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+anno_start	anno_end	anno_text	entity_type	sentence	section
+0	17	Crystal Structure	evidence	Crystal Structure and Activity Studies of the C11 Cysteine Peptidase from Parabacteroides merdae in the Human Gut Microbiome*	TITLE
+22	38	Activity Studies	experimental_method	Crystal Structure and Activity Studies of the C11 Cysteine Peptidase from Parabacteroides merdae in the Human Gut Microbiome*	TITLE
+46	49	C11	protein_type	Crystal Structure and Activity Studies of the C11 Cysteine Peptidase from Parabacteroides merdae in the Human Gut Microbiome*	TITLE
+50	68	Cysteine Peptidase	protein_type	Crystal Structure and Activity Studies of the C11 Cysteine Peptidase from Parabacteroides merdae in the Human Gut Microbiome*	TITLE
+74	96	Parabacteroides merdae	species	Crystal Structure and Activity Studies of the C11 Cysteine Peptidase from Parabacteroides merdae in the Human Gut Microbiome*	TITLE
+104	109	Human	species	Crystal Structure and Activity Studies of the C11 Cysteine Peptidase from Parabacteroides merdae in the Human Gut Microbiome*	TITLE
+0	27	Clan CD cysteine peptidases	protein_type	Clan CD cysteine peptidases, a structurally related group of peptidases that include mammalian caspases, exhibit a wide range of important functions, along with a variety of specificities and activation mechanisms.	ABSTRACT
+61	71	peptidases	protein_type	Clan CD cysteine peptidases, a structurally related group of peptidases that include mammalian caspases, exhibit a wide range of important functions, along with a variety of specificities and activation mechanisms.	ABSTRACT
+85	94	mammalian	taxonomy_domain	Clan CD cysteine peptidases, a structurally related group of peptidases that include mammalian caspases, exhibit a wide range of important functions, along with a variety of specificities and activation mechanisms.	ABSTRACT
+95	103	caspases	protein_type	Clan CD cysteine peptidases, a structurally related group of peptidases that include mammalian caspases, exhibit a wide range of important functions, along with a variety of specificities and activation mechanisms.	ABSTRACT
+17	35	clostripain family	protein_type	However, for the clostripain family (denoted C11), little is currently known.	ABSTRACT
+45	48	C11	protein_type	However, for the clostripain family (denoted C11), little is currently known.	ABSTRACT
+28	45	crystal structure	evidence	Here, we describe the first crystal structure of a C11 protein from the human gut bacterium, Parabacteroides merdae (PmC11), determined to 1.7-Å resolution.	ABSTRACT
+51	54	C11	protein_type	Here, we describe the first crystal structure of a C11 protein from the human gut bacterium, Parabacteroides merdae (PmC11), determined to 1.7-Å resolution.	ABSTRACT
+72	77	human	species	Here, we describe the first crystal structure of a C11 protein from the human gut bacterium, Parabacteroides merdae (PmC11), determined to 1.7-Å resolution.	ABSTRACT
+82	91	bacterium	taxonomy_domain	Here, we describe the first crystal structure of a C11 protein from the human gut bacterium, Parabacteroides merdae (PmC11), determined to 1.7-Å resolution.	ABSTRACT
+93	115	Parabacteroides merdae	species	Here, we describe the first crystal structure of a C11 protein from the human gut bacterium, Parabacteroides merdae (PmC11), determined to 1.7-Å resolution.	ABSTRACT
+117	122	PmC11	protein	Here, we describe the first crystal structure of a C11 protein from the human gut bacterium, Parabacteroides merdae (PmC11), determined to 1.7-Å resolution.	ABSTRACT
+0	5	PmC11	protein	PmC11 is a monomeric cysteine peptidase that comprises an extended caspase-like α/β/α sandwich and an unusual C-terminal domain.	ABSTRACT
+11	20	monomeric	oligomeric_state	PmC11 is a monomeric cysteine peptidase that comprises an extended caspase-like α/β/α sandwich and an unusual C-terminal domain.	ABSTRACT
+21	39	cysteine peptidase	protein_type	PmC11 is a monomeric cysteine peptidase that comprises an extended caspase-like α/β/α sandwich and an unusual C-terminal domain.	ABSTRACT
+58	94	extended caspase-like α/β/α sandwich	structure_element	PmC11 is a monomeric cysteine peptidase that comprises an extended caspase-like α/β/α sandwich and an unusual C-terminal domain.	ABSTRACT
+110	127	C-terminal domain	structure_element	PmC11 is a monomeric cysteine peptidase that comprises an extended caspase-like α/β/α sandwich and an unusual C-terminal domain.	ABSTRACT
+40	67	clan CD cysteine peptidases	protein_type	It shares core structural elements with clan CD cysteine peptidases but otherwise structurally differs from the other families in the clan.	ABSTRACT
+77	83	Lys147	residue_name_number	These studies also revealed a well ordered break in the polypeptide chain at Lys147, resulting in a large conformational rearrangement close to the active site.	ABSTRACT
+148	159	active site	site	These studies also revealed a well ordered break in the polypeptide chain at Lys147, resulting in a large conformational rearrangement close to the active site.	ABSTRACT
+0	32	Biochemical and kinetic analysis	experimental_method	Biochemical and kinetic analysis revealed Lys147 to be an intramolecular processing site at which cleavage is required for full activation of the enzyme, suggesting an autoinhibitory mechanism for self-preservation.	ABSTRACT
+42	48	Lys147	residue_name_number	Biochemical and kinetic analysis revealed Lys147 to be an intramolecular processing site at which cleavage is required for full activation of the enzyme, suggesting an autoinhibitory mechanism for self-preservation.	ABSTRACT
+58	88	intramolecular processing site	site	Biochemical and kinetic analysis revealed Lys147 to be an intramolecular processing site at which cleavage is required for full activation of the enzyme, suggesting an autoinhibitory mechanism for self-preservation.	ABSTRACT
+98	106	cleavage	ptm	Biochemical and kinetic analysis revealed Lys147 to be an intramolecular processing site at which cleavage is required for full activation of the enzyme, suggesting an autoinhibitory mechanism for self-preservation.	ABSTRACT
+123	138	full activation	protein_state	Biochemical and kinetic analysis revealed Lys147 to be an intramolecular processing site at which cleavage is required for full activation of the enzyme, suggesting an autoinhibitory mechanism for self-preservation.	ABSTRACT
+146	152	enzyme	protein	Biochemical and kinetic analysis revealed Lys147 to be an intramolecular processing site at which cleavage is required for full activation of the enzyme, suggesting an autoinhibitory mechanism for self-preservation.	ABSTRACT
+0	5	PmC11	protein	PmC11 has an acidic binding pocket and a preference for basic substrates, and accepts substrates with Arg and Lys in P1 and does not require Ca2+ for activity.	ABSTRACT
+13	34	acidic binding pocket	site	PmC11 has an acidic binding pocket and a preference for basic substrates, and accepts substrates with Arg and Lys in P1 and does not require Ca2+ for activity.	ABSTRACT
+102	105	Arg	residue_name	PmC11 has an acidic binding pocket and a preference for basic substrates, and accepts substrates with Arg and Lys in P1 and does not require Ca2+ for activity.	ABSTRACT
+110	113	Lys	residue_name	PmC11 has an acidic binding pocket and a preference for basic substrates, and accepts substrates with Arg and Lys in P1 and does not require Ca2+ for activity.	ABSTRACT
+117	119	P1	residue_number	PmC11 has an acidic binding pocket and a preference for basic substrates, and accepts substrates with Arg and Lys in P1 and does not require Ca2+ for activity.	ABSTRACT
+141	145	Ca2+	chemical	PmC11 has an acidic binding pocket and a preference for basic substrates, and accepts substrates with Arg and Lys in P1 and does not require Ca2+ for activity.	ABSTRACT
+77	82	PmC11	protein	Collectively, these data provide insights into the mechanism and activity of PmC11 and a detailed framework for studies on C11 peptidases from other phylogenetic kingdoms.	ABSTRACT
+123	137	C11 peptidases	protein_type	Collectively, these data provide insights into the mechanism and activity of PmC11 and a detailed framework for studies on C11 peptidases from other phylogenetic kingdoms.	ABSTRACT
+0	19	Cysteine peptidases	protein_type	Cysteine peptidases play crucial roles in the virulence of bacterial and other eukaryotic pathogens.	INTRO
+59	68	bacterial	taxonomy_domain	Cysteine peptidases play crucial roles in the virulence of bacterial and other eukaryotic pathogens.	INTRO
+79	89	eukaryotic	taxonomy_domain	Cysteine peptidases play crucial roles in the virulence of bacterial and other eukaryotic pathogens.	INTRO
+34	41	clan CD	protein_type	In the MEROPS peptidase database, clan CD contains groups (or families) of cysteine peptidases that share some highly conserved structural elements.	INTRO
+75	94	cysteine peptidases	protein_type	In the MEROPS peptidase database, clan CD contains groups (or families) of cysteine peptidases that share some highly conserved structural elements.	INTRO
+111	127	highly conserved	protein_state	In the MEROPS peptidase database, clan CD contains groups (or families) of cysteine peptidases that share some highly conserved structural elements.	INTRO
+0	16	Clan CD families	protein_type	Clan CD families are typically described using the name of their archetypal, or founding, member and also given an identification number preceded by a “C,” to denote cysteine peptidase.	INTRO
+166	184	cysteine peptidase	protein_type	Clan CD families are typically described using the name of their archetypal, or founding, member and also given an identification number preceded by a “C,” to denote cysteine peptidase.	INTRO
+110	128	crystal structures	evidence	Although seven families (C14 is additionally split into three subfamilies) have been described for this clan, crystal structures have only been determined from four: legumain (C13), caspase (C14a), paracaspase (C14b(P), metacaspase (C14b(M), gingipain (C25), and the cysteine peptidase domain (CPD) of various toxins (C80).	INTRO
+166	174	legumain	protein	Although seven families (C14 is additionally split into three subfamilies) have been described for this clan, crystal structures have only been determined from four: legumain (C13), caspase (C14a), paracaspase (C14b(P), metacaspase (C14b(M), gingipain (C25), and the cysteine peptidase domain (CPD) of various toxins (C80).	INTRO
+176	179	C13	protein_type	Although seven families (C14 is additionally split into three subfamilies) have been described for this clan, crystal structures have only been determined from four: legumain (C13), caspase (C14a), paracaspase (C14b(P), metacaspase (C14b(M), gingipain (C25), and the cysteine peptidase domain (CPD) of various toxins (C80).	INTRO
+182	189	caspase	protein	Although seven families (C14 is additionally split into three subfamilies) have been described for this clan, crystal structures have only been determined from four: legumain (C13), caspase (C14a), paracaspase (C14b(P), metacaspase (C14b(M), gingipain (C25), and the cysteine peptidase domain (CPD) of various toxins (C80).	INTRO
+191	195	C14a	protein_type	Although seven families (C14 is additionally split into three subfamilies) have been described for this clan, crystal structures have only been determined from four: legumain (C13), caspase (C14a), paracaspase (C14b(P), metacaspase (C14b(M), gingipain (C25), and the cysteine peptidase domain (CPD) of various toxins (C80).	INTRO
+198	209	paracaspase	protein	Although seven families (C14 is additionally split into three subfamilies) have been described for this clan, crystal structures have only been determined from four: legumain (C13), caspase (C14a), paracaspase (C14b(P), metacaspase (C14b(M), gingipain (C25), and the cysteine peptidase domain (CPD) of various toxins (C80).	INTRO
+211	217	C14b(P	protein_type	Although seven families (C14 is additionally split into three subfamilies) have been described for this clan, crystal structures have only been determined from four: legumain (C13), caspase (C14a), paracaspase (C14b(P), metacaspase (C14b(M), gingipain (C25), and the cysteine peptidase domain (CPD) of various toxins (C80).	INTRO
+220	231	metacaspase	protein	Although seven families (C14 is additionally split into three subfamilies) have been described for this clan, crystal structures have only been determined from four: legumain (C13), caspase (C14a), paracaspase (C14b(P), metacaspase (C14b(M), gingipain (C25), and the cysteine peptidase domain (CPD) of various toxins (C80).	INTRO
+233	239	C14b(M	protein_type	Although seven families (C14 is additionally split into three subfamilies) have been described for this clan, crystal structures have only been determined from four: legumain (C13), caspase (C14a), paracaspase (C14b(P), metacaspase (C14b(M), gingipain (C25), and the cysteine peptidase domain (CPD) of various toxins (C80).	INTRO
+242	251	gingipain	protein	Although seven families (C14 is additionally split into three subfamilies) have been described for this clan, crystal structures have only been determined from four: legumain (C13), caspase (C14a), paracaspase (C14b(P), metacaspase (C14b(M), gingipain (C25), and the cysteine peptidase domain (CPD) of various toxins (C80).	INTRO
+253	256	C25	protein_type	Although seven families (C14 is additionally split into three subfamilies) have been described for this clan, crystal structures have only been determined from four: legumain (C13), caspase (C14a), paracaspase (C14b(P), metacaspase (C14b(M), gingipain (C25), and the cysteine peptidase domain (CPD) of various toxins (C80).	INTRO
+267	292	cysteine peptidase domain	structure_element	Although seven families (C14 is additionally split into three subfamilies) have been described for this clan, crystal structures have only been determined from four: legumain (C13), caspase (C14a), paracaspase (C14b(P), metacaspase (C14b(M), gingipain (C25), and the cysteine peptidase domain (CPD) of various toxins (C80).	INTRO
+294	297	CPD	structure_element	Although seven families (C14 is additionally split into three subfamilies) have been described for this clan, crystal structures have only been determined from four: legumain (C13), caspase (C14a), paracaspase (C14b(P), metacaspase (C14b(M), gingipain (C25), and the cysteine peptidase domain (CPD) of various toxins (C80).	INTRO
+318	321	C80	protein_type	Although seven families (C14 is additionally split into three subfamilies) have been described for this clan, crystal structures have only been determined from four: legumain (C13), caspase (C14a), paracaspase (C14b(P), metacaspase (C14b(M), gingipain (C25), and the cysteine peptidase domain (CPD) of various toxins (C80).	INTRO
+43	54	clostripain	protein	No structural information is available for clostripain (C11), separase (C50), or PrtH-peptidase (C85).	INTRO
+56	59	C11	protein_type	No structural information is available for clostripain (C11), separase (C50), or PrtH-peptidase (C85).	INTRO
+62	70	separase	protein	No structural information is available for clostripain (C11), separase (C50), or PrtH-peptidase (C85).	INTRO
+72	75	C50	protein_type	No structural information is available for clostripain (C11), separase (C50), or PrtH-peptidase (C85).	INTRO
+81	95	PrtH-peptidase	protein	No structural information is available for clostripain (C11), separase (C50), or PrtH-peptidase (C85).	INTRO
+97	100	C85	protein_type	No structural information is available for clostripain (C11), separase (C50), or PrtH-peptidase (C85).	INTRO
+0	15	Clan CD enzymes	protein_type	Clan CD enzymes have a highly conserved His/Cys catalytic dyad and exhibit strict specificity for the P1 residue of their substrates.	INTRO
+23	39	highly conserved	protein_state	Clan CD enzymes have a highly conserved His/Cys catalytic dyad and exhibit strict specificity for the P1 residue of their substrates.	INTRO
+40	62	His/Cys catalytic dyad	site	Clan CD enzymes have a highly conserved His/Cys catalytic dyad and exhibit strict specificity for the P1 residue of their substrates.	INTRO
+102	104	P1	residue_number	Clan CD enzymes have a highly conserved His/Cys catalytic dyad and exhibit strict specificity for the P1 residue of their substrates.	INTRO
+37	44	clan CD	protein_type	However, despite these similarities, clan CD forms a functionally diverse group of enzymes: the overall structural diversity between (and at times within) the various families provides these peptidases with a wide variety of substrate specificities and activation mechanisms.	INTRO
+191	201	peptidases	protein_type	However, despite these similarities, clan CD forms a functionally diverse group of enzymes: the overall structural diversity between (and at times within) the various families provides these peptidases with a wide variety of substrate specificities and activation mechanisms.	INTRO
+75	84	mammalian	taxonomy_domain	The archetypal and arguably most notable family in the clan is that of the mammalian caspases (C14a), although clan CD members are distributed throughout the entire phylogenetic kingdom and are often required in fundamental biological processes.	INTRO
+85	93	caspases	protein_type	The archetypal and arguably most notable family in the clan is that of the mammalian caspases (C14a), although clan CD members are distributed throughout the entire phylogenetic kingdom and are often required in fundamental biological processes.	INTRO
+95	99	C14a	protein_type	The archetypal and arguably most notable family in the clan is that of the mammalian caspases (C14a), although clan CD members are distributed throughout the entire phylogenetic kingdom and are often required in fundamental biological processes.	INTRO
+111	118	clan CD	protein_type	The archetypal and arguably most notable family in the clan is that of the mammalian caspases (C14a), although clan CD members are distributed throughout the entire phylogenetic kingdom and are often required in fundamental biological processes.	INTRO
+70	73	C11	protein_type	Interestingly, little is known about the structure or function of the C11 proteins, despite their widespread distribution and its archetypal member, clostripain from Clostridium histolyticum, first reported in the literature in 1938.	INTRO
+149	160	clostripain	protein	Interestingly, little is known about the structure or function of the C11 proteins, despite their widespread distribution and its archetypal member, clostripain from Clostridium histolyticum, first reported in the literature in 1938.	INTRO
+166	190	Clostridium histolyticum	species	Interestingly, little is known about the structure or function of the C11 proteins, despite their widespread distribution and its archetypal member, clostripain from Clostridium histolyticum, first reported in the literature in 1938.	INTRO
+0	11	Clostripain	protein	Clostripain has been described as an arginine-specific peptidase with a requirement for Ca2+ and loss of an internal nonapeptide for full activation; lack of structural information on the family appears to have prohibited further investigation.	INTRO
+37	64	arginine-specific peptidase	protein_type	Clostripain has been described as an arginine-specific peptidase with a requirement for Ca2+ and loss of an internal nonapeptide for full activation; lack of structural information on the family appears to have prohibited further investigation.	INTRO
+88	92	Ca2+	chemical	Clostripain has been described as an arginine-specific peptidase with a requirement for Ca2+ and loss of an internal nonapeptide for full activation; lack of structural information on the family appears to have prohibited further investigation.	INTRO
+108	128	internal nonapeptide	structure_element	Clostripain has been described as an arginine-specific peptidase with a requirement for Ca2+ and loss of an internal nonapeptide for full activation; lack of structural information on the family appears to have prohibited further investigation.	INTRO
