcC (A), pink for LdcIa (C) and blue for LdcI in LdcI-LARA (E).	FIG
+34	38	wing	structure_element	In the rest of the protomers, the wing, core and C-terminal domains are colored from light to dark in shades of green for LdcC (A), pink for LdcIa (C) and blue for LdcI in LdcI-LARA (E).	FIG
+40	44	core	structure_element	In the rest of the protomers, the wing, core and C-terminal domains are colored from light to dark in shades of green for LdcC (A), pink for LdcIa (C) and blue for LdcI in LdcI-LARA (E).	FIG
+49	67	C-terminal domains	structure_element	In the rest of the protomers, the wing, core and C-terminal domains are colored from light to dark in shades of green for LdcC (A), pink for LdcIa (C) and blue for LdcI in LdcI-LARA (E).	FIG
+122	126	LdcC	protein	In the rest of the protomers, the wing, core and C-terminal domains are colored from light to dark in shades of green for LdcC (A), pink for LdcIa (C) and blue for LdcI in LdcI-LARA (E).	FIG
+141	146	LdcIa	protein	In the rest of the protomers, the wing, core and C-terminal domains are colored from light to dark in shades of green for LdcC (A), pink for LdcIa (C) and blue for LdcI in LdcI-LARA (E).	FIG
+164	168	LdcI	protein	In the rest of the protomers, the wing, core and C-terminal domains are colored from light to dark in shades of green for LdcC (A), pink for LdcIa (C) and blue for LdcI in LdcI-LARA (E).	FIG
+172	181	LdcI-LARA	complex_assembly	In the rest of the protomers, the wing, core and C-terminal domains are colored from light to dark in shades of green for LdcC (A), pink for LdcIa (C) and blue for LdcI in LdcI-LARA (E).	FIG
+13	24	LARA domain	structure_element	 In (E), the LARA domain density is shown in dark grey.	FIG
+4	12	monomers	oligomeric_state	Two monomers making a dimer are delineated.	FIG
+22	27	dimer	oligomeric_state	Two monomers making a dimer are delineated.	FIG
+28	36	protomer	oligomeric_state	Scale bar 50 Å. (B,D,F) One protomer from the cryoEM map of the LdcC (B), LdcIa (D) and LdcI-LARA (F) in light grey with the pseudoatomic model represented as cartoons and colored as the densities in (A,C,E).	FIG
+46	52	cryoEM	experimental_method	Scale bar 50 Å. (B,D,F) One protomer from the cryoEM map of the LdcC (B), LdcIa (D) and LdcI-LARA (F) in light grey with the pseudoatomic model represented as cartoons and colored as the densities in (A,C,E).	FIG
+53	56	map	evidence	Scale bar 50 Å. (B,D,F) One protomer from the cryoEM map of the LdcC (B), LdcIa (D) and LdcI-LARA (F) in light grey with the pseudoatomic model represented as cartoons and colored as the densities in (A,C,E).	FIG
+64	68	LdcC	protein	Scale bar 50 Å. (B,D,F) One protomer from the cryoEM map of the LdcC (B), LdcIa (D) and LdcI-LARA (F) in light grey with the pseudoatomic model represented as cartoons and colored as the densities in (A,C,E).	FIG
+74	79	LdcIa	protein	Scale bar 50 Å. (B,D,F) One protomer from the cryoEM map of the LdcC (B), LdcIa (D) and LdcI-LARA (F) in light grey with the pseudoatomic model represented as cartoons and colored as the densities in (A,C,E).	FIG
+88	97	LdcI-LARA	complex_assembly	Scale bar 50 Å. (B,D,F) One protomer from the cryoEM map of the LdcC (B), LdcIa (D) and LdcI-LARA (F) in light grey with the pseudoatomic model represented as cartoons and colored as the densities in (A,C,E).	FIG
+125	143	pseudoatomic model	evidence	Scale bar 50 Å. (B,D,F) One protomer from the cryoEM map of the LdcC (B), LdcIa (D) and LdcI-LARA (F) in light grey with the pseudoatomic model represented as cartoons and colored as the densities in (A,C,E).	FIG
+0	13	Superposition	experimental_method	Superposition of the pseudoatomic models of LdcC, LdcI from LdcI-LARA and LdcIa colored as in Fig. 1, and the crystal structure of LdcIi in shades of yellow.	FIG
