annotation_CSV/PMC4832331.csv

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