+133	148	full activation	protein_state	Clostripain has been described as an arginine-specific peptidase with a requirement for Ca2+ and loss of an internal nonapeptide for full activation; lack of structural information on the family appears to have prohibited further investigation.	INTRO
+56	64	bacteria	taxonomy_domain	As part of an ongoing project to characterize commensal bacteria in the microbiome that inhabit the human gut, the structure of C11 peptidase, PmC11, from Parabacteroides merdae was determined using the Joint Center for Structural Genomics (JCSG)4 HTP structural biology pipeline.	INTRO
+100	105	human	species	As part of an ongoing project to characterize commensal bacteria in the microbiome that inhabit the human gut, the structure of C11 peptidase, PmC11, from Parabacteroides merdae was determined using the Joint Center for Structural Genomics (JCSG)4 HTP structural biology pipeline.	INTRO
+115	124	structure	evidence	As part of an ongoing project to characterize commensal bacteria in the microbiome that inhabit the human gut, the structure of C11 peptidase, PmC11, from Parabacteroides merdae was determined using the Joint Center for Structural Genomics (JCSG)4 HTP structural biology pipeline.	INTRO
+128	141	C11 peptidase	protein_type	As part of an ongoing project to characterize commensal bacteria in the microbiome that inhabit the human gut, the structure of C11 peptidase, PmC11, from Parabacteroides merdae was determined using the Joint Center for Structural Genomics (JCSG)4 HTP structural biology pipeline.	INTRO
+143	148	PmC11	protein	As part of an ongoing project to characterize commensal bacteria in the microbiome that inhabit the human gut, the structure of C11 peptidase, PmC11, from Parabacteroides merdae was determined using the Joint Center for Structural Genomics (JCSG)4 HTP structural biology pipeline.	INTRO
+155	177	Parabacteroides merdae	species	As part of an ongoing project to characterize commensal bacteria in the microbiome that inhabit the human gut, the structure of C11 peptidase, PmC11, from Parabacteroides merdae was determined using the Joint Center for Structural Genomics (JCSG)4 HTP structural biology pipeline.	INTRO
+4	26	structure was analyzed	experimental_method	The structure was analyzed, and the enzyme was biochemically characterized to provide the first structure/function correlation for a C11 peptidase.	INTRO
+47	74	biochemically characterized	experimental_method	The structure was analyzed, and the enzyme was biochemically characterized to provide the first structure/function correlation for a C11 peptidase.	INTRO
+133	146	C11 peptidase	protein_type	The structure was analyzed, and the enzyme was biochemically characterized to provide the first structure/function correlation for a C11 peptidase.	INTRO
+0	9	Structure	evidence	Structure of PmC11	RESULTS
+13	18	PmC11	protein	Structure of PmC11	RESULTS
+4	21	crystal structure	evidence	The crystal structure of the catalytically active form of PmC11 revealed an extended caspase-like α/β/α sandwich architecture comprised of a central nine-stranded β-sheet, with an unusual C-terminal domain (CTD), starting at Lys250.	RESULTS
+29	49	catalytically active	protein_state	The crystal structure of the catalytically active form of PmC11 revealed an extended caspase-like α/β/α sandwich architecture comprised of a central nine-stranded β-sheet, with an unusual C-terminal domain (CTD), starting at Lys250.	RESULTS
+58	63	PmC11	protein	The crystal structure of the catalytically active form of PmC11 revealed an extended caspase-like α/β/α sandwich architecture comprised of a central nine-stranded β-sheet, with an unusual C-terminal domain (CTD), starting at Lys250.	RESULTS
+76	112	extended caspase-like α/β/α sandwich	structure_element	The crystal structure of the catalytically active form of PmC11 revealed an extended caspase-like α/β/α sandwich architecture comprised of a central nine-stranded β-sheet, with an unusual C-terminal domain (CTD), starting at Lys250.	RESULTS
+149	170	nine-stranded β-sheet	structure_element	The crystal structure of the catalytically active form of PmC11 revealed an extended caspase-like α/β/α sandwich architecture comprised of a central nine-stranded β-sheet, with an unusual C-terminal domain (CTD), starting at Lys250.	RESULTS
+188	205	C-terminal domain	structure_element	The crystal structure of the catalytically active form of PmC11 revealed an extended caspase-like α/β/α sandwich architecture comprised of a central nine-stranded β-sheet, with an unusual C-terminal domain (CTD), starting at Lys250.	RESULTS
+207	210	CTD	structure_element	The crystal structure of the catalytically active form of PmC11 revealed an extended caspase-like α/β/α sandwich architecture comprised of a central nine-stranded β-sheet, with an unusual C-terminal domain (CTD), starting at Lys250.	RESULTS
+225	231	Lys250	residue_name_number	The crystal structure of the catalytically active form of PmC11 revealed an extended caspase-like α/β/α sandwich architecture comprised of a central nine-stranded β-sheet, with an unusual C-terminal domain (CTD), starting at Lys250.	RESULTS
+2	17	single cleavage	ptm	A single cleavage was observed in the polypeptide chain at Lys147 (Fig. 1, A and B), where both ends of the cleavage site are fully visible and well ordered in the electron density.	RESULTS
+59	65	Lys147	residue_name_number	A single cleavage was observed in the polypeptide chain at Lys147 (Fig. 1, A and B), where both ends of the cleavage site are fully visible and well ordered in the electron density.	RESULTS
+108	121	cleavage site	site	A single cleavage was observed in the polypeptide chain at Lys147 (Fig. 1, A and B), where both ends of the cleavage site are fully visible and well ordered in the electron density.	RESULTS
+164	180	electron density	evidence	A single cleavage was observed in the polypeptide chain at Lys147 (Fig. 1, A and B), where both ends of the cleavage site are fully visible and well ordered in the electron density.	RESULTS
+12	33	nine-stranded β-sheet	structure_element	The central nine-stranded β-sheet (β1–β9) of PmC11 consists of six parallel and three anti-parallel β-strands with 4↑3↓2↑1↑5↑6↑7↓8↓9↑ topology (Fig. 1A) and the overall structure includes 14 α-helices with six (α1–α2 and α4–α7) closely surrounding the β-sheet in an approximately parallel orientation.	RESULTS
+35	40	β1–β9	structure_element	The central nine-stranded β-sheet (β1–β9) of PmC11 consists of six parallel and three anti-parallel β-strands with 4↑3↓2↑1↑5↑6↑7↓8↓9↑ topology (Fig. 1A) and the overall structure includes 14 α-helices with six (α1–α2 and α4–α7) closely surrounding the β-sheet in an approximately parallel orientation.	RESULTS
+45	50	PmC11	protein	The central nine-stranded β-sheet (β1–β9) of PmC11 consists of six parallel and three anti-parallel β-strands with 4↑3↓2↑1↑5↑6↑7↓8↓9↑ topology (Fig. 1A) and the overall structure includes 14 α-helices with six (α1–α2 and α4–α7) closely surrounding the β-sheet in an approximately parallel orientation.	RESULTS
+67	75	parallel	structure_element	The central nine-stranded β-sheet (β1–β9) of PmC11 consists of six parallel and three anti-parallel β-strands with 4↑3↓2↑1↑5↑6↑7↓8↓9↑ topology (Fig. 1A) and the overall structure includes 14 α-helices with six (α1–α2 and α4–α7) closely surrounding the β-sheet in an approximately parallel orientation.	RESULTS
+86	109	anti-parallel β-strands	structure_element	The central nine-stranded β-sheet (β1–β9) of PmC11 consists of six parallel and three anti-parallel β-strands with 4↑3↓2↑1↑5↑6↑7↓8↓9↑ topology (Fig. 1A) and the overall structure includes 14 α-helices with six (α1–α2 and α4–α7) closely surrounding the β-sheet in an approximately parallel orientation.	RESULTS
+169	178	structure	evidence	The central nine-stranded β-sheet (β1–β9) of PmC11 consists of six parallel and three anti-parallel β-strands with 4↑3↓2↑1↑5↑6↑7↓8↓9↑ topology (Fig. 1A) and the overall structure includes 14 α-helices with six (α1–α2 and α4–α7) closely surrounding the β-sheet in an approximately parallel orientation.	RESULTS
+191	200	α-helices	structure_element	The central nine-stranded β-sheet (β1–β9) of PmC11 consists of six parallel and three anti-parallel β-strands with 4↑3↓2↑1↑5↑6↑7↓8↓9↑ topology (Fig. 1A) and the overall structure includes 14 α-helices with six (α1–α2 and α4–α7) closely surrounding the β-sheet in an approximately parallel orientation.	RESULTS
+211	216	α1–α2	structure_element	The central nine-stranded β-sheet (β1–β9) of PmC11 consists of six parallel and three anti-parallel β-strands with 4↑3↓2↑1↑5↑6↑7↓8↓9↑ topology (Fig. 1A) and the overall structure includes 14 α-helices with six (α1–α2 and α4–α7) closely surrounding the β-sheet in an approximately parallel orientation.	RESULTS
+221	226	α4–α7	structure_element	The central nine-stranded β-sheet (β1–β9) of PmC11 consists of six parallel and three anti-parallel β-strands with 4↑3↓2↑1↑5↑6↑7↓8↓9↑ topology (Fig. 1A) and the overall structure includes 14 α-helices with six (α1–α2 and α4–α7) closely surrounding the β-sheet in an approximately parallel orientation.	RESULTS
+252	259	β-sheet	structure_element	The central nine-stranded β-sheet (β1–β9) of PmC11 consists of six parallel and three anti-parallel β-strands with 4↑3↓2↑1↑5↑6↑7↓8↓9↑ topology (Fig. 1A) and the overall structure includes 14 α-helices with six (α1–α2 and α4–α7) closely surrounding the β-sheet in an approximately parallel orientation.	RESULTS
+0	7	Helices	structure_element	Helices α1, α7, and α6 are located on one side of the β-sheet with α2, α4, and α5 on the opposite side (Fig. 1A).	RESULTS
+8	10	α1	structure_element	Helices α1, α7, and α6 are located on one side of the β-sheet with α2, α4, and α5 on the opposite side (Fig. 1A).	RESULTS
+12	14	α7	structure_element	Helices α1, α7, and α6 are located on one side of the β-sheet with α2, α4, and α5 on the opposite side (Fig. 1A).	RESULTS
+20	22	α6	structure_element	Helices α1, α7, and α6 are located on one side of the β-sheet with α2, α4, and α5 on the opposite side (Fig. 1A).	RESULTS
+54	61	β-sheet	structure_element	Helices α1, α7, and α6 are located on one side of the β-sheet with α2, α4, and α5 on the opposite side (Fig. 1A).	RESULTS
+67	69	α2	structure_element	Helices α1, α7, and α6 are located on one side of the β-sheet with α2, α4, and α5 on the opposite side (Fig. 1A).	RESULTS
+71	73	α4	structure_element	Helices α1, α7, and α6 are located on one side of the β-sheet with α2, α4, and α5 on the opposite side (Fig. 1A).	RESULTS
+79	81	α5	structure_element	Helices α1, α7, and α6 are located on one side of the β-sheet with α2, α4, and α5 on the opposite side (Fig. 1A).	RESULTS
+0	5	Helix	structure_element	Helix α3 sits at the end of the loop following β5 (L5), just preceding the Lys147 cleavage site, with both L5 and α3 pointing away from the central β-sheet and toward the CTD, which starts with α8.	RESULTS
+6	8	α3	structure_element	Helix α3 sits at the end of the loop following β5 (L5), just preceding the Lys147 cleavage site, with both L5 and α3 pointing away from the central β-sheet and toward the CTD, which starts with α8.	RESULTS
+32	36	loop	structure_element	Helix α3 sits at the end of the loop following β5 (L5), just preceding the Lys147 cleavage site, with both L5 and α3 pointing away from the central β-sheet and toward the CTD, which starts with α8.	RESULTS
+47	49	β5	structure_element	Helix α3 sits at the end of the loop following β5 (L5), just preceding the Lys147 cleavage site, with both L5 and α3 pointing away from the central β-sheet and toward the CTD, which starts with α8.	RESULTS
+51	53	L5	structure_element	Helix α3 sits at the end of the loop following β5 (L5), just preceding the Lys147 cleavage site, with both L5 and α3 pointing away from the central β-sheet and toward the CTD, which starts with α8.	RESULTS
+75	81	Lys147	residue_name_number	Helix α3 sits at the end of the loop following β5 (L5), just preceding the Lys147 cleavage site, with both L5 and α3 pointing away from the central β-sheet and toward the CTD, which starts with α8.	RESULTS
+82	95	cleavage site	site	Helix α3 sits at the end of the loop following β5 (L5), just preceding the Lys147 cleavage site, with both L5 and α3 pointing away from the central β-sheet and toward the CTD, which starts with α8.	RESULTS
+107	109	L5	structure_element	Helix α3 sits at the end of the loop following β5 (L5), just preceding the Lys147 cleavage site, with both L5 and α3 pointing away from the central β-sheet and toward the CTD, which starts with α8.	RESULTS
+114	116	α3	structure_element	Helix α3 sits at the end of the loop following β5 (L5), just preceding the Lys147 cleavage site, with both L5 and α3 pointing away from the central β-sheet and toward the CTD, which starts with α8.	RESULTS
+148	155	β-sheet	structure_element	Helix α3 sits at the end of the loop following β5 (L5), just preceding the Lys147 cleavage site, with both L5 and α3 pointing away from the central β-sheet and toward the CTD, which starts with α8.	RESULTS
+171	174	CTD	structure_element	Helix α3 sits at the end of the loop following β5 (L5), just preceding the Lys147 cleavage site, with both L5 and α3 pointing away from the central β-sheet and toward the CTD, which starts with α8.	RESULTS
+194	196	α8	structure_element	Helix α3 sits at the end of the loop following β5 (L5), just preceding the Lys147 cleavage site, with both L5 and α3 pointing away from the central β-sheet and toward the CTD, which starts with α8.	RESULTS
+4	13	structure	evidence	The structure also includes two short β-hairpins (βA–βB and βD–βE) and a small β-sheet (βC–βF), which is formed from two distinct regions of the sequence (βC precedes α11, α12 and β9, whereas βF follows the βD-βE hairpin) in the middle of the CTD (Fig. 1B).	RESULTS
+38	48	β-hairpins	structure_element	The structure also includes two short β-hairpins (βA–βB and βD–βE) and a small β-sheet (βC–βF), which is formed from two distinct regions of the sequence (βC precedes α11, α12 and β9, whereas βF follows the βD-βE hairpin) in the middle of the CTD (Fig. 1B).	RESULTS
+50	55	βA–βB	structure_element	The structure also includes two short β-hairpins (βA–βB and βD–βE) and a small β-sheet (βC–βF), which is formed from two distinct regions of the sequence (βC precedes α11, α12 and β9, whereas βF follows the βD-βE hairpin) in the middle of the CTD (Fig. 1B).	RESULTS
+60	65	βD–βE	structure_element	The structure also includes two short β-hairpins (βA–βB and βD–βE) and a small β-sheet (βC–βF), which is formed from two distinct regions of the sequence (βC precedes α11, α12 and β9, whereas βF follows the βD-βE hairpin) in the middle of the CTD (Fig. 1B).	RESULTS
+73	86	small β-sheet	structure_element	The structure also includes two short β-hairpins (βA–βB and βD–βE) and a small β-sheet (βC–βF), which is formed from two distinct regions of the sequence (βC precedes α11, α12 and β9, whereas βF follows the βD-βE hairpin) in the middle of the CTD (Fig. 1B).	RESULTS
+88	93	βC–βF	structure_element	The structure also includes two short β-hairpins (βA–βB and βD–βE) and a small β-sheet (βC–βF), which is formed from two distinct regions of the sequence (βC precedes α11, α12 and β9, whereas βF follows the βD-βE hairpin) in the middle of the CTD (Fig. 1B).	RESULTS
+155	157	βC	structure_element	The structure also includes two short β-hairpins (βA–βB and βD–βE) and a small β-sheet (βC–βF), which is formed from two distinct regions of the sequence (βC precedes α11, α12 and β9, whereas βF follows the βD-βE hairpin) in the middle of the CTD (Fig. 1B).	RESULTS
+167	170	α11	structure_element	The structure also includes two short β-hairpins (βA–βB and βD–βE) and a small β-sheet (βC–βF), which is formed from two distinct regions of the sequence (βC precedes α11, α12 and β9, whereas βF follows the βD-βE hairpin) in the middle of the CTD (Fig. 1B).	RESULTS
+172	175	α12	structure_element	The structure also includes two short β-hairpins (βA–βB and βD–βE) and a small β-sheet (βC–βF), which is formed from two distinct regions of the sequence (βC precedes α11, α12 and β9, whereas βF follows the βD-βE hairpin) in the middle of the CTD (Fig. 1B).	RESULTS
+180	182	β9	structure_element	The structure also includes two short β-hairpins (βA–βB and βD–βE) and a small β-sheet (βC–βF), which is formed from two distinct regions of the sequence (βC precedes α11, α12 and β9, whereas βF follows the βD-βE hairpin) in the middle of the CTD (Fig. 1B).	RESULTS
+192	194	βF	structure_element	The structure also includes two short β-hairpins (βA–βB and βD–βE) and a small β-sheet (βC–βF), which is formed from two distinct regions of the sequence (βC precedes α11, α12 and β9, whereas βF follows the βD-βE hairpin) in the middle of the CTD (Fig. 1B).	RESULTS
+207	212	βD-βE	structure_element	The structure also includes two short β-hairpins (βA–βB and βD–βE) and a small β-sheet (βC–βF), which is formed from two distinct regions of the sequence (βC precedes α11, α12 and β9, whereas βF follows the βD-βE hairpin) in the middle of the CTD (Fig. 1B).	RESULTS
+213	220	hairpin	structure_element	The structure also includes two short β-hairpins (βA–βB and βD–βE) and a small β-sheet (βC–βF), which is formed from two distinct regions of the sequence (βC precedes α11, α12 and β9, whereas βF follows the βD-βE hairpin) in the middle of the CTD (Fig. 1B).	RESULTS
+243	246	CTD	structure_element	The structure also includes two short β-hairpins (βA–βB and βD–βE) and a small β-sheet (βC–βF), which is formed from two distinct regions of the sequence (βC precedes α11, α12 and β9, whereas βF follows the βD-βE hairpin) in the middle of the CTD (Fig. 1B).	RESULTS
+0	17	Crystal structure	evidence	Crystal structure of a C11 peptidase from P. merdae.	FIG
+23	36	C11 peptidase	protein_type	Crystal structure of a C11 peptidase from P. merdae.	FIG
+42	51	P. merdae	species	Crystal structure of a C11 peptidase from P. merdae.	FIG
+4	30	primary sequence alignment	experimental_method	 A, primary sequence alignment of PmC11 (Uniprot ID A7A9N3) and clostripain (Uniprot ID P09870) from C. histolyticum with identical residues highlighted in gray shading.	FIG
+34	39	PmC11	protein	 A, primary sequence alignment of PmC11 (Uniprot ID A7A9N3) and clostripain (Uniprot ID P09870) from C. histolyticum with identical residues highlighted in gray shading.	FIG
+64	75	clostripain	protein	 A, primary sequence alignment of PmC11 (Uniprot ID A7A9N3) and clostripain (Uniprot ID P09870) from C. histolyticum with identical residues highlighted in gray shading.	FIG
+101	116	C. histolyticum	species	 A, primary sequence alignment of PmC11 (Uniprot ID A7A9N3) and clostripain (Uniprot ID P09870) from C. histolyticum with identical residues highlighted in gray shading.	FIG
+27	32	PmC11	protein	The secondary structure of PmC11 from the crystal structure is mapped onto its sequence with the position of the PmC11 catalytic dyad, autocatalytic cleavage site (Lys147), and S1 binding pocket Asp (Asp177) highlighted by a red star, a red downturned triangle, and a red upturned triangle, respectively.	FIG
+42	59	crystal structure	evidence	The secondary structure of PmC11 from the crystal structure is mapped onto its sequence with the position of the PmC11 catalytic dyad, autocatalytic cleavage site (Lys147), and S1 binding pocket Asp (Asp177) highlighted by a red star, a red downturned triangle, and a red upturned triangle, respectively.	FIG
+113	118	PmC11	protein	The secondary structure of PmC11 from the crystal structure is mapped onto its sequence with the position of the PmC11 catalytic dyad, autocatalytic cleavage site (Lys147), and S1 binding pocket Asp (Asp177) highlighted by a red star, a red downturned triangle, and a red upturned triangle, respectively.	FIG