+21	40	pseudoatomic models	evidence	Superposition of the pseudoatomic models of LdcC, LdcI from LdcI-LARA and LdcIa colored as in Fig. 1, and the crystal structure of LdcIi in shades of yellow.	FIG
+44	48	LdcC	protein	Superposition of the pseudoatomic models of LdcC, LdcI from LdcI-LARA and LdcIa colored as in Fig. 1, and the crystal structure of LdcIi in shades of yellow.	FIG
+50	54	LdcI	protein	Superposition of the pseudoatomic models of LdcC, LdcI from LdcI-LARA and LdcIa colored as in Fig. 1, and the crystal structure of LdcIi in shades of yellow.	FIG
+60	69	LdcI-LARA	complex_assembly	Superposition of the pseudoatomic models of LdcC, LdcI from LdcI-LARA and LdcIa colored as in Fig. 1, and the crystal structure of LdcIi in shades of yellow.	FIG
+74	79	LdcIa	protein	Superposition of the pseudoatomic models of LdcC, LdcI from LdcI-LARA and LdcIa colored as in Fig. 1, and the crystal structure of LdcIi in shades of yellow.	FIG
+110	127	crystal structure	evidence	Superposition of the pseudoatomic models of LdcC, LdcI from LdcI-LARA and LdcIa colored as in Fig. 1, and the crystal structure of LdcIi in shades of yellow.	FIG
+131	136	LdcIi	protein	Superposition of the pseudoatomic models of LdcC, LdcI from LdcI-LARA and LdcIa colored as in Fig. 1, and the crystal structure of LdcIi in shades of yellow.	FIG
+20	25	rings	structure_element	Only one of the two rings of the double toroid is shown for clarity.	FIG
+33	46	double toroid	structure_element	Only one of the two rings of the double toroid is shown for clarity.	FIG
+40	46	region	structure_element	The dashed circle indicates the central region that remains virtually unchanged between all the structures, while the periphery undergoes visible movements.	FIG
+96	106	structures	evidence	The dashed circle indicates the central region that remains virtually unchanged between all the structures, while the periphery undergoes visible movements.	FIG
+44	55	active site	site	Conformational rearrangements in the enzyme active site.	FIG
+4	9	LdcIi	protein	(A) LdcIi crystal structure, with one ring represented as a grey surface and the second as a cartoon.	FIG
+10	27	crystal structure	evidence	(A) LdcIi crystal structure, with one ring represented as a grey surface and the second as a cartoon.	FIG
+38	42	ring	structure_element	(A) LdcIi crystal structure, with one ring represented as a grey surface and the second as a cartoon.	FIG
+2	9	monomer	oligomeric_state	A monomer with its PLP cofactor is delineated.	FIG
+19	22	PLP	chemical	A monomer with its PLP cofactor is delineated.	FIG
+4	7	PLP	chemical	The PLP moieties of the cartoon ring are shown in red.	FIG
+32	36	ring	structure_element	The PLP moieties of the cartoon ring are shown in red.	FIG
+9	14	LdcIi	protein	 (B) The LdcIi dimer extracted from the crystal structure of the decamer.	FIG
+15	20	dimer	oligomeric_state	 (B) The LdcIi dimer extracted from the crystal structure of the decamer.	FIG
+40	57	crystal structure	evidence	 (B) The LdcIi dimer extracted from the crystal structure of the decamer.	FIG
+65	72	decamer	oligomeric_state	 (B) The LdcIi dimer extracted from the crystal structure of the decamer.	FIG
+4	11	monomer	oligomeric_state	One monomer is colored in shades of yellow as in Figs 1 and 2, while the monomer related by C2 symmetry is grey.	FIG
+73	80	monomer	oligomeric_state	One monomer is colored in shades of yellow as in Figs 1 and 2, while the monomer related by C2 symmetry is grey.	FIG
+4	7	PLP	chemical	The PLP is red.	FIG
+4	15	active site	site	The active site is boxed.	FIG
+18	22	LdcI	protein	Stretching of the LdcI monomer upon pH-dependent enzyme activation and LARA binding.	FIG
+23	30	monomer	oligomeric_state	Stretching of the LdcI monomer upon pH-dependent enzyme activation and LARA binding.	FIG
+36	48	pH-dependent	protein_state	Stretching of the LdcI monomer upon pH-dependent enzyme activation and LARA binding.	FIG
+71	75	LARA	structure_element	Stretching of the LdcI monomer upon pH-dependent enzyme activation and LARA binding.	FIG
+26	45	pseudoatomic models	evidence	(A–C) A slice through the pseudoatomic models of the LdcI monomers extracted from the superimposed decamers (Fig. 2) The rectangle indicates the regions enlarged in (D–F).	FIG
+53	57	LdcI	protein	(A–C) A slice through the pseudoatomic models of the LdcI monomers extracted from the superimposed decamers (Fig. 2) The rectangle indicates the regions enlarged in (D–F).	FIG
+58	66	monomers	oligomeric_state	(A–C) A slice through the pseudoatomic models of the LdcI monomers extracted from the superimposed decamers (Fig. 2) The rectangle indicates the regions enlarged in (D–F).	FIG
+86	98	superimposed	experimental_method	(A–C) A slice through the pseudoatomic models of the LdcI monomers extracted from the superimposed decamers (Fig. 2) The rectangle indicates the regions enlarged in (D–F).	FIG
+99	107	decamers	oligomeric_state	(A–C) A slice through the pseudoatomic models of the LdcI monomers extracted from the superimposed decamers (Fig. 2) The rectangle indicates the regions enlarged in (D–F).	FIG
+13	18	LdcIi	protein	(A) compares LdcIi (yellow) and LdcIa (pink), (B) compares LdcIa (pink) and LdcI-LARA (blue), and (C) compares LdcIi (yellow), LdcIa (pink) and LdcI-LARA (blue) simultaneously in order to show the progressive stretching described in the text.	FIG
+32	37	LdcIa	protein	(A) compares LdcIi (yellow) and LdcIa (pink), (B) compares LdcIa (pink) and LdcI-LARA (blue), and (C) compares LdcIi (yellow), LdcIa (pink) and LdcI-LARA (blue) simultaneously in order to show the progressive stretching described in the text.	FIG
+59	64	LdcIa	protein	(A) compares LdcIi (yellow) and LdcIa (pink), (B) compares LdcIa (pink) and LdcI-LARA (blue), and (C) compares LdcIi (yellow), LdcIa (pink) and LdcI-LARA (blue) simultaneously in order to show the progressive stretching described in the text.	FIG
+76	85	LdcI-LARA	complex_assembly	(A) compares LdcIi (yellow) and LdcIa (pink), (B) compares LdcIa (pink) and LdcI-LARA (blue), and (C) compares LdcIi (yellow), LdcIa (pink) and LdcI-LARA (blue) simultaneously in order to show the progressive stretching described in the text.	FIG
+111	116	LdcIi	protein	(A) compares LdcIi (yellow) and LdcIa (pink), (B) compares LdcIa (pink) and LdcI-LARA (blue), and (C) compares LdcIi (yellow), LdcIa (pink) and LdcI-LARA (blue) simultaneously in order to show the progressive stretching described in the text.	FIG
+127	132	LdcIa	protein	(A) compares LdcIi (yellow) and LdcIa (pink), (B) compares LdcIa (pink) and LdcI-LARA (blue), and (C) compares LdcIi (yellow), LdcIa (pink) and LdcI-LARA (blue) simultaneously in order to show the progressive stretching described in the text.	FIG
+144	153	LdcI-LARA	complex_assembly	(A) compares LdcIi (yellow) and LdcIa (pink), (B) compares LdcIa (pink) and LdcI-LARA (blue), and (C) compares LdcIi (yellow), LdcIa (pink) and LdcI-LARA (blue) simultaneously in order to show the progressive stretching described in the text.	FIG
+4	10	cryoEM	experimental_method	The cryoEM density of the LARA domain is represented as a grey surface to show the position of the binding site and the direction of the movement.	FIG
+11	18	density	evidence	The cryoEM density of the LARA domain is represented as a grey surface to show the position of the binding site and the direction of the movement.	FIG
+26	37	LARA domain	structure_element	The cryoEM density of the LARA domain is represented as a grey surface to show the position of the binding site and the direction of the movement.	FIG