+119	133	catalytic dyad	site	The secondary structure of PmC11 from the crystal structure is mapped onto its sequence with the position of the PmC11 catalytic dyad, autocatalytic cleavage site (Lys147), and S1 binding pocket Asp (Asp177) highlighted by a red star, a red downturned triangle, and a red upturned triangle, respectively.	FIG
+135	162	autocatalytic cleavage site	site	The secondary structure of PmC11 from the crystal structure is mapped onto its sequence with the position of the PmC11 catalytic dyad, autocatalytic cleavage site (Lys147), and S1 binding pocket Asp (Asp177) highlighted by a red star, a red downturned triangle, and a red upturned triangle, respectively.	FIG
+164	170	Lys147	residue_name_number	The secondary structure of PmC11 from the crystal structure is mapped onto its sequence with the position of the PmC11 catalytic dyad, autocatalytic cleavage site (Lys147), and S1 binding pocket Asp (Asp177) highlighted by a red star, a red downturned triangle, and a red upturned triangle, respectively.	FIG
+177	194	S1 binding pocket	site	The secondary structure of PmC11 from the crystal structure is mapped onto its sequence with the position of the PmC11 catalytic dyad, autocatalytic cleavage site (Lys147), and S1 binding pocket Asp (Asp177) highlighted by a red star, a red downturned triangle, and a red upturned triangle, respectively.	FIG
+195	198	Asp	residue_name	The secondary structure of PmC11 from the crystal structure is mapped onto its sequence with the position of the PmC11 catalytic dyad, autocatalytic cleavage site (Lys147), and S1 binding pocket Asp (Asp177) highlighted by a red star, a red downturned triangle, and a red upturned triangle, respectively.	FIG
+200	206	Asp177	residue_name_number	The secondary structure of PmC11 from the crystal structure is mapped onto its sequence with the position of the PmC11 catalytic dyad, autocatalytic cleavage site (Lys147), and S1 binding pocket Asp (Asp177) highlighted by a red star, a red downturned triangle, and a red upturned triangle, respectively.	FIG
+11	16	loops	structure_element	Connecting loops are colored gray, the main β-sheet is in orange, with other strands in olive, α-helices are in blue, and the nonapeptide linker of clostripain that is excised upon autocleavage is underlined in red.	FIG
+44	51	β-sheet	structure_element	Connecting loops are colored gray, the main β-sheet is in orange, with other strands in olive, α-helices are in blue, and the nonapeptide linker of clostripain that is excised upon autocleavage is underlined in red.	FIG
+95	104	α-helices	structure_element	Connecting loops are colored gray, the main β-sheet is in orange, with other strands in olive, α-helices are in blue, and the nonapeptide linker of clostripain that is excised upon autocleavage is underlined in red.	FIG
+126	144	nonapeptide linker	structure_element	Connecting loops are colored gray, the main β-sheet is in orange, with other strands in olive, α-helices are in blue, and the nonapeptide linker of clostripain that is excised upon autocleavage is underlined in red.	FIG
+148	159	clostripain	protein	Connecting loops are colored gray, the main β-sheet is in orange, with other strands in olive, α-helices are in blue, and the nonapeptide linker of clostripain that is excised upon autocleavage is underlined in red.	FIG
+181	193	autocleavage	ptm	Connecting loops are colored gray, the main β-sheet is in orange, with other strands in olive, α-helices are in blue, and the nonapeptide linker of clostripain that is excised upon autocleavage is underlined in red.	FIG
+21	35	catalytic site	site	Sequences around the catalytic site of clostripain and PmC11 align well.	FIG
+39	50	clostripain	protein	Sequences around the catalytic site of clostripain and PmC11 align well.	FIG
+55	60	PmC11	protein	Sequences around the catalytic site of clostripain and PmC11 align well.	FIG
+23	28	PmC11	protein	B, topology diagram of PmC11 colored as in A except that additional (non-core) β-strands are in yellow.	FIG
+79	88	β-strands	structure_element	B, topology diagram of PmC11 colored as in A except that additional (non-core) β-strands are in yellow.	FIG
+44	51	β-sheet	structure_element	Helices found on either side of the central β-sheet are shown above and below the sheet, respectively.	FIG
+82	87	sheet	structure_element	Helices found on either side of the central β-sheet are shown above and below the sheet, respectively.	FIG
+20	34	catalytic dyad	site	The position of the catalytic dyad (H, C) and the processing site (Lys147) are highlighted.	FIG
+36	37	H	residue_name	The position of the catalytic dyad (H, C) and the processing site (Lys147) are highlighted.	FIG
+39	40	C	residue_name	The position of the catalytic dyad (H, C) and the processing site (Lys147) are highlighted.	FIG
+50	65	processing site	site	The position of the catalytic dyad (H, C) and the processing site (Lys147) are highlighted.	FIG
+67	73	Lys147	residue_name_number	The position of the catalytic dyad (H, C) and the processing site (Lys147) are highlighted.	FIG
+19	28	β-strands	structure_element	Helices (1–14) and β-strands (1–9 and A-F) are numbered from the N terminus.	FIG
+4	21	core caspase-fold	structure_element	The core caspase-fold is highlighted in a box.	FIG
+25	30	PmC11	protein	C, tertiary structure of PmC11.	FIG
+33	38	PmC11	protein	The N and C termini (N and C) of PmC11 along with the central β-sheet (1–9), helix α5, and helices α8, α11, and α13 from the C-terminal domain, are all labeled.	FIG
+62	69	β-sheet	structure_element	The N and C termini (N and C) of PmC11 along with the central β-sheet (1–9), helix α5, and helices α8, α11, and α13 from the C-terminal domain, are all labeled.	FIG
+77	82	helix	structure_element	The N and C termini (N and C) of PmC11 along with the central β-sheet (1–9), helix α5, and helices α8, α11, and α13 from the C-terminal domain, are all labeled.	FIG
+83	85	α5	structure_element	The N and C termini (N and C) of PmC11 along with the central β-sheet (1–9), helix α5, and helices α8, α11, and α13 from the C-terminal domain, are all labeled.	FIG
+91	98	helices	structure_element	The N and C termini (N and C) of PmC11 along with the central β-sheet (1–9), helix α5, and helices α8, α11, and α13 from the C-terminal domain, are all labeled.	FIG
+99	101	α8	structure_element	The N and C termini (N and C) of PmC11 along with the central β-sheet (1–9), helix α5, and helices α8, α11, and α13 from the C-terminal domain, are all labeled.	FIG
+103	106	α11	structure_element	The N and C termini (N and C) of PmC11 along with the central β-sheet (1–9), helix α5, and helices α8, α11, and α13 from the C-terminal domain, are all labeled.	FIG
+112	115	α13	structure_element	The N and C termini (N and C) of PmC11 along with the central β-sheet (1–9), helix α5, and helices α8, α11, and α13 from the C-terminal domain, are all labeled.	FIG
+125	142	C-terminal domain	structure_element	The N and C termini (N and C) of PmC11 along with the central β-sheet (1–9), helix α5, and helices α8, α11, and α13 from the C-terminal domain, are all labeled.	FIG
+33	40	β-sheet	structure_element	Loops are colored gray, the main β-sheet is in orange, with other β-strands in yellow, and α-helices are in blue.	FIG
+66	75	β-strands	structure_element	Loops are colored gray, the main β-sheet is in orange, with other β-strands in yellow, and α-helices are in blue.	FIG
+91	100	α-helices	structure_element	Loops are colored gray, the main β-sheet is in orange, with other β-strands in yellow, and α-helices are in blue.	FIG
+4	7	CTD	structure_element	The CTD of PmC11 is composed of a tight helical bundle formed from helices α8–α14 and includes strands βC and βF, and β-hairpin βD–βE. The CTD sits entirely on one side of the enzyme interacting only with α3, α5, β9, and the loops surrounding β8.	RESULTS
+11	16	PmC11	protein	The CTD of PmC11 is composed of a tight helical bundle formed from helices α8–α14 and includes strands βC and βF, and β-hairpin βD–βE. The CTD sits entirely on one side of the enzyme interacting only with α3, α5, β9, and the loops surrounding β8.	RESULTS
+34	54	tight helical bundle	structure_element	The CTD of PmC11 is composed of a tight helical bundle formed from helices α8–α14 and includes strands βC and βF, and β-hairpin βD–βE. The CTD sits entirely on one side of the enzyme interacting only with α3, α5, β9, and the loops surrounding β8.	RESULTS
+67	74	helices	structure_element	The CTD of PmC11 is composed of a tight helical bundle formed from helices α8–α14 and includes strands βC and βF, and β-hairpin βD–βE. The CTD sits entirely on one side of the enzyme interacting only with α3, α5, β9, and the loops surrounding β8.	RESULTS
+75	81	α8–α14	structure_element	The CTD of PmC11 is composed of a tight helical bundle formed from helices α8–α14 and includes strands βC and βF, and β-hairpin βD–βE. The CTD sits entirely on one side of the enzyme interacting only with α3, α5, β9, and the loops surrounding β8.	RESULTS
+95	102	strands	structure_element	The CTD of PmC11 is composed of a tight helical bundle formed from helices α8–α14 and includes strands βC and βF, and β-hairpin βD–βE. The CTD sits entirely on one side of the enzyme interacting only with α3, α5, β9, and the loops surrounding β8.	RESULTS
+103	105	βC	structure_element	The CTD of PmC11 is composed of a tight helical bundle formed from helices α8–α14 and includes strands βC and βF, and β-hairpin βD–βE. The CTD sits entirely on one side of the enzyme interacting only with α3, α5, β9, and the loops surrounding β8.	RESULTS
+110	112	βF	structure_element	The CTD of PmC11 is composed of a tight helical bundle formed from helices α8–α14 and includes strands βC and βF, and β-hairpin βD–βE. The CTD sits entirely on one side of the enzyme interacting only with α3, α5, β9, and the loops surrounding β8.	RESULTS
+118	127	β-hairpin	structure_element	The CTD of PmC11 is composed of a tight helical bundle formed from helices α8–α14 and includes strands βC and βF, and β-hairpin βD–βE. The CTD sits entirely on one side of the enzyme interacting only with α3, α5, β9, and the loops surrounding β8.	RESULTS
+128	133	βD–βE	structure_element	The CTD of PmC11 is composed of a tight helical bundle formed from helices α8–α14 and includes strands βC and βF, and β-hairpin βD–βE. The CTD sits entirely on one side of the enzyme interacting only with α3, α5, β9, and the loops surrounding β8.	RESULTS
+139	142	CTD	structure_element	The CTD of PmC11 is composed of a tight helical bundle formed from helices α8–α14 and includes strands βC and βF, and β-hairpin βD–βE. The CTD sits entirely on one side of the enzyme interacting only with α3, α5, β9, and the loops surrounding β8.	RESULTS
+205	207	α3	structure_element	The CTD of PmC11 is composed of a tight helical bundle formed from helices α8–α14 and includes strands βC and βF, and β-hairpin βD–βE. The CTD sits entirely on one side of the enzyme interacting only with α3, α5, β9, and the loops surrounding β8.	RESULTS
+209	211	α5	structure_element	The CTD of PmC11 is composed of a tight helical bundle formed from helices α8–α14 and includes strands βC and βF, and β-hairpin βD–βE. The CTD sits entirely on one side of the enzyme interacting only with α3, α5, β9, and the loops surrounding β8.	RESULTS
+213	215	β9	structure_element	The CTD of PmC11 is composed of a tight helical bundle formed from helices α8–α14 and includes strands βC and βF, and β-hairpin βD–βE. The CTD sits entirely on one side of the enzyme interacting only with α3, α5, β9, and the loops surrounding β8.	RESULTS
+225	230	loops	structure_element	The CTD of PmC11 is composed of a tight helical bundle formed from helices α8–α14 and includes strands βC and βF, and β-hairpin βD–βE. The CTD sits entirely on one side of the enzyme interacting only with α3, α5, β9, and the loops surrounding β8.	RESULTS
+243	245	β8	structure_element	The CTD of PmC11 is composed of a tight helical bundle formed from helices α8–α14 and includes strands βC and βF, and β-hairpin βD–βE. The CTD sits entirely on one side of the enzyme interacting only with α3, α5, β9, and the loops surrounding β8.	RESULTS
+49	51	α5	structure_element	Of the interacting secondary structure elements, α5 is perhaps the most interesting.	RESULTS
+0	10	This helix	structure_element	This helix makes a total of eight hydrogen bonds with the CTD, including one salt bridge (Arg191-Asp255) and is surrounded by the CTD on one side and the main core of the enzyme on the other, acting like a linchpin holding both components together (Fig. 1C).	RESULTS
+58	61	CTD	structure_element	This helix makes a total of eight hydrogen bonds with the CTD, including one salt bridge (Arg191-Asp255) and is surrounded by the CTD on one side and the main core of the enzyme on the other, acting like a linchpin holding both components together (Fig. 1C).	RESULTS
+90	96	Arg191	residue_name_number	This helix makes a total of eight hydrogen bonds with the CTD, including one salt bridge (Arg191-Asp255) and is surrounded by the CTD on one side and the main core of the enzyme on the other, acting like a linchpin holding both components together (Fig. 1C).	RESULTS
+97	103	Asp255	residue_name_number	This helix makes a total of eight hydrogen bonds with the CTD, including one salt bridge (Arg191-Asp255) and is surrounded by the CTD on one side and the main core of the enzyme on the other, acting like a linchpin holding both components together (Fig. 1C).	RESULTS
+130	133	CTD	structure_element	This helix makes a total of eight hydrogen bonds with the CTD, including one salt bridge (Arg191-Asp255) and is surrounded by the CTD on one side and the main core of the enzyme on the other, acting like a linchpin holding both components together (Fig. 1C).	RESULTS
+154	163	main core	structure_element	This helix makes a total of eight hydrogen bonds with the CTD, including one salt bridge (Arg191-Asp255) and is surrounded by the CTD on one side and the main core of the enzyme on the other, acting like a linchpin holding both components together (Fig. 1C).	RESULTS
+0	5	PmC11	protein	PmC11 is, as expected, most structurally similar to other members of clan CD with the top hits in a search of known structures being caspase-7, gingipain-K, and legumain (PBD codes 4hq0, 4tkx, and 4aw9, respectively) (Table 2).	RESULTS
+69	76	clan CD	protein_type	PmC11 is, as expected, most structurally similar to other members of clan CD with the top hits in a search of known structures being caspase-7, gingipain-K, and legumain (PBD codes 4hq0, 4tkx, and 4aw9, respectively) (Table 2).	RESULTS
+116	126	structures	evidence	PmC11 is, as expected, most structurally similar to other members of clan CD with the top hits in a search of known structures being caspase-7, gingipain-K, and legumain (PBD codes 4hq0, 4tkx, and 4aw9, respectively) (Table 2).	RESULTS
+133	142	caspase-7	protein	PmC11 is, as expected, most structurally similar to other members of clan CD with the top hits in a search of known structures being caspase-7, gingipain-K, and legumain (PBD codes 4hq0, 4tkx, and 4aw9, respectively) (Table 2).	RESULTS
+144	155	gingipain-K	protein	PmC11 is, as expected, most structurally similar to other members of clan CD with the top hits in a search of known structures being caspase-7, gingipain-K, and legumain (PBD codes 4hq0, 4tkx, and 4aw9, respectively) (Table 2).	RESULTS
+161	169	legumain	protein	PmC11 is, as expected, most structurally similar to other members of clan CD with the top hits in a search of known structures being caspase-7, gingipain-K, and legumain (PBD codes 4hq0, 4tkx, and 4aw9, respectively) (Table 2).	RESULTS
+4	21	C-terminal domain	structure_element	The C-terminal domain is unique to PmC11 within clan CD and structure comparisons for this domain alone does not produce any hits in the PDB (DaliLite, PDBeFold), suggesting a completely novel fold.	RESULTS
+35	40	PmC11	protein	The C-terminal domain is unique to PmC11 within clan CD and structure comparisons for this domain alone does not produce any hits in the PDB (DaliLite, PDBeFold), suggesting a completely novel fold.	RESULTS
+48	55	clan CD	protein_type	The C-terminal domain is unique to PmC11 within clan CD and structure comparisons for this domain alone does not produce any hits in the PDB (DaliLite, PDBeFold), suggesting a completely novel fold.	RESULTS
+60	81	structure comparisons	experimental_method	The C-terminal domain is unique to PmC11 within clan CD and structure comparisons for this domain alone does not produce any hits in the PDB (DaliLite, PDBeFold), suggesting a completely novel fold.	RESULTS
+86	103	this domain alone	structure_element	The C-terminal domain is unique to PmC11 within clan CD and structure comparisons for this domain alone does not produce any hits in the PDB (DaliLite, PDBeFold), suggesting a completely novel fold.	RESULTS
+142	150	DaliLite	experimental_method	The C-terminal domain is unique to PmC11 within clan CD and structure comparisons for this domain alone does not produce any hits in the PDB (DaliLite, PDBeFold), suggesting a completely novel fold.	RESULTS
+152	160	PDBeFold	experimental_method	The C-terminal domain is unique to PmC11 within clan CD and structure comparisons for this domain alone does not produce any hits in the PDB (DaliLite, PDBeFold), suggesting a completely novel fold.	RESULTS
+59	66	clan CD	protein_type	As the archetypal and arguably most well studied member of clan CD, the caspases were used as the basis to investigate the structure/function relationships in PmC11, with caspase-7 as the representative member.	RESULTS
+72	80	caspases	protein_type	As the archetypal and arguably most well studied member of clan CD, the caspases were used as the basis to investigate the structure/function relationships in PmC11, with caspase-7 as the representative member.	RESULTS
+159	164	PmC11	protein	As the archetypal and arguably most well studied member of clan CD, the caspases were used as the basis to investigate the structure/function relationships in PmC11, with caspase-7 as the representative member.	RESULTS
+171	180	caspase-7	protein	As the archetypal and arguably most well studied member of clan CD, the caspases were used as the basis to investigate the structure/function relationships in PmC11, with caspase-7 as the representative member.	RESULTS
+19	28	β-strands	structure_element	Six of the central β-strands in PmC11 (β1–β2 and β5–β8) share the same topology as the six-stranded β-sheet found in caspases, with strands β3, β4, and β9 located on the outside of this core structure (Fig. 1B, box).	RESULTS
+32	37	PmC11	protein	Six of the central β-strands in PmC11 (β1–β2 and β5–β8) share the same topology as the six-stranded β-sheet found in caspases, with strands β3, β4, and β9 located on the outside of this core structure (Fig. 1B, box).	RESULTS
+39	44	β1–β2	structure_element	Six of the central β-strands in PmC11 (β1–β2 and β5–β8) share the same topology as the six-stranded β-sheet found in caspases, with strands β3, β4, and β9 located on the outside of this core structure (Fig. 1B, box).	RESULTS
+49	54	β5–β8	structure_element	Six of the central β-strands in PmC11 (β1–β2 and β5–β8) share the same topology as the six-stranded β-sheet found in caspases, with strands β3, β4, and β9 located on the outside of this core structure (Fig. 1B, box).	RESULTS
+87	107	six-stranded β-sheet	structure_element	Six of the central β-strands in PmC11 (β1–β2 and β5–β8) share the same topology as the six-stranded β-sheet found in caspases, with strands β3, β4, and β9 located on the outside of this core structure (Fig. 1B, box).	RESULTS
+117	125	caspases	protein_type	Six of the central β-strands in PmC11 (β1–β2 and β5–β8) share the same topology as the six-stranded β-sheet found in caspases, with strands β3, β4, and β9 located on the outside of this core structure (Fig. 1B, box).	RESULTS
+132	139	strands	structure_element	Six of the central β-strands in PmC11 (β1–β2 and β5–β8) share the same topology as the six-stranded β-sheet found in caspases, with strands β3, β4, and β9 located on the outside of this core structure (Fig. 1B, box).	RESULTS
+140	142	β3	structure_element	Six of the central β-strands in PmC11 (β1–β2 and β5–β8) share the same topology as the six-stranded β-sheet found in caspases, with strands β3, β4, and β9 located on the outside of this core structure (Fig. 1B, box).	RESULTS
+144	146	β4	structure_element	Six of the central β-strands in PmC11 (β1–β2 and β5–β8) share the same topology as the six-stranded β-sheet found in caspases, with strands β3, β4, and β9 located on the outside of this core structure (Fig. 1B, box).	RESULTS
+152	154	β9	structure_element	Six of the central β-strands in PmC11 (β1–β2 and β5–β8) share the same topology as the six-stranded β-sheet found in caspases, with strands β3, β4, and β9 located on the outside of this core structure (Fig. 1B, box).	RESULTS
+186	200	core structure	structure_element	Six of the central β-strands in PmC11 (β1–β2 and β5–β8) share the same topology as the six-stranded β-sheet found in caspases, with strands β3, β4, and β9 located on the outside of this core structure (Fig. 1B, box).	RESULTS
+0	6	His133	residue_name_number	His133 and Cys179 were found at locations structurally homologous to the caspase catalytic dyad, and other clan CD structures, at the C termini of strands β5 and β6, respectively (Figs. 1, A and B, and 2A).	RESULTS
+11	17	Cys179	residue_name_number	His133 and Cys179 were found at locations structurally homologous to the caspase catalytic dyad, and other clan CD structures, at the C termini of strands β5 and β6, respectively (Figs. 1, A and B, and 2A).	RESULTS
+73	80	caspase	protein_type	His133 and Cys179 were found at locations structurally homologous to the caspase catalytic dyad, and other clan CD structures, at the C termini of strands β5 and β6, respectively (Figs. 1, A and B, and 2A).	RESULTS
+81	95	catalytic dyad	site	His133 and Cys179 were found at locations structurally homologous to the caspase catalytic dyad, and other clan CD structures, at the C termini of strands β5 and β6, respectively (Figs. 1, A and B, and 2A).	RESULTS
+107	114	clan CD	protein_type	His133 and Cys179 were found at locations structurally homologous to the caspase catalytic dyad, and other clan CD structures, at the C termini of strands β5 and β6, respectively (Figs. 1, A and B, and 2A).	RESULTS
+115	125	structures	evidence	His133 and Cys179 were found at locations structurally homologous to the caspase catalytic dyad, and other clan CD structures, at the C termini of strands β5 and β6, respectively (Figs. 1, A and B, and 2A).	RESULTS
+147	154	strands	structure_element	His133 and Cys179 were found at locations structurally homologous to the caspase catalytic dyad, and other clan CD structures, at the C termini of strands β5 and β6, respectively (Figs. 1, A and B, and 2A).	RESULTS
+155	157	β5	structure_element	His133 and Cys179 were found at locations structurally homologous to the caspase catalytic dyad, and other clan CD structures, at the C termini of strands β5 and β6, respectively (Figs. 1, A and B, and 2A).	RESULTS
+162	164	β6	structure_element	His133 and Cys179 were found at locations structurally homologous to the caspase catalytic dyad, and other clan CD structures, at the C termini of strands β5 and β6, respectively (Figs. 1, A and B, and 2A).	RESULTS
+2	29	multiple sequence alignment	experimental_method	A multiple sequence alignment of C11 proteins revealed that these residues are highly conserved (data not shown).	RESULTS
+33	36	C11	protein_type	A multiple sequence alignment of C11 proteins revealed that these residues are highly conserved (data not shown).	RESULTS
+79	95	highly conserved	protein_state	A multiple sequence alignment of C11 proteins revealed that these residues are highly conserved (data not shown).	RESULTS
+11	33	PDBeFOLD superposition	experimental_method	Summary of PDBeFOLD superposition of structures found to be most similar to PmC11 in the PBD based on DaliLite	TABLE
+76	81	PmC11	protein	Summary of PDBeFOLD superposition of structures found to be most similar to PmC11 in the PBD based on DaliLite	TABLE
+102	110	DaliLite	experimental_method	Summary of PDBeFOLD superposition of structures found to be most similar to PmC11 in the PBD based on DaliLite	TABLE
+0	43	Biochemical and structural characterization	experimental_method	Biochemical and structural characterization of PmC11.	FIG
+47	52	PmC11	protein	Biochemical and structural characterization of PmC11.	FIG
+54	59	PmC11	protein	 A, ribbon representation of the overall structure of PmC11 illustrating the catalytic site, cleavage site displacement, and potential S1 binding site.	FIG
+77	91	catalytic site	site	 A, ribbon representation of the overall structure of PmC11 illustrating the catalytic site, cleavage site displacement, and potential S1 binding site.	FIG
+135	150	S1 binding site	site	 A, ribbon representation of the overall structure of PmC11 illustrating the catalytic site, cleavage site displacement, and potential S1 binding site.	FIG
+12	21	structure	evidence	The overall structure of PmC11 is shown in gray, looking down into the catalytic site with the catalytic dyad in red.	FIG
+25	30	PmC11	protein	The overall structure of PmC11 is shown in gray, looking down into the catalytic site with the catalytic dyad in red.	FIG
+71	85	catalytic site	site	The overall structure of PmC11 is shown in gray, looking down into the catalytic site with the catalytic dyad in red.	FIG
+95	109	catalytic dyad	site	The overall structure of PmC11 is shown in gray, looking down into the catalytic site with the catalytic dyad in red.	FIG
+20	43	autolytic cleavage site	site	The two ends of the autolytic cleavage site (Lys147 and Ala148, green) are displaced by 19.5 Å (thin black line) from one another and residues in the potential substrate binding pocket are highlighted in blue.	FIG
+45	51	Lys147	residue_name_number	The two ends of the autolytic cleavage site (Lys147 and Ala148, green) are displaced by 19.5 Å (thin black line) from one another and residues in the potential substrate binding pocket are highlighted in blue.	FIG
+45	51	Lys147	residue_name_number	The two ends of the autolytic cleavage site (Lys147 and Ala148, green) are displaced by 19.5 Å (thin black line) from one another and residues in the potential substrate binding pocket are highlighted in blue.	FIG
+56	62	Ala148	residue_name_number	The two ends of the autolytic cleavage site (Lys147 and Ala148, green) are displaced by 19.5 Å (thin black line) from one another and residues in the potential substrate binding pocket are highlighted in blue.	FIG
+160	184	substrate binding pocket	site	The two ends of the autolytic cleavage site (Lys147 and Ala148, green) are displaced by 19.5 Å (thin black line) from one another and residues in the potential substrate binding pocket are highlighted in blue.	FIG
+3	32	size exclusion chromatography	experimental_method	B, size exclusion chromatography of PmC11.	FIG
+36	41	PmC11	protein	B, size exclusion chromatography of PmC11.	FIG
+20	27	monomer	oligomeric_state	PmC11 migrates as a monomer with a molecular mass around 41 kDa calculated from protein standards of known molecular weights.	FIG
+63	71	SDS-PAGE	experimental_method	Elution fractions across the major peak (1–6) were analyzed by SDS-PAGE on a 4–12% gel in MES buffer.	FIG
+7	13	active	protein_state	C, the active form of PmC11 and two mutants, PmC11C179A (C) and PmC11K147A (K), were examined by SDS-PAGE (lane 1) and Western blot analysis using an anti-His antibody (lane 2) show that PmC11 autoprocesses, whereas mutants, PmC11C179A and PmC11K147A, do not show autoprocessing in vitro.	FIG
+22	27	PmC11	protein	C, the active form of PmC11 and two mutants, PmC11C179A (C) and PmC11K147A (K), were examined by SDS-PAGE (lane 1) and Western blot analysis using an anti-His antibody (lane 2) show that PmC11 autoprocesses, whereas mutants, PmC11C179A and PmC11K147A, do not show autoprocessing in vitro.	FIG
+45	55	PmC11C179A	mutant	C, the active form of PmC11 and two mutants, PmC11C179A (C) and PmC11K147A (K), were examined by SDS-PAGE (lane 1) and Western blot analysis using an anti-His antibody (lane 2) show that PmC11 autoprocesses, whereas mutants, PmC11C179A and PmC11K147A, do not show autoprocessing in vitro.	FIG
+64	74	PmC11K147A	mutant	C, the active form of PmC11 and two mutants, PmC11C179A (C) and PmC11K147A (K), were examined by SDS-PAGE (lane 1) and Western blot analysis using an anti-His antibody (lane 2) show that PmC11 autoprocesses, whereas mutants, PmC11C179A and PmC11K147A, do not show autoprocessing in vitro.	FIG
+97	105	SDS-PAGE	experimental_method	C, the active form of PmC11 and two mutants, PmC11C179A (C) and PmC11K147A (K), were examined by SDS-PAGE (lane 1) and Western blot analysis using an anti-His antibody (lane 2) show that PmC11 autoprocesses, whereas mutants, PmC11C179A and PmC11K147A, do not show autoprocessing in vitro.	FIG
+119	131	Western blot	experimental_method	C, the active form of PmC11 and two mutants, PmC11C179A (C) and PmC11K147A (K), were examined by SDS-PAGE (lane 1) and Western blot analysis using an anti-His antibody (lane 2) show that PmC11 autoprocesses, whereas mutants, PmC11C179A and PmC11K147A, do not show autoprocessing in vitro.	FIG
+187	192	PmC11	protein	C, the active form of PmC11 and two mutants, PmC11C179A (C) and PmC11K147A (K), were examined by SDS-PAGE (lane 1) and Western blot analysis using an anti-His antibody (lane 2) show that PmC11 autoprocesses, whereas mutants, PmC11C179A and PmC11K147A, do not show autoprocessing in vitro.	FIG
+193	206	autoprocesses	ptm	C, the active form of PmC11 and two mutants, PmC11C179A (C) and PmC11K147A (K), were examined by SDS-PAGE (lane 1) and Western blot analysis using an anti-His antibody (lane 2) show that PmC11 autoprocesses, whereas mutants, PmC11C179A and PmC11K147A, do not show autoprocessing in vitro.	FIG
+225	235	PmC11C179A	mutant	C, the active form of PmC11 and two mutants, PmC11C179A (C) and PmC11K147A (K), were examined by SDS-PAGE (lane 1) and Western blot analysis using an anti-His antibody (lane 2) show that PmC11 autoprocesses, whereas mutants, PmC11C179A and PmC11K147A, do not show autoprocessing in vitro.	FIG
+240	250	PmC11K147A	mutant	C, the active form of PmC11 and two mutants, PmC11C179A (C) and PmC11K147A (K), were examined by SDS-PAGE (lane 1) and Western blot analysis using an anti-His antibody (lane 2) show that PmC11 autoprocesses, whereas mutants, PmC11C179A and PmC11K147A, do not show autoprocessing in vitro.	FIG
+264	278	autoprocessing	ptm	C, the active form of PmC11 and two mutants, PmC11C179A (C) and PmC11K147A (K), were examined by SDS-PAGE (lane 1) and Western blot analysis using an anti-His antibody (lane 2) show that PmC11 autoprocesses, whereas mutants, PmC11C179A and PmC11K147A, do not show autoprocessing in vitro.	FIG
+34	39	PmC11	protein	D, cysteine peptidase activity of PmC11.	FIG
+7	11	Vmax	evidence	Km and Vmax of PmC11 and K147A mutant were determined by monitoring change in the fluorescence corresponding to AMC release from Bz-R-AMC.	FIG
+15	20	PmC11	protein	Km and Vmax of PmC11 and K147A mutant were determined by monitoring change in the fluorescence corresponding to AMC release from Bz-R-AMC.	FIG
+25	30	K147A	mutant	Km and Vmax of PmC11 and K147A mutant were determined by monitoring change in the fluorescence corresponding to AMC release from Bz-R-AMC.	FIG
+129	137	Bz-R-AMC	chemical	Km and Vmax of PmC11 and K147A mutant were determined by monitoring change in the fluorescence corresponding to AMC release from Bz-R-AMC.	FIG
+3	28	intermolecular processing	ptm	E, intermolecular processing of PmC11C179A by PmC11.	FIG
+32	42	PmC11C179A	mutant	E, intermolecular processing of PmC11C179A by PmC11.	FIG
+46	51	PmC11	protein	E, intermolecular processing of PmC11C179A by PmC11.	FIG
+89	94	PmC11	protein	PmC11C179A (20 μg) was incubated overnight at 37 °C with increasing amounts of processed PmC11 and analyzed on a 10% SDS-PAGE gel.	FIG
+117	125	SDS-PAGE	experimental_method	PmC11C179A (20 μg) was incubated overnight at 37 °C with increasing amounts of processed PmC11 and analyzed on a 10% SDS-PAGE gel.	FIG
+9	19	PmC11C179A	mutant	Inactive PmC11C179A was not processed to a major extent by active PmC11 until around a ratio of 1:4 (5 μg of active PmC11).	FIG
+59	65	active	protein_state	Inactive PmC11C179A was not processed to a major extent by active PmC11 until around a ratio of 1:4 (5 μg of active PmC11).	FIG
+66	71	PmC11	protein	Inactive PmC11C179A was not processed to a major extent by active PmC11 until around a ratio of 1:4 (5 μg of active PmC11).	FIG
+109	115	active	protein_state	Inactive PmC11C179A was not processed to a major extent by active PmC11 until around a ratio of 1:4 (5 μg of active PmC11).	FIG
+116	121	PmC11	protein	Inactive PmC11C179A was not processed to a major extent by active PmC11 until around a ratio of 1:4 (5 μg of active PmC11).	FIG
+26	32	active	protein_state	A single lane of 20 μg of active PmC11 (labeled 20) is shown for comparison.	FIG
+33	38	PmC11	protein	A single lane of 20 μg of active PmC11 (labeled 20) is shown for comparison.	FIG
+3	11	activity	evidence	F, activity of PmC11 against basic substrates.	FIG
+15	20	PmC11	protein	F, activity of PmC11 against basic substrates.	FIG
+38	43	PmC11	protein	G, electrostatic surface potential of PmC11 shown in a similar orientation, where blue and red denote positively and negatively charged surface potential, respectively, contoured at ±5 kT/e.	FIG
+20	34	catalytic dyad	site	The position of the catalytic dyad, one potential key substrate binding residue Asp177, and the ends of the cleavage site Lys147 and Ala148 are indicated.	FIG
+50	79	key substrate binding residue	site	The position of the catalytic dyad, one potential key substrate binding residue Asp177, and the ends of the cleavage site Lys147 and Ala148 are indicated.	FIG
+80	86	Asp177	residue_name_number	The position of the catalytic dyad, one potential key substrate binding residue Asp177, and the ends of the cleavage site Lys147 and Ala148 are indicated.	FIG
+108	121	cleavage site	site	The position of the catalytic dyad, one potential key substrate binding residue Asp177, and the ends of the cleavage site Lys147 and Ala148 are indicated.	FIG
+122	128	Lys147	residue_name_number	The position of the catalytic dyad, one potential key substrate binding residue Asp177, and the ends of the cleavage site Lys147 and Ala148 are indicated.	FIG
+133	139	Ala148	residue_name_number	The position of the catalytic dyad, one potential key substrate binding residue Asp177, and the ends of the cleavage site Lys147 and Ala148 are indicated.	FIG
+12	21	α-helices	structure_element	Five of the α-helices surrounding the β-sheet of PmC11 (α1, α2, α4, α6, and α7) are found in similar positions to the five structurally conserved helices in caspases and other members of clan CD, apart from family C80.	RESULTS
+38	45	β-sheet	structure_element	Five of the α-helices surrounding the β-sheet of PmC11 (α1, α2, α4, α6, and α7) are found in similar positions to the five structurally conserved helices in caspases and other members of clan CD, apart from family C80.	RESULTS
+49	54	PmC11	protein	Five of the α-helices surrounding the β-sheet of PmC11 (α1, α2, α4, α6, and α7) are found in similar positions to the five structurally conserved helices in caspases and other members of clan CD, apart from family C80.	RESULTS
+56	58	α1	structure_element	Five of the α-helices surrounding the β-sheet of PmC11 (α1, α2, α4, α6, and α7) are found in similar positions to the five structurally conserved helices in caspases and other members of clan CD, apart from family C80.	RESULTS
+60	62	α2	structure_element	Five of the α-helices surrounding the β-sheet of PmC11 (α1, α2, α4, α6, and α7) are found in similar positions to the five structurally conserved helices in caspases and other members of clan CD, apart from family C80.	RESULTS
+64	66	α4	structure_element	Five of the α-helices surrounding the β-sheet of PmC11 (α1, α2, α4, α6, and α7) are found in similar positions to the five structurally conserved helices in caspases and other members of clan CD, apart from family C80.	RESULTS
+68	70	α6	structure_element	Five of the α-helices surrounding the β-sheet of PmC11 (α1, α2, α4, α6, and α7) are found in similar positions to the five structurally conserved helices in caspases and other members of clan CD, apart from family C80.	RESULTS
+76	78	α7	structure_element	Five of the α-helices surrounding the β-sheet of PmC11 (α1, α2, α4, α6, and α7) are found in similar positions to the five structurally conserved helices in caspases and other members of clan CD, apart from family C80.	RESULTS
+123	145	structurally conserved	protein_state	Five of the α-helices surrounding the β-sheet of PmC11 (α1, α2, α4, α6, and α7) are found in similar positions to the five structurally conserved helices in caspases and other members of clan CD, apart from family C80.	RESULTS
+146	153	helices	structure_element	Five of the α-helices surrounding the β-sheet of PmC11 (α1, α2, α4, α6, and α7) are found in similar positions to the five structurally conserved helices in caspases and other members of clan CD, apart from family C80.	RESULTS
+157	165	caspases	protein_type	Five of the α-helices surrounding the β-sheet of PmC11 (α1, α2, α4, α6, and α7) are found in similar positions to the five structurally conserved helices in caspases and other members of clan CD, apart from family C80.	RESULTS
+187	194	clan CD	protein_type	Five of the α-helices surrounding the β-sheet of PmC11 (α1, α2, α4, α6, and α7) are found in similar positions to the five structurally conserved helices in caspases and other members of clan CD, apart from family C80.	RESULTS
+214	217	C80	protein_type	Five of the α-helices surrounding the β-sheet of PmC11 (α1, α2, α4, α6, and α7) are found in similar positions to the five structurally conserved helices in caspases and other members of clan CD, apart from family C80.	RESULTS
+20	36	extended β-sheet	structure_element	Other than its more extended β-sheet, PmC11 differs most significantly from other clan CD members at its C terminus, where the CTD contains a further seven α-helices and four β-strands after β8.	RESULTS
+38	43	PmC11	protein	Other than its more extended β-sheet, PmC11 differs most significantly from other clan CD members at its C terminus, where the CTD contains a further seven α-helices and four β-strands after β8.	RESULTS
+82	89	clan CD	protein_type	Other than its more extended β-sheet, PmC11 differs most significantly from other clan CD members at its C terminus, where the CTD contains a further seven α-helices and four β-strands after β8.	RESULTS
+127	130	CTD	structure_element	Other than its more extended β-sheet, PmC11 differs most significantly from other clan CD members at its C terminus, where the CTD contains a further seven α-helices and four β-strands after β8.	RESULTS
+156	165	α-helices	structure_element	Other than its more extended β-sheet, PmC11 differs most significantly from other clan CD members at its C terminus, where the CTD contains a further seven α-helices and four β-strands after β8.	RESULTS
+175	184	β-strands	structure_element	Other than its more extended β-sheet, PmC11 differs most significantly from other clan CD members at its C terminus, where the CTD contains a further seven α-helices and four β-strands after β8.	RESULTS