+99	111	binding site	site	The cryoEM density of the LARA domain is represented as a grey surface to show the position of the binding site and the direction of the movement.	FIG
+29	32	CTD	structure_element	(D–F) Inserts zooming at the CTD part in proximity of the LARA binding site.	FIG
+58	75	LARA binding site	site	(D–F) Inserts zooming at the CTD part in proximity of the LARA binding site.	FIG
+16	21	LdcIC	mutant	Analysis of the LdcIC and LdcCI chimeras.	FIG
+26	31	LdcCI	mutant	Analysis of the LdcIC and LdcCI chimeras.	FIG
+32	40	chimeras	mutant	Analysis of the LdcIC and LdcCI chimeras.	FIG
+24	43	pseudoatomic models	evidence	(A) A slice through the pseudoatomic models of the LdcIa (purple) and LdcC (green) monomers extracted from the superimposed decamers (Fig. 2). (B) The C-terminal β-sheet in LdcIa and LdcC enlarged from (A,C) Exchanged primary sequences (capital letters) and their immediate vicinity (lower case letters) colored as in (A,B), with the corresponding secondary structure elements and the amino acid numbering shown.	FIG
+51	56	LdcIa	protein	(A) A slice through the pseudoatomic models of the LdcIa (purple) and LdcC (green) monomers extracted from the superimposed decamers (Fig. 2). (B) The C-terminal β-sheet in LdcIa and LdcC enlarged from (A,C) Exchanged primary sequences (capital letters) and their immediate vicinity (lower case letters) colored as in (A,B), with the corresponding secondary structure elements and the amino acid numbering shown.	FIG
+70	74	LdcC	protein	(A) A slice through the pseudoatomic models of the LdcIa (purple) and LdcC (green) monomers extracted from the superimposed decamers (Fig. 2). (B) The C-terminal β-sheet in LdcIa and LdcC enlarged from (A,C) Exchanged primary sequences (capital letters) and their immediate vicinity (lower case letters) colored as in (A,B), with the corresponding secondary structure elements and the amino acid numbering shown.	FIG
+83	91	monomers	oligomeric_state	(A) A slice through the pseudoatomic models of the LdcIa (purple) and LdcC (green) monomers extracted from the superimposed decamers (Fig. 2). (B) The C-terminal β-sheet in LdcIa and LdcC enlarged from (A,C) Exchanged primary sequences (capital letters) and their immediate vicinity (lower case letters) colored as in (A,B), with the corresponding secondary structure elements and the amino acid numbering shown.	FIG
+111	123	superimposed	experimental_method	(A) A slice through the pseudoatomic models of the LdcIa (purple) and LdcC (green) monomers extracted from the superimposed decamers (Fig. 2). (B) The C-terminal β-sheet in LdcIa and LdcC enlarged from (A,C) Exchanged primary sequences (capital letters) and their immediate vicinity (lower case letters) colored as in (A,B), with the corresponding secondary structure elements and the amino acid numbering shown.	FIG
+124	132	decamers	oligomeric_state	(A) A slice through the pseudoatomic models of the LdcIa (purple) and LdcC (green) monomers extracted from the superimposed decamers (Fig. 2). (B) The C-terminal β-sheet in LdcIa and LdcC enlarged from (A,C) Exchanged primary sequences (capital letters) and their immediate vicinity (lower case letters) colored as in (A,B), with the corresponding secondary structure elements and the amino acid numbering shown.	FIG
+162	169	β-sheet	structure_element	(A) A slice through the pseudoatomic models of the LdcIa (purple) and LdcC (green) monomers extracted from the superimposed decamers (Fig. 2). (B) The C-terminal β-sheet in LdcIa and LdcC enlarged from (A,C) Exchanged primary sequences (capital letters) and their immediate vicinity (lower case letters) colored as in (A,B), with the corresponding secondary structure elements and the amino acid numbering shown.	FIG