+191	193	β8	structure_element	Other than its more extended β-sheet, PmC11 differs most significantly from other clan CD members at its C terminus, where the CTD contains a further seven α-helices and four β-strands after β8.	RESULTS
+0	14	Autoprocessing	ptm	Autoprocessing of PmC11	RESULTS
+18	23	PmC11	protein	Autoprocessing of PmC11	RESULTS
+0	12	Purification	experimental_method	Purification of recombinant PmC11 (molecular mass = 42.6 kDa) revealed partial processing into two cleavage products of 26.4 and 16.2 kDa, related to the observed cleavage at Lys147 in the crystal structure (Fig. 2A).	RESULTS
+28	33	PmC11	protein	Purification of recombinant PmC11 (molecular mass = 42.6 kDa) revealed partial processing into two cleavage products of 26.4 and 16.2 kDa, related to the observed cleavage at Lys147 in the crystal structure (Fig. 2A).	RESULTS
+163	171	cleavage	ptm	Purification of recombinant PmC11 (molecular mass = 42.6 kDa) revealed partial processing into two cleavage products of 26.4 and 16.2 kDa, related to the observed cleavage at Lys147 in the crystal structure (Fig. 2A).	RESULTS
+175	181	Lys147	residue_name_number	Purification of recombinant PmC11 (molecular mass = 42.6 kDa) revealed partial processing into two cleavage products of 26.4 and 16.2 kDa, related to the observed cleavage at Lys147 in the crystal structure (Fig. 2A).	RESULTS
+189	206	crystal structure	evidence	Purification of recombinant PmC11 (molecular mass = 42.6 kDa) revealed partial processing into two cleavage products of 26.4 and 16.2 kDa, related to the observed cleavage at Lys147 in the crystal structure (Fig. 2A).	RESULTS
+0	10	Incubation	experimental_method	Incubation of PmC11 at 37 °C for 16 h, resulted in a fully processed enzyme that remained as an intact monomer when applied to a size-exclusion column (Fig. 2B).	RESULTS
+14	19	PmC11	protein	Incubation of PmC11 at 37 °C for 16 h, resulted in a fully processed enzyme that remained as an intact monomer when applied to a size-exclusion column (Fig. 2B).	RESULTS
+53	68	fully processed	protein_state	Incubation of PmC11 at 37 °C for 16 h, resulted in a fully processed enzyme that remained as an intact monomer when applied to a size-exclusion column (Fig. 2B).	RESULTS
+96	102	intact	protein_state	Incubation of PmC11 at 37 °C for 16 h, resulted in a fully processed enzyme that remained as an intact monomer when applied to a size-exclusion column (Fig. 2B).	RESULTS
+103	110	monomer	oligomeric_state	Incubation of PmC11 at 37 °C for 16 h, resulted in a fully processed enzyme that remained as an intact monomer when applied to a size-exclusion column (Fig. 2B).	RESULTS
+11	24	cleavage site	site	The single cleavage site of PmC11 at Lys147 is found immediately after α3, in loop L5 within the central β-sheet (Figs. 1, A and B, and 2A).	RESULTS
+28	33	PmC11	protein	The single cleavage site of PmC11 at Lys147 is found immediately after α3, in loop L5 within the central β-sheet (Figs. 1, A and B, and 2A).	RESULTS
+37	43	Lys147	residue_name_number	The single cleavage site of PmC11 at Lys147 is found immediately after α3, in loop L5 within the central β-sheet (Figs. 1, A and B, and 2A).	RESULTS
+71	73	α3	structure_element	The single cleavage site of PmC11 at Lys147 is found immediately after α3, in loop L5 within the central β-sheet (Figs. 1, A and B, and 2A).	RESULTS
+78	82	loop	structure_element	The single cleavage site of PmC11 at Lys147 is found immediately after α3, in loop L5 within the central β-sheet (Figs. 1, A and B, and 2A).	RESULTS
+83	85	L5	structure_element	The single cleavage site of PmC11 at Lys147 is found immediately after α3, in loop L5 within the central β-sheet (Figs. 1, A and B, and 2A).	RESULTS
+105	112	β-sheet	structure_element	The single cleavage site of PmC11 at Lys147 is found immediately after α3, in loop L5 within the central β-sheet (Figs. 1, A and B, and 2A).	RESULTS
+20	33	cleavage site	site	The two ends of the cleavage site are remarkably well ordered in the crystal structure and displaced from one another by 19.5 Å (Fig. 2A).	RESULTS
+69	86	crystal structure	evidence	The two ends of the cleavage site are remarkably well ordered in the crystal structure and displaced from one another by 19.5 Å (Fig. 2A).	RESULTS
+37	50	cleavage site	site	Moreover, the C-terminal side of the cleavage site resides near the catalytic dyad with Ala148 being 4.5 and 5.7 Å from His133 and Cys179, respectively.	RESULTS
+68	82	catalytic dyad	site	Moreover, the C-terminal side of the cleavage site resides near the catalytic dyad with Ala148 being 4.5 and 5.7 Å from His133 and Cys179, respectively.	RESULTS
+88	94	Ala148	residue_name_number	Moreover, the C-terminal side of the cleavage site resides near the catalytic dyad with Ala148 being 4.5 and 5.7 Å from His133 and Cys179, respectively.	RESULTS
+120	126	His133	residue_name_number	Moreover, the C-terminal side of the cleavage site resides near the catalytic dyad with Ala148 being 4.5 and 5.7 Å from His133 and Cys179, respectively.	RESULTS
+131	137	Cys179	residue_name_number	Moreover, the C-terminal side of the cleavage site resides near the catalytic dyad with Ala148 being 4.5 and 5.7 Å from His133 and Cys179, respectively.	RESULTS
+43	48	helix	structure_element	Consequently, it appears feasible that the helix attached to Lys147 (α3) could be responsible for steric autoinhibition of PmC11 when Lys147 is covalently bonded to Ala148.	RESULTS
+61	67	Lys147	residue_name_number	Consequently, it appears feasible that the helix attached to Lys147 (α3) could be responsible for steric autoinhibition of PmC11 when Lys147 is covalently bonded to Ala148.	RESULTS
+69	71	α3	structure_element	Consequently, it appears feasible that the helix attached to Lys147 (α3) could be responsible for steric autoinhibition of PmC11 when Lys147 is covalently bonded to Ala148.	RESULTS
+123	128	PmC11	protein	Consequently, it appears feasible that the helix attached to Lys147 (α3) could be responsible for steric autoinhibition of PmC11 when Lys147 is covalently bonded to Ala148.	RESULTS
+134	140	Lys147	residue_name_number	Consequently, it appears feasible that the helix attached to Lys147 (α3) could be responsible for steric autoinhibition of PmC11 when Lys147 is covalently bonded to Ala148.	RESULTS
+165	171	Ala148	residue_name_number	Consequently, it appears feasible that the helix attached to Lys147 (α3) could be responsible for steric autoinhibition of PmC11 when Lys147 is covalently bonded to Ala148.	RESULTS
+10	18	cleavage	ptm	Thus, the cleavage would be required for full activation of PmC11.	RESULTS
+41	56	full activation	protein_state	Thus, the cleavage would be required for full activation of PmC11.	RESULTS
+60	65	PmC11	protein	Thus, the cleavage would be required for full activation of PmC11.	RESULTS
+78	88	PmC11C179A	mutant	To investigate this possibility, two mutant forms of the enzyme were created: PmC11C179A (a catalytically inactive mutant) and PmC11K147A (a cleavage-site mutant).	RESULTS
+92	121	catalytically inactive mutant	protein_state	To investigate this possibility, two mutant forms of the enzyme were created: PmC11C179A (a catalytically inactive mutant) and PmC11K147A (a cleavage-site mutant).	RESULTS
+127	137	PmC11K147A	mutant	To investigate this possibility, two mutant forms of the enzyme were created: PmC11C179A (a catalytically inactive mutant) and PmC11K147A (a cleavage-site mutant).	RESULTS
+141	161	cleavage-site mutant	protein_state	To investigate this possibility, two mutant forms of the enzyme were created: PmC11C179A (a catalytically inactive mutant) and PmC11K147A (a cleavage-site mutant).	RESULTS
+8	16	SDS-PAGE	experimental_method	Initial SDS-PAGE and Western blot analysis of both mutants revealed no discernible processing occurred as compared with active PmC11 (Fig. 2C).	RESULTS
+21	33	Western blot	experimental_method	Initial SDS-PAGE and Western blot analysis of both mutants revealed no discernible processing occurred as compared with active PmC11 (Fig. 2C).	RESULTS
+120	126	active	protein_state	Initial SDS-PAGE and Western blot analysis of both mutants revealed no discernible processing occurred as compared with active PmC11 (Fig. 2C).	RESULTS
+127	132	PmC11	protein	Initial SDS-PAGE and Western blot analysis of both mutants revealed no discernible processing occurred as compared with active PmC11 (Fig. 2C).	RESULTS
+4	14	PmC11K147A	mutant	The PmC11K147A mutant enzyme had a markedly different reaction rate (Vmax) compared with WT, where the reaction velocity of PmC11 was 10 times greater than that of PmC11K147A (Fig. 2D).	RESULTS
+15	21	mutant	protein_state	The PmC11K147A mutant enzyme had a markedly different reaction rate (Vmax) compared with WT, where the reaction velocity of PmC11 was 10 times greater than that of PmC11K147A (Fig. 2D).	RESULTS
+54	67	reaction rate	evidence	The PmC11K147A mutant enzyme had a markedly different reaction rate (Vmax) compared with WT, where the reaction velocity of PmC11 was 10 times greater than that of PmC11K147A (Fig. 2D).	RESULTS
+69	73	Vmax	evidence	The PmC11K147A mutant enzyme had a markedly different reaction rate (Vmax) compared with WT, where the reaction velocity of PmC11 was 10 times greater than that of PmC11K147A (Fig. 2D).	RESULTS
+89	91	WT	protein_state	The PmC11K147A mutant enzyme had a markedly different reaction rate (Vmax) compared with WT, where the reaction velocity of PmC11 was 10 times greater than that of PmC11K147A (Fig. 2D).	RESULTS
+103	120	reaction velocity	evidence	The PmC11K147A mutant enzyme had a markedly different reaction rate (Vmax) compared with WT, where the reaction velocity of PmC11 was 10 times greater than that of PmC11K147A (Fig. 2D).	RESULTS
+124	129	PmC11	protein	The PmC11K147A mutant enzyme had a markedly different reaction rate (Vmax) compared with WT, where the reaction velocity of PmC11 was 10 times greater than that of PmC11K147A (Fig. 2D).	RESULTS
+164	174	PmC11K147A	mutant	The PmC11K147A mutant enzyme had a markedly different reaction rate (Vmax) compared with WT, where the reaction velocity of PmC11 was 10 times greater than that of PmC11K147A (Fig. 2D).	RESULTS
+39	44	PmC11	protein	Taken together, these data reveal that PmC11 requires processing at Lys147 for optimum activity.	RESULTS
+68	74	Lys147	residue_name_number	Taken together, these data reveal that PmC11 requires processing at Lys147 for optimum activity.	RESULTS
+88	98	PmC11C179A	mutant	To investigate whether processing is a result of intra- or intermolecular cleavage, the PmC11C179A mutant was incubated with increasing concentrations of processed and activated PmC11.	RESULTS
+99	105	mutant	protein_state	To investigate whether processing is a result of intra- or intermolecular cleavage, the PmC11C179A mutant was incubated with increasing concentrations of processed and activated PmC11.	RESULTS
+110	150	incubated with increasing concentrations	experimental_method	To investigate whether processing is a result of intra- or intermolecular cleavage, the PmC11C179A mutant was incubated with increasing concentrations of processed and activated PmC11.	RESULTS
+154	163	processed	protein_state	To investigate whether processing is a result of intra- or intermolecular cleavage, the PmC11C179A mutant was incubated with increasing concentrations of processed and activated PmC11.	RESULTS
+168	177	activated	protein_state	To investigate whether processing is a result of intra- or intermolecular cleavage, the PmC11C179A mutant was incubated with increasing concentrations of processed and activated PmC11.	RESULTS
+178	183	PmC11	protein	To investigate whether processing is a result of intra- or intermolecular cleavage, the PmC11C179A mutant was incubated with increasing concentrations of processed and activated PmC11.	RESULTS
+62	72	PmC11C179A	mutant	These studies revealed that there was no apparent cleavage of PmC11C179A by the active enzyme at low concentrations of PmC11 and that only limited cleavage was observed when the ratio of active enzyme (PmC11:PmC11C179A) was increased to ∼1:10 and 1:4, with complete cleavage observed at a ratio of 1:1 (Fig. 2E).	RESULTS
+80	86	active	protein_state	These studies revealed that there was no apparent cleavage of PmC11C179A by the active enzyme at low concentrations of PmC11 and that only limited cleavage was observed when the ratio of active enzyme (PmC11:PmC11C179A) was increased to ∼1:10 and 1:4, with complete cleavage observed at a ratio of 1:1 (Fig. 2E).	RESULTS
+94	115	at low concentrations	experimental_method	These studies revealed that there was no apparent cleavage of PmC11C179A by the active enzyme at low concentrations of PmC11 and that only limited cleavage was observed when the ratio of active enzyme (PmC11:PmC11C179A) was increased to ∼1:10 and 1:4, with complete cleavage observed at a ratio of 1:1 (Fig. 2E).	RESULTS
+119	124	PmC11	protein	These studies revealed that there was no apparent cleavage of PmC11C179A by the active enzyme at low concentrations of PmC11 and that only limited cleavage was observed when the ratio of active enzyme (PmC11:PmC11C179A) was increased to ∼1:10 and 1:4, with complete cleavage observed at a ratio of 1:1 (Fig. 2E).	RESULTS
+187	193	active	protein_state	These studies revealed that there was no apparent cleavage of PmC11C179A by the active enzyme at low concentrations of PmC11 and that only limited cleavage was observed when the ratio of active enzyme (PmC11:PmC11C179A) was increased to ∼1:10 and 1:4, with complete cleavage observed at a ratio of 1:1 (Fig. 2E).	RESULTS
+202	207	PmC11	protein	These studies revealed that there was no apparent cleavage of PmC11C179A by the active enzyme at low concentrations of PmC11 and that only limited cleavage was observed when the ratio of active enzyme (PmC11:PmC11C179A) was increased to ∼1:10 and 1:4, with complete cleavage observed at a ratio of 1:1 (Fig. 2E).	RESULTS
+208	218	PmC11C179A	mutant	These studies revealed that there was no apparent cleavage of PmC11C179A by the active enzyme at low concentrations of PmC11 and that only limited cleavage was observed when the ratio of active enzyme (PmC11:PmC11C179A) was increased to ∼1:10 and 1:4, with complete cleavage observed at a ratio of 1:1 (Fig. 2E).	RESULTS
+224	250	increased to ∼1:10 and 1:4	experimental_method	These studies revealed that there was no apparent cleavage of PmC11C179A by the active enzyme at low concentrations of PmC11 and that only limited cleavage was observed when the ratio of active enzyme (PmC11:PmC11C179A) was increased to ∼1:10 and 1:4, with complete cleavage observed at a ratio of 1:1 (Fig. 2E).	RESULTS
+289	301	ratio of 1:1	experimental_method	These studies revealed that there was no apparent cleavage of PmC11C179A by the active enzyme at low concentrations of PmC11 and that only limited cleavage was observed when the ratio of active enzyme (PmC11:PmC11C179A) was increased to ∼1:10 and 1:4, with complete cleavage observed at a ratio of 1:1 (Fig. 2E).	RESULTS
+19	27	cleavage	ptm	This suggests that cleavage of PmC11C179A was most likely an effect of the increasing concentration of PmC11 and intermolecular cleavage.	RESULTS
+31	41	PmC11C179A	mutant	This suggests that cleavage of PmC11C179A was most likely an effect of the increasing concentration of PmC11 and intermolecular cleavage.	RESULTS
+103	108	PmC11	protein	This suggests that cleavage of PmC11C179A was most likely an effect of the increasing concentration of PmC11 and intermolecular cleavage.	RESULTS
+42	50	pro-form	protein_state	Collectively, these data suggest that the pro-form of PmC11 is autoinhibited by a section of L5 blocking access to the active site, prior to intramolecular cleavage at Lys147.	RESULTS
+54	59	PmC11	protein	Collectively, these data suggest that the pro-form of PmC11 is autoinhibited by a section of L5 blocking access to the active site, prior to intramolecular cleavage at Lys147.	RESULTS
+63	76	autoinhibited	protein_state	Collectively, these data suggest that the pro-form of PmC11 is autoinhibited by a section of L5 blocking access to the active site, prior to intramolecular cleavage at Lys147.	RESULTS
+93	95	L5	structure_element	Collectively, these data suggest that the pro-form of PmC11 is autoinhibited by a section of L5 blocking access to the active site, prior to intramolecular cleavage at Lys147.	RESULTS
+119	130	active site	site	Collectively, these data suggest that the pro-form of PmC11 is autoinhibited by a section of L5 blocking access to the active site, prior to intramolecular cleavage at Lys147.	RESULTS
+141	164	intramolecular cleavage	ptm	Collectively, these data suggest that the pro-form of PmC11 is autoinhibited by a section of L5 blocking access to the active site, prior to intramolecular cleavage at Lys147.	RESULTS
+168	174	Lys147	residue_name_number	Collectively, these data suggest that the pro-form of PmC11 is autoinhibited by a section of L5 blocking access to the active site, prior to intramolecular cleavage at Lys147.	RESULTS
+5	13	cleavage	ptm	This cleavage subsequently allows movement of the region containing Lys147 and the active site to open up for substrate access.	RESULTS
+68	74	Lys147	residue_name_number	This cleavage subsequently allows movement of the region containing Lys147 and the active site to open up for substrate access.	RESULTS
+83	94	active site	site	This cleavage subsequently allows movement of the region containing Lys147 and the active site to open up for substrate access.	RESULTS
+98	102	open	protein_state	This cleavage subsequently allows movement of the region containing Lys147 and the active site to open up for substrate access.	RESULTS
+25	30	PmC11	protein	Substrate Specificity of PmC11	RESULTS
+4	26	autocatalytic cleavage	ptm	The autocatalytic cleavage of PmC11 at Lys147 (sequence KLK∧A) demonstrates that the enzyme accepts substrates with Lys in the P1 position.	RESULTS
+30	35	PmC11	protein	The autocatalytic cleavage of PmC11 at Lys147 (sequence KLK∧A) demonstrates that the enzyme accepts substrates with Lys in the P1 position.	RESULTS
+39	45	Lys147	residue_name_number	The autocatalytic cleavage of PmC11 at Lys147 (sequence KLK∧A) demonstrates that the enzyme accepts substrates with Lys in the P1 position.	RESULTS
+116	119	Lys	residue_name	The autocatalytic cleavage of PmC11 at Lys147 (sequence KLK∧A) demonstrates that the enzyme accepts substrates with Lys in the P1 position.	RESULTS
+127	129	P1	residue_number	The autocatalytic cleavage of PmC11 at Lys147 (sequence KLK∧A) demonstrates that the enzyme accepts substrates with Lys in the P1 position.	RESULTS
+13	18	PmC11	protein	As expected, PmC11 showed no activity against substrates with Pro or Asp in P1 but was active toward substrates with a basic residue in P1 such as Bz-R-AMC, Z-GGR-AMC, and BOC-VLK-AMC.	RESULTS
+62	65	Pro	residue_name	As expected, PmC11 showed no activity against substrates with Pro or Asp in P1 but was active toward substrates with a basic residue in P1 such as Bz-R-AMC, Z-GGR-AMC, and BOC-VLK-AMC.	RESULTS
+69	72	Asp	residue_name	As expected, PmC11 showed no activity against substrates with Pro or Asp in P1 but was active toward substrates with a basic residue in P1 such as Bz-R-AMC, Z-GGR-AMC, and BOC-VLK-AMC.	RESULTS
+76	78	P1	residue_number	As expected, PmC11 showed no activity against substrates with Pro or Asp in P1 but was active toward substrates with a basic residue in P1 such as Bz-R-AMC, Z-GGR-AMC, and BOC-VLK-AMC.	RESULTS
+87	93	active	protein_state	As expected, PmC11 showed no activity against substrates with Pro or Asp in P1 but was active toward substrates with a basic residue in P1 such as Bz-R-AMC, Z-GGR-AMC, and BOC-VLK-AMC.	RESULTS
+136	138	P1	residue_number	As expected, PmC11 showed no activity against substrates with Pro or Asp in P1 but was active toward substrates with a basic residue in P1 such as Bz-R-AMC, Z-GGR-AMC, and BOC-VLK-AMC.	RESULTS
+147	155	Bz-R-AMC	chemical	As expected, PmC11 showed no activity against substrates with Pro or Asp in P1 but was active toward substrates with a basic residue in P1 such as Bz-R-AMC, Z-GGR-AMC, and BOC-VLK-AMC.	RESULTS
+157	166	Z-GGR-AMC	chemical	As expected, PmC11 showed no activity against substrates with Pro or Asp in P1 but was active toward substrates with a basic residue in P1 such as Bz-R-AMC, Z-GGR-AMC, and BOC-VLK-AMC.	RESULTS
+172	183	BOC-VLK-AMC	chemical	As expected, PmC11 showed no activity against substrates with Pro or Asp in P1 but was active toward substrates with a basic residue in P1 such as Bz-R-AMC, Z-GGR-AMC, and BOC-VLK-AMC.	RESULTS
+59	62	Arg	residue_name	The rate of cleavage was ∼3-fold greater toward the single Arg substrate Bz-R-AMC than for the other two (Fig. 2F) and, unexpectedly, PmC11 showed no activity toward BOC-K-AMC.	RESULTS
+73	81	Bz-R-AMC	chemical	The rate of cleavage was ∼3-fold greater toward the single Arg substrate Bz-R-AMC than for the other two (Fig. 2F) and, unexpectedly, PmC11 showed no activity toward BOC-K-AMC.	RESULTS
+134	139	PmC11	protein	The rate of cleavage was ∼3-fold greater toward the single Arg substrate Bz-R-AMC than for the other two (Fig. 2F) and, unexpectedly, PmC11 showed no activity toward BOC-K-AMC.	RESULTS
+166	175	BOC-K-AMC	chemical	The rate of cleavage was ∼3-fold greater toward the single Arg substrate Bz-R-AMC than for the other two (Fig. 2F) and, unexpectedly, PmC11 showed no activity toward BOC-K-AMC.	RESULTS
+27	32	PmC11	protein	These results confirm that PmC11 accepts substrates containing Arg or Lys in P1 with a possible preference for Arg.	RESULTS
+63	66	Arg	residue_name	These results confirm that PmC11 accepts substrates containing Arg or Lys in P1 with a possible preference for Arg.	RESULTS
+70	73	Lys	residue_name	These results confirm that PmC11 accepts substrates containing Arg or Lys in P1 with a possible preference for Arg.	RESULTS
+77	79	P1	residue_number	These results confirm that PmC11 accepts substrates containing Arg or Lys in P1 with a possible preference for Arg.	RESULTS
+111	114	Arg	residue_name	These results confirm that PmC11 accepts substrates containing Arg or Lys in P1 with a possible preference for Arg.	RESULTS
+4	18	catalytic dyad	site	The catalytic dyad of PmC11 sits near the bottom of an open pocket on the surface of the enzyme at a conserved location in the clan CD family.	RESULTS
+22	27	PmC11	protein	The catalytic dyad of PmC11 sits near the bottom of an open pocket on the surface of the enzyme at a conserved location in the clan CD family.	RESULTS
+55	59	open	protein_state	The catalytic dyad of PmC11 sits near the bottom of an open pocket on the surface of the enzyme at a conserved location in the clan CD family.	RESULTS
+60	66	pocket	site	The catalytic dyad of PmC11 sits near the bottom of an open pocket on the surface of the enzyme at a conserved location in the clan CD family.	RESULTS
+101	119	conserved location	protein_state	The catalytic dyad of PmC11 sits near the bottom of an open pocket on the surface of the enzyme at a conserved location in the clan CD family.	RESULTS
+132	141	CD family	protein_type	The catalytic dyad of PmC11 sits near the bottom of an open pocket on the surface of the enzyme at a conserved location in the clan CD family.	RESULTS
+4	9	PmC11	protein	The PmC11 structure reveals that the catalytic dyad forms part of a large acidic pocket (Fig. 2G), consistent with a binding site for a basic substrate.	RESULTS
+10	19	structure	evidence	The PmC11 structure reveals that the catalytic dyad forms part of a large acidic pocket (Fig. 2G), consistent with a binding site for a basic substrate.	RESULTS
+37	51	catalytic dyad	site	The PmC11 structure reveals that the catalytic dyad forms part of a large acidic pocket (Fig. 2G), consistent with a binding site for a basic substrate.	RESULTS
+74	87	acidic pocket	site	The PmC11 structure reveals that the catalytic dyad forms part of a large acidic pocket (Fig. 2G), consistent with a binding site for a basic substrate.	RESULTS
+117	129	binding site	site	The PmC11 structure reveals that the catalytic dyad forms part of a large acidic pocket (Fig. 2G), consistent with a binding site for a basic substrate.	RESULTS
+5	11	pocket	site	This pocket is lined with the potential functional side chains of Asn50, Asp177, and Thr204 with Gly134, Asp207, and Met205 also contributing to the pocket (Fig. 2A).	RESULTS
+66	71	Asn50	residue_name_number	This pocket is lined with the potential functional side chains of Asn50, Asp177, and Thr204 with Gly134, Asp207, and Met205 also contributing to the pocket (Fig. 2A).	RESULTS
+73	79	Asp177	residue_name_number	This pocket is lined with the potential functional side chains of Asn50, Asp177, and Thr204 with Gly134, Asp207, and Met205 also contributing to the pocket (Fig. 2A).	RESULTS
+85	91	Thr204	residue_name_number	This pocket is lined with the potential functional side chains of Asn50, Asp177, and Thr204 with Gly134, Asp207, and Met205 also contributing to the pocket (Fig. 2A).	RESULTS
+97	103	Gly134	residue_name_number	This pocket is lined with the potential functional side chains of Asn50, Asp177, and Thr204 with Gly134, Asp207, and Met205 also contributing to the pocket (Fig. 2A).	RESULTS
+105	111	Asp207	residue_name_number	This pocket is lined with the potential functional side chains of Asn50, Asp177, and Thr204 with Gly134, Asp207, and Met205 also contributing to the pocket (Fig. 2A).	RESULTS
+117	123	Met205	residue_name_number	This pocket is lined with the potential functional side chains of Asn50, Asp177, and Thr204 with Gly134, Asp207, and Met205 also contributing to the pocket (Fig. 2A).	RESULTS
+149	155	pocket	site	This pocket is lined with the potential functional side chains of Asn50, Asp177, and Thr204 with Gly134, Asp207, and Met205 also contributing to the pocket (Fig. 2A).	RESULTS
+54	74	structurally similar	protein_state	Interestingly, these residues are in regions that are structurally similar to those involved in the S1 binding pockets of other clan CD members (shown in Ref.).	RESULTS
+100	118	S1 binding pockets	site	Interestingly, these residues are in regions that are structurally similar to those involved in the S1 binding pockets of other clan CD members (shown in Ref.).	RESULTS
+128	143	clan CD members	protein_type	Interestingly, these residues are in regions that are structurally similar to those involved in the S1 binding pockets of other clan CD members (shown in Ref.).	RESULTS
+8	13	PmC11	protein	Because PmC11 recognizes basic substrates, the tetrapeptide inhibitor Z-VRPR-FMK was tested as an enzyme inhibitor and was found to inhibit both the autoprocessing and activity of PmC11 (Fig. 3A).	RESULTS
+70	80	Z-VRPR-FMK	chemical	Because PmC11 recognizes basic substrates, the tetrapeptide inhibitor Z-VRPR-FMK was tested as an enzyme inhibitor and was found to inhibit both the autoprocessing and activity of PmC11 (Fig. 3A).	RESULTS
+132	139	inhibit	protein_state	Because PmC11 recognizes basic substrates, the tetrapeptide inhibitor Z-VRPR-FMK was tested as an enzyme inhibitor and was found to inhibit both the autoprocessing and activity of PmC11 (Fig. 3A).	RESULTS
+149	163	autoprocessing	ptm	Because PmC11 recognizes basic substrates, the tetrapeptide inhibitor Z-VRPR-FMK was tested as an enzyme inhibitor and was found to inhibit both the autoprocessing and activity of PmC11 (Fig. 3A).	RESULTS
+180	185	PmC11	protein	Because PmC11 recognizes basic substrates, the tetrapeptide inhibitor Z-VRPR-FMK was tested as an enzyme inhibitor and was found to inhibit both the autoprocessing and activity of PmC11 (Fig. 3A).	RESULTS
+0	10	Z-VRPR-FMK	chemical	Z-VRPR-FMK was also shown to bind to the enzyme: a size-shift was observed, by SDS-PAGE analysis, in the larger processed product of PmC11 suggesting that the inhibitor bound to the active site (Fig. 3B).	RESULTS
+51	61	size-shift	evidence	Z-VRPR-FMK was also shown to bind to the enzyme: a size-shift was observed, by SDS-PAGE analysis, in the larger processed product of PmC11 suggesting that the inhibitor bound to the active site (Fig. 3B).	RESULTS
+79	87	SDS-PAGE	experimental_method	Z-VRPR-FMK was also shown to bind to the enzyme: a size-shift was observed, by SDS-PAGE analysis, in the larger processed product of PmC11 suggesting that the inhibitor bound to the active site (Fig. 3B).	RESULTS
+133	138	PmC11	protein	Z-VRPR-FMK was also shown to bind to the enzyme: a size-shift was observed, by SDS-PAGE analysis, in the larger processed product of PmC11 suggesting that the inhibitor bound to the active site (Fig. 3B).	RESULTS
+159	174	inhibitor bound	protein_state	Z-VRPR-FMK was also shown to bind to the enzyme: a size-shift was observed, by SDS-PAGE analysis, in the larger processed product of PmC11 suggesting that the inhibitor bound to the active site (Fig. 3B).	RESULTS
+182	193	active site	site	Z-VRPR-FMK was also shown to bind to the enzyme: a size-shift was observed, by SDS-PAGE analysis, in the larger processed product of PmC11 suggesting that the inhibitor bound to the active site (Fig. 3B).	RESULTS
+2	19	structure overlay	experimental_method	A structure overlay of PmC11 with the MALT1-paracacaspase (MALT1-P), in complex with Z-VRPR-FMK, revealed that the PmC11 dyad sits in a very similar position to that of active MALT1-P and that Asn50, Asp177, and Asp207 superimpose well with the principal MALT1-P inhibitor binding residues (Asp365, Asp462, and Glu500, respectively (VRPR-FMK from MALT1-P with the corresponding PmC11 residues from the structural overlay is shown in Fig. 1D), as described in Ref.).	RESULTS
+23	28	PmC11	protein	A structure overlay of PmC11 with the MALT1-paracacaspase (MALT1-P), in complex with Z-VRPR-FMK, revealed that the PmC11 dyad sits in a very similar position to that of active MALT1-P and that Asn50, Asp177, and Asp207 superimpose well with the principal MALT1-P inhibitor binding residues (Asp365, Asp462, and Glu500, respectively (VRPR-FMK from MALT1-P with the corresponding PmC11 residues from the structural overlay is shown in Fig. 1D), as described in Ref.).	RESULTS
+38	57	MALT1-paracacaspase	protein	A structure overlay of PmC11 with the MALT1-paracacaspase (MALT1-P), in complex with Z-VRPR-FMK, revealed that the PmC11 dyad sits in a very similar position to that of active MALT1-P and that Asn50, Asp177, and Asp207 superimpose well with the principal MALT1-P inhibitor binding residues (Asp365, Asp462, and Glu500, respectively (VRPR-FMK from MALT1-P with the corresponding PmC11 residues from the structural overlay is shown in Fig. 1D), as described in Ref.).	RESULTS
+59	66	MALT1-P	protein	A structure overlay of PmC11 with the MALT1-paracacaspase (MALT1-P), in complex with Z-VRPR-FMK, revealed that the PmC11 dyad sits in a very similar position to that of active MALT1-P and that Asn50, Asp177, and Asp207 superimpose well with the principal MALT1-P inhibitor binding residues (Asp365, Asp462, and Glu500, respectively (VRPR-FMK from MALT1-P with the corresponding PmC11 residues from the structural overlay is shown in Fig. 1D), as described in Ref.).	RESULTS
+72	79	complex	protein_state	A structure overlay of PmC11 with the MALT1-paracacaspase (MALT1-P), in complex with Z-VRPR-FMK, revealed that the PmC11 dyad sits in a very similar position to that of active MALT1-P and that Asn50, Asp177, and Asp207 superimpose well with the principal MALT1-P inhibitor binding residues (Asp365, Asp462, and Glu500, respectively (VRPR-FMK from MALT1-P with the corresponding PmC11 residues from the structural overlay is shown in Fig. 1D), as described in Ref.).	RESULTS
+85	95	Z-VRPR-FMK	chemical	A structure overlay of PmC11 with the MALT1-paracacaspase (MALT1-P), in complex with Z-VRPR-FMK, revealed that the PmC11 dyad sits in a very similar position to that of active MALT1-P and that Asn50, Asp177, and Asp207 superimpose well with the principal MALT1-P inhibitor binding residues (Asp365, Asp462, and Glu500, respectively (VRPR-FMK from MALT1-P with the corresponding PmC11 residues from the structural overlay is shown in Fig. 1D), as described in Ref.).	RESULTS
+115	120	PmC11	protein	A structure overlay of PmC11 with the MALT1-paracacaspase (MALT1-P), in complex with Z-VRPR-FMK, revealed that the PmC11 dyad sits in a very similar position to that of active MALT1-P and that Asn50, Asp177, and Asp207 superimpose well with the principal MALT1-P inhibitor binding residues (Asp365, Asp462, and Glu500, respectively (VRPR-FMK from MALT1-P with the corresponding PmC11 residues from the structural overlay is shown in Fig. 1D), as described in Ref.).	RESULTS
+121	125	dyad	site	A structure overlay of PmC11 with the MALT1-paracacaspase (MALT1-P), in complex with Z-VRPR-FMK, revealed that the PmC11 dyad sits in a very similar position to that of active MALT1-P and that Asn50, Asp177, and Asp207 superimpose well with the principal MALT1-P inhibitor binding residues (Asp365, Asp462, and Glu500, respectively (VRPR-FMK from MALT1-P with the corresponding PmC11 residues from the structural overlay is shown in Fig. 1D), as described in Ref.).	RESULTS
+169	175	active	protein_state	A structure overlay of PmC11 with the MALT1-paracacaspase (MALT1-P), in complex with Z-VRPR-FMK, revealed that the PmC11 dyad sits in a very similar position to that of active MALT1-P and that Asn50, Asp177, and Asp207 superimpose well with the principal MALT1-P inhibitor binding residues (Asp365, Asp462, and Glu500, respectively (VRPR-FMK from MALT1-P with the corresponding PmC11 residues from the structural overlay is shown in Fig. 1D), as described in Ref.).	RESULTS
+176	183	MALT1-P	protein	A structure overlay of PmC11 with the MALT1-paracacaspase (MALT1-P), in complex with Z-VRPR-FMK, revealed that the PmC11 dyad sits in a very similar position to that of active MALT1-P and that Asn50, Asp177, and Asp207 superimpose well with the principal MALT1-P inhibitor binding residues (Asp365, Asp462, and Glu500, respectively (VRPR-FMK from MALT1-P with the corresponding PmC11 residues from the structural overlay is shown in Fig. 1D), as described in Ref.).	RESULTS
+193	198	Asn50	residue_name_number	A structure overlay of PmC11 with the MALT1-paracacaspase (MALT1-P), in complex with Z-VRPR-FMK, revealed that the PmC11 dyad sits in a very similar position to that of active MALT1-P and that Asn50, Asp177, and Asp207 superimpose well with the principal MALT1-P inhibitor binding residues (Asp365, Asp462, and Glu500, respectively (VRPR-FMK from MALT1-P with the corresponding PmC11 residues from the structural overlay is shown in Fig. 1D), as described in Ref.).	RESULTS
+200	206	Asp177	residue_name_number	A structure overlay of PmC11 with the MALT1-paracacaspase (MALT1-P), in complex with Z-VRPR-FMK, revealed that the PmC11 dyad sits in a very similar position to that of active MALT1-P and that Asn50, Asp177, and Asp207 superimpose well with the principal MALT1-P inhibitor binding residues (Asp365, Asp462, and Glu500, respectively (VRPR-FMK from MALT1-P with the corresponding PmC11 residues from the structural overlay is shown in Fig. 1D), as described in Ref.).	RESULTS
+212	218	Asp207	residue_name_number	A structure overlay of PmC11 with the MALT1-paracacaspase (MALT1-P), in complex with Z-VRPR-FMK, revealed that the PmC11 dyad sits in a very similar position to that of active MALT1-P and that Asn50, Asp177, and Asp207 superimpose well with the principal MALT1-P inhibitor binding residues (Asp365, Asp462, and Glu500, respectively (VRPR-FMK from MALT1-P with the corresponding PmC11 residues from the structural overlay is shown in Fig. 1D), as described in Ref.).	RESULTS
+255	262	MALT1-P	protein	A structure overlay of PmC11 with the MALT1-paracacaspase (MALT1-P), in complex with Z-VRPR-FMK, revealed that the PmC11 dyad sits in a very similar position to that of active MALT1-P and that Asn50, Asp177, and Asp207 superimpose well with the principal MALT1-P inhibitor binding residues (Asp365, Asp462, and Glu500, respectively (VRPR-FMK from MALT1-P with the corresponding PmC11 residues from the structural overlay is shown in Fig. 1D), as described in Ref.).	RESULTS
+263	289	inhibitor binding residues	site	A structure overlay of PmC11 with the MALT1-paracacaspase (MALT1-P), in complex with Z-VRPR-FMK, revealed that the PmC11 dyad sits in a very similar position to that of active MALT1-P and that Asn50, Asp177, and Asp207 superimpose well with the principal MALT1-P inhibitor binding residues (Asp365, Asp462, and Glu500, respectively (VRPR-FMK from MALT1-P with the corresponding PmC11 residues from the structural overlay is shown in Fig. 1D), as described in Ref.).	RESULTS
+291	297	Asp365	residue_name_number	A structure overlay of PmC11 with the MALT1-paracacaspase (MALT1-P), in complex with Z-VRPR-FMK, revealed that the PmC11 dyad sits in a very similar position to that of active MALT1-P and that Asn50, Asp177, and Asp207 superimpose well with the principal MALT1-P inhibitor binding residues (Asp365, Asp462, and Glu500, respectively (VRPR-FMK from MALT1-P with the corresponding PmC11 residues from the structural overlay is shown in Fig. 1D), as described in Ref.).	RESULTS
+299	305	Asp462	residue_name_number	A structure overlay of PmC11 with the MALT1-paracacaspase (MALT1-P), in complex with Z-VRPR-FMK, revealed that the PmC11 dyad sits in a very similar position to that of active MALT1-P and that Asn50, Asp177, and Asp207 superimpose well with the principal MALT1-P inhibitor binding residues (Asp365, Asp462, and Glu500, respectively (VRPR-FMK from MALT1-P with the corresponding PmC11 residues from the structural overlay is shown in Fig. 1D), as described in Ref.).	RESULTS
+311	317	Glu500	residue_name_number	A structure overlay of PmC11 with the MALT1-paracacaspase (MALT1-P), in complex with Z-VRPR-FMK, revealed that the PmC11 dyad sits in a very similar position to that of active MALT1-P and that Asn50, Asp177, and Asp207 superimpose well with the principal MALT1-P inhibitor binding residues (Asp365, Asp462, and Glu500, respectively (VRPR-FMK from MALT1-P with the corresponding PmC11 residues from the structural overlay is shown in Fig. 1D), as described in Ref.).	RESULTS
+333	341	VRPR-FMK	chemical	A structure overlay of PmC11 with the MALT1-paracacaspase (MALT1-P), in complex with Z-VRPR-FMK, revealed that the PmC11 dyad sits in a very similar position to that of active MALT1-P and that Asn50, Asp177, and Asp207 superimpose well with the principal MALT1-P inhibitor binding residues (Asp365, Asp462, and Glu500, respectively (VRPR-FMK from MALT1-P with the corresponding PmC11 residues from the structural overlay is shown in Fig. 1D), as described in Ref.).	RESULTS
+347	354	MALT1-P	protein	A structure overlay of PmC11 with the MALT1-paracacaspase (MALT1-P), in complex with Z-VRPR-FMK, revealed that the PmC11 dyad sits in a very similar position to that of active MALT1-P and that Asn50, Asp177, and Asp207 superimpose well with the principal MALT1-P inhibitor binding residues (Asp365, Asp462, and Glu500, respectively (VRPR-FMK from MALT1-P with the corresponding PmC11 residues from the structural overlay is shown in Fig. 1D), as described in Ref.).	RESULTS
+378	383	PmC11	protein	A structure overlay of PmC11 with the MALT1-paracacaspase (MALT1-P), in complex with Z-VRPR-FMK, revealed that the PmC11 dyad sits in a very similar position to that of active MALT1-P and that Asn50, Asp177, and Asp207 superimpose well with the principal MALT1-P inhibitor binding residues (Asp365, Asp462, and Glu500, respectively (VRPR-FMK from MALT1-P with the corresponding PmC11 residues from the structural overlay is shown in Fig. 1D), as described in Ref.).	RESULTS