+173	178	LdcIa	protein	(A) A slice through the pseudoatomic models of the LdcIa (purple) and LdcC (green) monomers extracted from the superimposed decamers (Fig. 2). (B) The C-terminal β-sheet in LdcIa and LdcC enlarged from (A,C) Exchanged primary sequences (capital letters) and their immediate vicinity (lower case letters) colored as in (A,B), with the corresponding secondary structure elements and the amino acid numbering shown.	FIG
+183	187	LdcC	protein	(A) A slice through the pseudoatomic models of the LdcIa (purple) and LdcC (green) monomers extracted from the superimposed decamers (Fig. 2). (B) The C-terminal β-sheet in LdcIa and LdcC enlarged from (A,C) Exchanged primary sequences (capital letters) and their immediate vicinity (lower case letters) colored as in (A,B), with the corresponding secondary structure elements and the amino acid numbering shown.	FIG
+55	64	wild type	protein_state	(D,E) A gallery of negative stain EM images of (D) the wild type LdcI-RavA cage and (E) the LdcCI-RavA cage-like particles. (F) Some representative class averages of the LdcCI-RavA cage-like particles.	FIG
+65	74	LdcI-RavA	complex_assembly	(D,E) A gallery of negative stain EM images of (D) the wild type LdcI-RavA cage and (E) the LdcCI-RavA cage-like particles. (F) Some representative class averages of the LdcCI-RavA cage-like particles.	FIG
+92	122	LdcCI-RavA cage-like particles	mutant	(D,E) A gallery of negative stain EM images of (D) the wild type LdcI-RavA cage and (E) the LdcCI-RavA cage-like particles. (F) Some representative class averages of the LdcCI-RavA cage-like particles.	FIG
+170	200	LdcCI-RavA cage-like particles	mutant	(D,E) A gallery of negative stain EM images of (D) the wild type LdcI-RavA cage and (E) the LdcCI-RavA cage-like particles. (F) Some representative class averages of the LdcCI-RavA cage-like particles.	FIG
+0	17	Sequence analysis	experimental_method	Sequence analysis of enterobacterial lysine decarboxylases.	FIG
+21	36	enterobacterial	taxonomy_domain	Sequence analysis of enterobacterial lysine decarboxylases.	FIG
+37	58	lysine decarboxylases	protein_type	Sequence analysis of enterobacterial lysine decarboxylases.	FIG
+4	27	Maximum likelihood tree	evidence	(A) Maximum likelihood tree with the “LdcC-like” and the “LdcI-like” groups highlighted in green and pink, respectively.	FIG
+38	47	LdcC-like	protein_type	(A) Maximum likelihood tree with the “LdcC-like” and the “LdcI-like” groups highlighted in green and pink, respectively.	FIG
+58	67	LdcI-like	protein_type	(A) Maximum likelihood tree with the “LdcC-like” and the “LdcI-like” groups highlighted in green and pink, respectively.	FIG
+27	36	LdcI-like	protein_type	(B) Analysis of consensus “LdcI-like” and “LdcC-like” sequences around the first and second C-terminal β-strands.	FIG
+43	52	LdcC-like	protein_type	(B) Analysis of consensus “LdcI-like” and “LdcC-like” sequences around the first and second C-terminal β-strands.	FIG
+103	112	β-strands	structure_element	(B) Analysis of consensus “LdcI-like” and “LdcC-like” sequences around the first and second C-terminal β-strands.	FIG
+16	23	E. coli	species	Numbering as in E. coli.	FIG
+28	32	LdcI	protein	 (C) Signature sequences of LdcI and LdcC in the C-terminal β-sheet.	FIG
+37	41	LdcC	protein	 (C) Signature sequences of LdcI and LdcC in the C-terminal β-sheet.	FIG
+60	67	β-sheet	structure_element	 (C) Signature sequences of LdcI and LdcC in the C-terminal β-sheet.	FIG
+116	122	cryoEM	experimental_method	Polarity differences are highlighted. (D) Position and nature of these differences at the surface of the respective cryoEM maps with the color code as in B. See also Fig. S7 and Tables S3 and S4.	FIG
+123	127	maps	evidence	Polarity differences are highlighted. (D) Position and nature of these differences at the surface of the respective cryoEM maps with the color code as in B. See also Fig. S7 and Tables S3 and S4.	FIG