+402	420	structural overlay	experimental_method	A structure overlay of PmC11 with the MALT1-paracacaspase (MALT1-P), in complex with Z-VRPR-FMK, revealed that the PmC11 dyad sits in a very similar position to that of active MALT1-P and that Asn50, Asp177, and Asp207 superimpose well with the principal MALT1-P inhibitor binding residues (Asp365, Asp462, and Glu500, respectively (VRPR-FMK from MALT1-P with the corresponding PmC11 residues from the structural overlay is shown in Fig. 1D), as described in Ref.).	RESULTS
+0	6	Asp177	residue_name_number	Asp177 is located near the catalytic cysteine and is conserved throughout the C11 family, suggesting it is the primary S1 binding site residue.	RESULTS
+27	36	catalytic	protein_state	Asp177 is located near the catalytic cysteine and is conserved throughout the C11 family, suggesting it is the primary S1 binding site residue.	RESULTS
+37	45	cysteine	residue_name	Asp177 is located near the catalytic cysteine and is conserved throughout the C11 family, suggesting it is the primary S1 binding site residue.	RESULTS
+53	73	conserved throughout	protein_state	Asp177 is located near the catalytic cysteine and is conserved throughout the C11 family, suggesting it is the primary S1 binding site residue.	RESULTS
+78	88	C11 family	protein_type	Asp177 is located near the catalytic cysteine and is conserved throughout the C11 family, suggesting it is the primary S1 binding site residue.	RESULTS
+119	142	S1 binding site residue	site	Asp177 is located near the catalytic cysteine and is conserved throughout the C11 family, suggesting it is the primary S1 binding site residue.	RESULTS
+7	16	structure	evidence	In the structure of PmC11, Asp207 resides on a flexible loop pointing away from the S1 binding pocket (Fig. 3C).	RESULTS
+20	25	PmC11	protein	In the structure of PmC11, Asp207 resides on a flexible loop pointing away from the S1 binding pocket (Fig. 3C).	RESULTS
+27	33	Asp207	residue_name_number	In the structure of PmC11, Asp207 resides on a flexible loop pointing away from the S1 binding pocket (Fig. 3C).	RESULTS
+56	60	loop	structure_element	In the structure of PmC11, Asp207 resides on a flexible loop pointing away from the S1 binding pocket (Fig. 3C).	RESULTS
+84	101	S1 binding pocket	site	In the structure of PmC11, Asp207 resides on a flexible loop pointing away from the S1 binding pocket (Fig. 3C).	RESULTS
+14	18	loop	structure_element	However, this loop has been shown to be important for substrate binding in clan CD and this residue could easily rotate and be involved in substrate binding in PmC11.	RESULTS
+75	82	clan CD	protein_type	However, this loop has been shown to be important for substrate binding in clan CD and this residue could easily rotate and be involved in substrate binding in PmC11.	RESULTS
+160	165	PmC11	protein	However, this loop has been shown to be important for substrate binding in clan CD and this residue could easily rotate and be involved in substrate binding in PmC11.	RESULTS
+6	11	Asn50	residue_name_number	Thus, Asn50, Asp177, and Asp207 are most likely responsible for the substrate specificity of PmC11.	RESULTS
+13	19	Asp177	residue_name_number	Thus, Asn50, Asp177, and Asp207 are most likely responsible for the substrate specificity of PmC11.	RESULTS
+25	31	Asp207	residue_name_number	Thus, Asn50, Asp177, and Asp207 are most likely responsible for the substrate specificity of PmC11.	RESULTS
+93	98	PmC11	protein	Thus, Asn50, Asp177, and Asp207 are most likely responsible for the substrate specificity of PmC11.	RESULTS
+0	6	Asp177	residue_name_number	Asp177 is highly conserved throughout the clan CD C11 peptidases and is thought to be primarily responsible for substrate specificity of the clan CD enzymes, as also illustrated from the proximity of these residues relative to the inhibitor Z-VRPR-FMK when PmC11 is overlaid on the MALT1-P structure (Fig. 3C).	RESULTS
+10	26	highly conserved	protein_state	Asp177 is highly conserved throughout the clan CD C11 peptidases and is thought to be primarily responsible for substrate specificity of the clan CD enzymes, as also illustrated from the proximity of these residues relative to the inhibitor Z-VRPR-FMK when PmC11 is overlaid on the MALT1-P structure (Fig. 3C).	RESULTS
+42	64	clan CD C11 peptidases	protein_type	Asp177 is highly conserved throughout the clan CD C11 peptidases and is thought to be primarily responsible for substrate specificity of the clan CD enzymes, as also illustrated from the proximity of these residues relative to the inhibitor Z-VRPR-FMK when PmC11 is overlaid on the MALT1-P structure (Fig. 3C).	RESULTS
+141	156	clan CD enzymes	protein_type	Asp177 is highly conserved throughout the clan CD C11 peptidases and is thought to be primarily responsible for substrate specificity of the clan CD enzymes, as also illustrated from the proximity of these residues relative to the inhibitor Z-VRPR-FMK when PmC11 is overlaid on the MALT1-P structure (Fig. 3C).	RESULTS
+241	251	Z-VRPR-FMK	chemical	Asp177 is highly conserved throughout the clan CD C11 peptidases and is thought to be primarily responsible for substrate specificity of the clan CD enzymes, as also illustrated from the proximity of these residues relative to the inhibitor Z-VRPR-FMK when PmC11 is overlaid on the MALT1-P structure (Fig. 3C).	RESULTS
+257	262	PmC11	protein	Asp177 is highly conserved throughout the clan CD C11 peptidases and is thought to be primarily responsible for substrate specificity of the clan CD enzymes, as also illustrated from the proximity of these residues relative to the inhibitor Z-VRPR-FMK when PmC11 is overlaid on the MALT1-P structure (Fig. 3C).	RESULTS
+266	274	overlaid	experimental_method	Asp177 is highly conserved throughout the clan CD C11 peptidases and is thought to be primarily responsible for substrate specificity of the clan CD enzymes, as also illustrated from the proximity of these residues relative to the inhibitor Z-VRPR-FMK when PmC11 is overlaid on the MALT1-P structure (Fig. 3C).	RESULTS
+282	289	MALT1-P	protein	Asp177 is highly conserved throughout the clan CD C11 peptidases and is thought to be primarily responsible for substrate specificity of the clan CD enzymes, as also illustrated from the proximity of these residues relative to the inhibitor Z-VRPR-FMK when PmC11 is overlaid on the MALT1-P structure (Fig. 3C).	RESULTS
+290	299	structure	evidence	Asp177 is highly conserved throughout the clan CD C11 peptidases and is thought to be primarily responsible for substrate specificity of the clan CD enzymes, as also illustrated from the proximity of these residues relative to the inhibitor Z-VRPR-FMK when PmC11 is overlaid on the MALT1-P structure (Fig. 3C).	RESULTS
+0	5	PmC11	protein	PmC11 binds and is inhibited by Z-VRPR-FMK and does not require Ca2+ for activity.	FIG
+32	42	Z-VRPR-FMK	chemical	PmC11 binds and is inhibited by Z-VRPR-FMK and does not require Ca2+ for activity.	FIG
+64	68	Ca2+	chemical	PmC11 binds and is inhibited by Z-VRPR-FMK and does not require Ca2+ for activity.	FIG
+35	45	Z-VRPR-FMK	chemical	 A, PmC11 activity is inhibited by Z-VRPR-FMK.	FIG
+12	20	Bz-R-AMC	chemical	Cleavage of Bz-R-AMC by PmC11 was measured in a fluorometric activity assay with (+, purple) and without (−, red) Z-VRPR-FMK.	FIG
+24	29	PmC11	protein	Cleavage of Bz-R-AMC by PmC11 was measured in a fluorometric activity assay with (+, purple) and without (−, red) Z-VRPR-FMK.	FIG
+48	75	fluorometric activity assay	experimental_method	Cleavage of Bz-R-AMC by PmC11 was measured in a fluorometric activity assay with (+, purple) and without (−, red) Z-VRPR-FMK.	FIG
+114	124	Z-VRPR-FMK	chemical	Cleavage of Bz-R-AMC by PmC11 was measured in a fluorometric activity assay with (+, purple) and without (−, red) Z-VRPR-FMK.	FIG
+3	18	gel-shift assay	experimental_method	B, gel-shift assay reveals that Z-VRPR-FMK binds to PmC11.	FIG
+32	42	Z-VRPR-FMK	chemical	B, gel-shift assay reveals that Z-VRPR-FMK binds to PmC11.	FIG
+52	57	PmC11	protein	B, gel-shift assay reveals that Z-VRPR-FMK binds to PmC11.	FIG
+10	19	incubated	experimental_method	PmC11 was incubated with (+) or without (−) Z-VRPR-FMK and the samples analyzed on a 10% SDS-PAGE gel.	FIG
+44	54	Z-VRPR-FMK	chemical	PmC11 was incubated with (+) or without (−) Z-VRPR-FMK and the samples analyzed on a 10% SDS-PAGE gel.	FIG
+89	97	SDS-PAGE	experimental_method	PmC11 was incubated with (+) or without (−) Z-VRPR-FMK and the samples analyzed on a 10% SDS-PAGE gel.	FIG
+2	12	size shift	evidence	A size shift can be observed in the larger processed product of PmC11 (26.1 kDa).	FIG
+64	69	PmC11	protein	A size shift can be observed in the larger processed product of PmC11 (26.1 kDa).	FIG
+3	8	PmC11	protein	C, PmC11 with the Z-VRPR-FMK from the MALT1-paracacaspase (MALT1-P) superimposed.	FIG
+18	28	Z-VRPR-FMK	chemical	C, PmC11 with the Z-VRPR-FMK from the MALT1-paracacaspase (MALT1-P) superimposed.	FIG
+38	57	MALT1-paracacaspase	protein	C, PmC11 with the Z-VRPR-FMK from the MALT1-paracacaspase (MALT1-P) superimposed.	FIG
+59	66	MALT1-P	protein	C, PmC11 with the Z-VRPR-FMK from the MALT1-paracacaspase (MALT1-P) superimposed.	FIG
+68	80	superimposed	experimental_method	C, PmC11 with the Z-VRPR-FMK from the MALT1-paracacaspase (MALT1-P) superimposed.	FIG
+2	38	three-dimensional structural overlay	experimental_method	A three-dimensional structural overlay of Z-VRPR-FMK from the MALT1-P complex onto PmC11.	FIG
+42	52	Z-VRPR-FMK	chemical	A three-dimensional structural overlay of Z-VRPR-FMK from the MALT1-P complex onto PmC11.	FIG
+62	69	MALT1-P	protein	A three-dimensional structural overlay of Z-VRPR-FMK from the MALT1-P complex onto PmC11.	FIG
+83	88	PmC11	protein	A three-dimensional structural overlay of Z-VRPR-FMK from the MALT1-P complex onto PmC11.	FIG
+32	42	Z-VRPR-FMK	chemical	The position and orientation of Z-VRPR-FMK was taken from superposition of the PmC11 and MALTI_P structures and indicates the presumed active site of PmC11.	FIG
+58	71	superposition	experimental_method	The position and orientation of Z-VRPR-FMK was taken from superposition of the PmC11 and MALTI_P structures and indicates the presumed active site of PmC11.	FIG
+79	84	PmC11	protein	The position and orientation of Z-VRPR-FMK was taken from superposition of the PmC11 and MALTI_P structures and indicates the presumed active site of PmC11.	FIG
+89	96	MALTI_P	protein	The position and orientation of Z-VRPR-FMK was taken from superposition of the PmC11 and MALTI_P structures and indicates the presumed active site of PmC11.	FIG
+97	107	structures	evidence	The position and orientation of Z-VRPR-FMK was taken from superposition of the PmC11 and MALTI_P structures and indicates the presumed active site of PmC11.	FIG
+135	146	active site	site	The position and orientation of Z-VRPR-FMK was taken from superposition of the PmC11 and MALTI_P structures and indicates the presumed active site of PmC11.	FIG
+150	155	PmC11	protein	The position and orientation of Z-VRPR-FMK was taken from superposition of the PmC11 and MALTI_P structures and indicates the presumed active site of PmC11.	FIG
+83	104	binding site residues	site	Residues surrounding the inhibitor are labeled and represent potentially important binding site residues, labeled in black and shown in an atomic representation.	FIG
+52	57	PmC11	protein	C, divalent cations do not increase the activity of PmC11.	FIG
+16	24	Bz-R-AMC	chemical	The cleavage of Bz-R-AMC by PmC11 was measured in the presence of the cations Ca2+, Mn2+, Zn2+, Co2+, Cu2+, Mg2+, and Fe3+ with EGTA as a negative control, and relative fluorescence measured against time (min).	FIG
+28	33	PmC11	protein	The cleavage of Bz-R-AMC by PmC11 was measured in the presence of the cations Ca2+, Mn2+, Zn2+, Co2+, Cu2+, Mg2+, and Fe3+ with EGTA as a negative control, and relative fluorescence measured against time (min).	FIG
+78	82	Ca2+	chemical	The cleavage of Bz-R-AMC by PmC11 was measured in the presence of the cations Ca2+, Mn2+, Zn2+, Co2+, Cu2+, Mg2+, and Fe3+ with EGTA as a negative control, and relative fluorescence measured against time (min).	FIG
+84	88	Mn2+	chemical	The cleavage of Bz-R-AMC by PmC11 was measured in the presence of the cations Ca2+, Mn2+, Zn2+, Co2+, Cu2+, Mg2+, and Fe3+ with EGTA as a negative control, and relative fluorescence measured against time (min).	FIG
+90	94	Zn2+	chemical	The cleavage of Bz-R-AMC by PmC11 was measured in the presence of the cations Ca2+, Mn2+, Zn2+, Co2+, Cu2+, Mg2+, and Fe3+ with EGTA as a negative control, and relative fluorescence measured against time (min).	FIG
+96	100	Co2+	chemical	The cleavage of Bz-R-AMC by PmC11 was measured in the presence of the cations Ca2+, Mn2+, Zn2+, Co2+, Cu2+, Mg2+, and Fe3+ with EGTA as a negative control, and relative fluorescence measured against time (min).	FIG
+102	106	Cu2+	chemical	The cleavage of Bz-R-AMC by PmC11 was measured in the presence of the cations Ca2+, Mn2+, Zn2+, Co2+, Cu2+, Mg2+, and Fe3+ with EGTA as a negative control, and relative fluorescence measured against time (min).	FIG
+108	112	Mg2+	chemical	The cleavage of Bz-R-AMC by PmC11 was measured in the presence of the cations Ca2+, Mn2+, Zn2+, Co2+, Cu2+, Mg2+, and Fe3+ with EGTA as a negative control, and relative fluorescence measured against time (min).	FIG
+118	122	Fe3+	chemical	The cleavage of Bz-R-AMC by PmC11 was measured in the presence of the cations Ca2+, Mn2+, Zn2+, Co2+, Cu2+, Mg2+, and Fe3+ with EGTA as a negative control, and relative fluorescence measured against time (min).	FIG
+128	132	EGTA	chemical	The cleavage of Bz-R-AMC by PmC11 was measured in the presence of the cations Ca2+, Mn2+, Zn2+, Co2+, Cu2+, Mg2+, and Fe3+ with EGTA as a negative control, and relative fluorescence measured against time (min).	FIG
+160	203	relative fluorescence measured against time	experimental_method	The cleavage of Bz-R-AMC by PmC11 was measured in the presence of the cations Ca2+, Mn2+, Zn2+, Co2+, Cu2+, Mg2+, and Fe3+ with EGTA as a negative control, and relative fluorescence measured against time (min).	FIG
+4	23	addition of cations	experimental_method	The addition of cations produced no improvement in activity of PmC11 when compared in the presence of EGTA, suggesting that PmC11 does not require metal ions for proteolytic activity.	FIG
+63	68	PmC11	protein	The addition of cations produced no improvement in activity of PmC11 when compared in the presence of EGTA, suggesting that PmC11 does not require metal ions for proteolytic activity.	FIG
+102	106	EGTA	chemical	The addition of cations produced no improvement in activity of PmC11 when compared in the presence of EGTA, suggesting that PmC11 does not require metal ions for proteolytic activity.	FIG
+124	129	PmC11	protein	The addition of cations produced no improvement in activity of PmC11 when compared in the presence of EGTA, suggesting that PmC11 does not require metal ions for proteolytic activity.	FIG
+13	17	Cu2+	chemical	Furthermore, Cu2+, Fe2+, and Zn2+ appear to inhibit PmC11.	FIG
+19	23	Fe2+	chemical	Furthermore, Cu2+, Fe2+, and Zn2+ appear to inhibit PmC11.	FIG
+29	33	Zn2+	chemical	Furthermore, Cu2+, Fe2+, and Zn2+ appear to inhibit PmC11.	FIG
+44	51	inhibit	protein_state	Furthermore, Cu2+, Fe2+, and Zn2+ appear to inhibit PmC11.	FIG
+52	57	PmC11	protein	Furthermore, Cu2+, Fe2+, and Zn2+ appear to inhibit PmC11.	FIG
+16	27	Clostripain	protein	Comparison with Clostripain	RESULTS
+0	11	Clostripain	protein	Clostripain from C. histolyticum is the founding member of the C11 family of peptidases and contains an additional 149 residues compared with PmC11.	RESULTS
+17	32	C. histolyticum	species	Clostripain from C. histolyticum is the founding member of the C11 family of peptidases and contains an additional 149 residues compared with PmC11.	RESULTS
+63	73	C11 family	protein_type	Clostripain from C. histolyticum is the founding member of the C11 family of peptidases and contains an additional 149 residues compared with PmC11.	RESULTS
+77	87	peptidases	protein_type	Clostripain from C. histolyticum is the founding member of the C11 family of peptidases and contains an additional 149 residues compared with PmC11.	RESULTS
+115	127	149 residues	residue_range	Clostripain from C. histolyticum is the founding member of the C11 family of peptidases and contains an additional 149 residues compared with PmC11.	RESULTS
+142	147	PmC11	protein	Clostripain from C. histolyticum is the founding member of the C11 family of peptidases and contains an additional 149 residues compared with PmC11.	RESULTS
+2	29	multiple sequence alignment	experimental_method	A multiple sequence alignment revealed that most of the secondary structural elements are conserved between the two enzymes, although they are only ∼23% identical (Fig. 1A).	RESULTS
+56	85	secondary structural elements	structure_element	A multiple sequence alignment revealed that most of the secondary structural elements are conserved between the two enzymes, although they are only ∼23% identical (Fig. 1A).	RESULTS
+90	99	conserved	protein_state	A multiple sequence alignment revealed that most of the secondary structural elements are conserved between the two enzymes, although they are only ∼23% identical (Fig. 1A).	RESULTS
+14	19	PmC11	protein	Nevertheless, PmC11 may be a good model for the core structure of clostripain.	RESULTS
+66	77	clostripain	protein	Nevertheless, PmC11 may be a good model for the core structure of clostripain.	RESULTS
+4	32	primary structural alignment	experimental_method	The primary structural alignment also shows that the catalytic dyad in PmC11 is structurally conserved in clostripain (Fig. 1A).	RESULTS
+53	67	catalytic dyad	site	The primary structural alignment also shows that the catalytic dyad in PmC11 is structurally conserved in clostripain (Fig. 1A).	RESULTS
+71	76	PmC11	protein	The primary structural alignment also shows that the catalytic dyad in PmC11 is structurally conserved in clostripain (Fig. 1A).	RESULTS
+80	102	structurally conserved	protein_state	The primary structural alignment also shows that the catalytic dyad in PmC11 is structurally conserved in clostripain (Fig. 1A).	RESULTS
+106	117	clostripain	protein	The primary structural alignment also shows that the catalytic dyad in PmC11 is structurally conserved in clostripain (Fig. 1A).	RESULTS
+7	12	PmC11	protein	Unlike PmC11, clostripain has two cleavage sites (Arg181 and Arg190), which results in the removal of a nonapeptide, and is required for full activation of the enzyme (highlighted in Fig. 1A).	RESULTS
+14	25	clostripain	protein	Unlike PmC11, clostripain has two cleavage sites (Arg181 and Arg190), which results in the removal of a nonapeptide, and is required for full activation of the enzyme (highlighted in Fig. 1A).	RESULTS
+34	48	cleavage sites	site	Unlike PmC11, clostripain has two cleavage sites (Arg181 and Arg190), which results in the removal of a nonapeptide, and is required for full activation of the enzyme (highlighted in Fig. 1A).	RESULTS
+50	56	Arg181	residue_name_number	Unlike PmC11, clostripain has two cleavage sites (Arg181 and Arg190), which results in the removal of a nonapeptide, and is required for full activation of the enzyme (highlighted in Fig. 1A).	RESULTS
+61	67	Arg190	residue_name_number	Unlike PmC11, clostripain has two cleavage sites (Arg181 and Arg190), which results in the removal of a nonapeptide, and is required for full activation of the enzyme (highlighted in Fig. 1A).	RESULTS
+104	115	nonapeptide	structure_element	Unlike PmC11, clostripain has two cleavage sites (Arg181 and Arg190), which results in the removal of a nonapeptide, and is required for full activation of the enzyme (highlighted in Fig. 1A).	RESULTS
+137	152	full activation	protein_state	Unlike PmC11, clostripain has two cleavage sites (Arg181 and Arg190), which results in the removal of a nonapeptide, and is required for full activation of the enzyme (highlighted in Fig. 1A).	RESULTS
+15	21	Arg190	residue_name_number	Interestingly, Arg190 was found to align with Lys147 in PmC11.	RESULTS
+46	52	Lys147	residue_name_number	Interestingly, Arg190 was found to align with Lys147 in PmC11.	RESULTS
+56	61	PmC11	protein	Interestingly, Arg190 was found to align with Lys147 in PmC11.	RESULTS
+35	53	S1-binding residue	site	In addition, the predicted primary S1-binding residue in PmC11 Asp177 also overlays with the residue predicted to be the P1 specificity determining residue in clostripain (Asp229, Fig. 1A).	RESULTS
+57	62	PmC11	protein	In addition, the predicted primary S1-binding residue in PmC11 Asp177 also overlays with the residue predicted to be the P1 specificity determining residue in clostripain (Asp229, Fig. 1A).	RESULTS
+63	69	Asp177	residue_name_number	In addition, the predicted primary S1-binding residue in PmC11 Asp177 also overlays with the residue predicted to be the P1 specificity determining residue in clostripain (Asp229, Fig. 1A).	RESULTS
+75	83	overlays	experimental_method	In addition, the predicted primary S1-binding residue in PmC11 Asp177 also overlays with the residue predicted to be the P1 specificity determining residue in clostripain (Asp229, Fig. 1A).	RESULTS
+121	155	P1 specificity determining residue	site	In addition, the predicted primary S1-binding residue in PmC11 Asp177 also overlays with the residue predicted to be the P1 specificity determining residue in clostripain (Asp229, Fig. 1A).	RESULTS
+159	170	clostripain	protein	In addition, the predicted primary S1-binding residue in PmC11 Asp177 also overlays with the residue predicted to be the P1 specificity determining residue in clostripain (Asp229, Fig. 1A).	RESULTS
+172	178	Asp229	residue_name_number	In addition, the predicted primary S1-binding residue in PmC11 Asp177 also overlays with the residue predicted to be the P1 specificity determining residue in clostripain (Asp229, Fig. 1A).	RESULTS
+14	25	clostripain	protein	As studies on clostripain revealed addition of Ca2+ ions are required for full activation, the Ca2+ dependence of PmC11 was examined.	RESULTS
+47	51	Ca2+	chemical	As studies on clostripain revealed addition of Ca2+ ions are required for full activation, the Ca2+ dependence of PmC11 was examined.	RESULTS
+74	89	full activation	protein_state	As studies on clostripain revealed addition of Ca2+ ions are required for full activation, the Ca2+ dependence of PmC11 was examined.	RESULTS
+95	99	Ca2+	chemical	As studies on clostripain revealed addition of Ca2+ ions are required for full activation, the Ca2+ dependence of PmC11 was examined.	RESULTS
+114	119	PmC11	protein	As studies on clostripain revealed addition of Ca2+ ions are required for full activation, the Ca2+ dependence of PmC11 was examined.	RESULTS
+14	18	Ca2+	chemical	Surprisingly, Ca2+ did not enhance PmC11 activity and, furthermore, other divalent cations, Mg2+, Mn2+, Co2+, Fe2+, Zn2+, and Cu2+, were not necessary for PmC11 activity (Fig. 3D).	RESULTS
+35	40	PmC11	protein	Surprisingly, Ca2+ did not enhance PmC11 activity and, furthermore, other divalent cations, Mg2+, Mn2+, Co2+, Fe2+, Zn2+, and Cu2+, were not necessary for PmC11 activity (Fig. 3D).	RESULTS
+92	96	Mg2+	chemical	Surprisingly, Ca2+ did not enhance PmC11 activity and, furthermore, other divalent cations, Mg2+, Mn2+, Co2+, Fe2+, Zn2+, and Cu2+, were not necessary for PmC11 activity (Fig. 3D).	RESULTS
+98	102	Mn2+	chemical	Surprisingly, Ca2+ did not enhance PmC11 activity and, furthermore, other divalent cations, Mg2+, Mn2+, Co2+, Fe2+, Zn2+, and Cu2+, were not necessary for PmC11 activity (Fig. 3D).	RESULTS
+104	108	Co2+	chemical	Surprisingly, Ca2+ did not enhance PmC11 activity and, furthermore, other divalent cations, Mg2+, Mn2+, Co2+, Fe2+, Zn2+, and Cu2+, were not necessary for PmC11 activity (Fig. 3D).	RESULTS
+110	114	Fe2+	chemical	Surprisingly, Ca2+ did not enhance PmC11 activity and, furthermore, other divalent cations, Mg2+, Mn2+, Co2+, Fe2+, Zn2+, and Cu2+, were not necessary for PmC11 activity (Fig. 3D).	RESULTS
+116	120	Zn2+	chemical	Surprisingly, Ca2+ did not enhance PmC11 activity and, furthermore, other divalent cations, Mg2+, Mn2+, Co2+, Fe2+, Zn2+, and Cu2+, were not necessary for PmC11 activity (Fig. 3D).	RESULTS
+126	130	Cu2+	chemical	Surprisingly, Ca2+ did not enhance PmC11 activity and, furthermore, other divalent cations, Mg2+, Mn2+, Co2+, Fe2+, Zn2+, and Cu2+, were not necessary for PmC11 activity (Fig. 3D).	RESULTS
+155	160	PmC11	protein	Surprisingly, Ca2+ did not enhance PmC11 activity and, furthermore, other divalent cations, Mg2+, Mn2+, Co2+, Fe2+, Zn2+, and Cu2+, were not necessary for PmC11 activity (Fig. 3D).	RESULTS
+30	34	EGTA	chemical	In support of these findings, EGTA did not inhibit PmC11 suggesting that, unlike clostripain, PmC11 does not require Ca2+ or other divalent cations, for activity.	RESULTS
+51	56	PmC11	protein	In support of these findings, EGTA did not inhibit PmC11 suggesting that, unlike clostripain, PmC11 does not require Ca2+ or other divalent cations, for activity.	RESULTS
+81	92	clostripain	protein	In support of these findings, EGTA did not inhibit PmC11 suggesting that, unlike clostripain, PmC11 does not require Ca2+ or other divalent cations, for activity.	RESULTS
+94	99	PmC11	protein	In support of these findings, EGTA did not inhibit PmC11 suggesting that, unlike clostripain, PmC11 does not require Ca2+ or other divalent cations, for activity.	RESULTS
+117	121	Ca2+	chemical	In support of these findings, EGTA did not inhibit PmC11 suggesting that, unlike clostripain, PmC11 does not require Ca2+ or other divalent cations, for activity.	RESULTS
+4	21	crystal structure	evidence	The crystal structure of PmC11 now provides three-dimensional information for a member of the clostripain C11 family of cysteine peptidases.	DISCUSS
+25	30	PmC11	protein	The crystal structure of PmC11 now provides three-dimensional information for a member of the clostripain C11 family of cysteine peptidases.	DISCUSS
+94	105	clostripain	protein	The crystal structure of PmC11 now provides three-dimensional information for a member of the clostripain C11 family of cysteine peptidases.	DISCUSS
+106	116	C11 family	protein_type	The crystal structure of PmC11 now provides three-dimensional information for a member of the clostripain C11 family of cysteine peptidases.	DISCUSS
+120	139	cysteine peptidases	protein_type	The crystal structure of PmC11 now provides three-dimensional information for a member of the clostripain C11 family of cysteine peptidases.	DISCUSS
+58	73	clan CD members	protein_type	The enzyme exhibits all of the key structural elements of clan CD members, but is unusual in that it has a nine-stranded central β-sheet with a novel C-terminal domain.	DISCUSS
+129	136	β-sheet	structure_element	The enzyme exhibits all of the key structural elements of clan CD members, but is unusual in that it has a nine-stranded central β-sheet with a novel C-terminal domain.	DISCUSS
+150	167	C-terminal domain	structure_element	The enzyme exhibits all of the key structural elements of clan CD members, but is unusual in that it has a nine-stranded central β-sheet with a novel C-terminal domain.	DISCUSS
+29	34	PmC11	protein	The structural similarity of PmC11 with its nearest structural neighbors in the PDB is decidedly low, overlaying better with six-stranded caspase-7 than any of the other larger members of the clan (Table 2).	DISCUSS
+138	147	caspase-7	protein	The structural similarity of PmC11 with its nearest structural neighbors in the PDB is decidedly low, overlaying better with six-stranded caspase-7 than any of the other larger members of the clan (Table 2).	DISCUSS
+29	34	PmC11	protein	The substrate specificity of PmC11 is Arg/Lys and the crystal structure revealed an acidic pocket for specific binding of such basic substrates.	DISCUSS
+38	41	Arg	residue_name	The substrate specificity of PmC11 is Arg/Lys and the crystal structure revealed an acidic pocket for specific binding of such basic substrates.	DISCUSS
+42	45	Lys	residue_name	The substrate specificity of PmC11 is Arg/Lys and the crystal structure revealed an acidic pocket for specific binding of such basic substrates.	DISCUSS
+54	71	crystal structure	evidence	The substrate specificity of PmC11 is Arg/Lys and the crystal structure revealed an acidic pocket for specific binding of such basic substrates.	DISCUSS
+84	97	acidic pocket	site	The substrate specificity of PmC11 is Arg/Lys and the crystal structure revealed an acidic pocket for specific binding of such basic substrates.	DISCUSS
+17	26	structure	evidence	In addition, the structure suggested a mechanism of self-inhibition in both PmC11 and clostripain and an activation mechanism that requires autoprocessing.	DISCUSS
+76	81	PmC11	protein	In addition, the structure suggested a mechanism of self-inhibition in both PmC11 and clostripain and an activation mechanism that requires autoprocessing.	DISCUSS
+86	97	clostripain	protein	In addition, the structure suggested a mechanism of self-inhibition in both PmC11 and clostripain and an activation mechanism that requires autoprocessing.	DISCUSS
+140	154	autoprocessing	ptm	In addition, the structure suggested a mechanism of self-inhibition in both PmC11 and clostripain and an activation mechanism that requires autoprocessing.	DISCUSS
+0	5	PmC11	protein	PmC11 differs from clostripain in that is does not appear to require divalent cations for activation.	DISCUSS
+19	30	clostripain	protein	PmC11 differs from clostripain in that is does not appear to require divalent cations for activation.	DISCUSS
+25	32	clan CD	protein_type	Several other members of clan CD require processing for full activation including legumain, gingipain-R, MARTX-CPD, and the effector caspases, e.g. caspase-7.	DISCUSS
+41	51	processing	ptm	Several other members of clan CD require processing for full activation including legumain, gingipain-R, MARTX-CPD, and the effector caspases, e.g. caspase-7.	DISCUSS
+56	71	full activation	protein_state	Several other members of clan CD require processing for full activation including legumain, gingipain-R, MARTX-CPD, and the effector caspases, e.g. caspase-7.	DISCUSS
+82	90	legumain	protein	Several other members of clan CD require processing for full activation including legumain, gingipain-R, MARTX-CPD, and the effector caspases, e.g. caspase-7.	DISCUSS
+92	103	gingipain-R	protein	Several other members of clan CD require processing for full activation including legumain, gingipain-R, MARTX-CPD, and the effector caspases, e.g. caspase-7.	DISCUSS
+105	114	MARTX-CPD	protein	Several other members of clan CD require processing for full activation including legumain, gingipain-R, MARTX-CPD, and the effector caspases, e.g. caspase-7.	DISCUSS
+124	141	effector caspases	protein_type	Several other members of clan CD require processing for full activation including legumain, gingipain-R, MARTX-CPD, and the effector caspases, e.g. caspase-7.	DISCUSS
+148	157	caspase-7	protein	Several other members of clan CD require processing for full activation including legumain, gingipain-R, MARTX-CPD, and the effector caspases, e.g. caspase-7.	DISCUSS
+13	30	effector caspases	protein_type	To date, the effector caspases are the only group of enzymes that require cleavage of a loop within the central β-sheet.	DISCUSS
+74	82	cleavage	ptm	To date, the effector caspases are the only group of enzymes that require cleavage of a loop within the central β-sheet.	DISCUSS
+88	92	loop	structure_element	To date, the effector caspases are the only group of enzymes that require cleavage of a loop within the central β-sheet.	DISCUSS
+112	119	β-sheet	structure_element	To date, the effector caspases are the only group of enzymes that require cleavage of a loop within the central β-sheet.	DISCUSS
+25	30	PmC11	protein	This is also the case in PmC11, although the cleavage loop is structurally different to that found in the caspases and follows the catalytic His (Fig. 1A), as opposed to the Cys in the caspases.	DISCUSS
+45	53	cleavage	ptm	This is also the case in PmC11, although the cleavage loop is structurally different to that found in the caspases and follows the catalytic His (Fig. 1A), as opposed to the Cys in the caspases.	DISCUSS
+54	58	loop	structure_element	This is also the case in PmC11, although the cleavage loop is structurally different to that found in the caspases and follows the catalytic His (Fig. 1A), as opposed to the Cys in the caspases.	DISCUSS
+106	114	caspases	protein_type	This is also the case in PmC11, although the cleavage loop is structurally different to that found in the caspases and follows the catalytic His (Fig. 1A), as opposed to the Cys in the caspases.	DISCUSS
+131	140	catalytic	protein_state	This is also the case in PmC11, although the cleavage loop is structurally different to that found in the caspases and follows the catalytic His (Fig. 1A), as opposed to the Cys in the caspases.	DISCUSS
+141	144	His	residue_name	This is also the case in PmC11, although the cleavage loop is structurally different to that found in the caspases and follows the catalytic His (Fig. 1A), as opposed to the Cys in the caspases.	DISCUSS
+174	177	Cys	residue_name	This is also the case in PmC11, although the cleavage loop is structurally different to that found in the caspases and follows the catalytic His (Fig. 1A), as opposed to the Cys in the caspases.	DISCUSS
+185	193	caspases	protein_type	This is also the case in PmC11, although the cleavage loop is structurally different to that found in the caspases and follows the catalytic His (Fig. 1A), as opposed to the Cys in the caspases.	DISCUSS
+10	25	clan CD members	protein_type	All other clan CD members requiring cleavage for full activation do so at sites external to their central sheets.	DISCUSS
+36	44	cleavage	ptm	All other clan CD members requiring cleavage for full activation do so at sites external to their central sheets.	DISCUSS
+49	64	full activation	protein_state	All other clan CD members requiring cleavage for full activation do so at sites external to their central sheets.	DISCUSS
+74	79	sites	site	All other clan CD members requiring cleavage for full activation do so at sites external to their central sheets.	DISCUSS
+106	112	sheets	structure_element	All other clan CD members requiring cleavage for full activation do so at sites external to their central sheets.	DISCUSS
+4	12	caspases	protein_type	The caspases and gingipain-R both undergo intermolecular (trans) cleavage and legumain and MARTX-CPD are reported to perform intramolecular (cis) cleavage.	DISCUSS
+17	28	gingipain-R	protein	The caspases and gingipain-R both undergo intermolecular (trans) cleavage and legumain and MARTX-CPD are reported to perform intramolecular (cis) cleavage.	DISCUSS
+42	73	intermolecular (trans) cleavage	ptm	The caspases and gingipain-R both undergo intermolecular (trans) cleavage and legumain and MARTX-CPD are reported to perform intramolecular (cis) cleavage.	DISCUSS
+78	86	legumain	protein	The caspases and gingipain-R both undergo intermolecular (trans) cleavage and legumain and MARTX-CPD are reported to perform intramolecular (cis) cleavage.	DISCUSS
+91	100	MARTX-CPD	protein	The caspases and gingipain-R both undergo intermolecular (trans) cleavage and legumain and MARTX-CPD are reported to perform intramolecular (cis) cleavage.	DISCUSS
+125	154	intramolecular (cis) cleavage	ptm	The caspases and gingipain-R both undergo intermolecular (trans) cleavage and legumain and MARTX-CPD are reported to perform intramolecular (cis) cleavage.	DISCUSS
+32	39	clan CD	protein_type	In addition, several members of clan CD exhibit self-inhibition, whereby regions of the enzyme block access to the active site.	DISCUSS
+73	80	regions	structure_element	In addition, several members of clan CD exhibit self-inhibition, whereby regions of the enzyme block access to the active site.	DISCUSS
+115	126	active site	site	In addition, several members of clan CD exhibit self-inhibition, whereby regions of the enzyme block access to the active site.	DISCUSS
+5	10	PmC11	protein	Like PmC11, these structures show preformed catalytic machinery and, for a substrate to gain access, movement and/or cleavage of the blocking region is required.	DISCUSS
+117	125	cleavage	ptm	Like PmC11, these structures show preformed catalytic machinery and, for a substrate to gain access, movement and/or cleavage of the blocking region is required.	DISCUSS
+133	148	blocking region	structure_element	Like PmC11, these structures show preformed catalytic machinery and, for a substrate to gain access, movement and/or cleavage of the blocking region is required.	DISCUSS
+4	13	structure	evidence	The structure of PmC11 gives the first insight into this class of relatively unexplored family of proteins and should allow important catalytic and substrate binding residues to be identified in a variety of orthologues.	DISCUSS
+17	22	PmC11	protein	The structure of PmC11 gives the first insight into this class of relatively unexplored family of proteins and should allow important catalytic and substrate binding residues to be identified in a variety of orthologues.	DISCUSS
+48	53	PmC11	protein	Indeed, insights gained from an analysis of the PmC11 structure revealed the identity of the Trypanosoma brucei PNT1 protein as a C11 cysteine peptidase with an essential role in organelle replication.	DISCUSS
+54	63	structure	evidence	Indeed, insights gained from an analysis of the PmC11 structure revealed the identity of the Trypanosoma brucei PNT1 protein as a C11 cysteine peptidase with an essential role in organelle replication.	DISCUSS
+93	111	Trypanosoma brucei	species	Indeed, insights gained from an analysis of the PmC11 structure revealed the identity of the Trypanosoma brucei PNT1 protein as a C11 cysteine peptidase with an essential role in organelle replication.	DISCUSS
+112	116	PNT1	protein	Indeed, insights gained from an analysis of the PmC11 structure revealed the identity of the Trypanosoma brucei PNT1 protein as a C11 cysteine peptidase with an essential role in organelle replication.	DISCUSS
+130	152	C11 cysteine peptidase	protein_type	Indeed, insights gained from an analysis of the PmC11 structure revealed the identity of the Trypanosoma brucei PNT1 protein as a C11 cysteine peptidase with an essential role in organelle replication.	DISCUSS
+4	9	PmC11	protein	The PmC11 structure should provide a good basis for structural modeling and, given the importance of other clan CD enzymes, this work should also advance the exploration of these peptidases and potentially identify new biologically important substrates.	DISCUSS
+10	19	structure	evidence	The PmC11 structure should provide a good basis for structural modeling and, given the importance of other clan CD enzymes, this work should also advance the exploration of these peptidases and potentially identify new biologically important substrates.	DISCUSS
+52	71	structural modeling	experimental_method	The PmC11 structure should provide a good basis for structural modeling and, given the importance of other clan CD enzymes, this work should also advance the exploration of these peptidases and potentially identify new biologically important substrates.	DISCUSS
+107	122	clan CD enzymes	protein_type	The PmC11 structure should provide a good basis for structural modeling and, given the importance of other clan CD enzymes, this work should also advance the exploration of these peptidases and potentially identify new biologically important substrates.	DISCUSS
+179	189	peptidases	protein_type	The PmC11 structure should provide a good basis for structural modeling and, given the importance of other clan CD enzymes, this work should also advance the exploration of these peptidases and potentially identify new biologically important substrates.	DISCUSS