4S2T

Crystal structure of X-prolyl aminopeptidase from Caenorhabditis elegans: a cytosolic enzyme with a di-nuclear active site

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A [auth P]	SCOP2B Superfamily	Creatinase/prolidase N-terminal domain-like	8054218	3000538	SCOP2B (2022-06-29)
A [auth P]	SCOP2B Superfamily	Peptidase M24 C-terminal domain-like	8054215	3002284	SCOP2B (2022-06-29)
A [auth P]	SCOP2B Superfamily	Creatinase/prolidase N-terminal domain-like	8054216	3000538	SCOP2B (2022-06-29)
A [auth P]	SCOP2B Superfamily	Creatinase/aminopeptidase catalytic domain-like	8054220	3000126	SCOP2B (2022-06-29)
B [auth Q]	SCOP2B Superfamily	Creatinase/prolidase N-terminal domain-like	8054216	3000538	SCOP2B (2022-06-29)
B [auth Q]	SCOP2B Superfamily	Creatinase/aminopeptidase catalytic domain-like	8054220	3000126	SCOP2B (2022-06-29)
B [auth Q]	SCOP2B Superfamily	Creatinase/prolidase N-terminal domain-like	8054218	3000538	SCOP2B (2022-06-29)
B [auth Q]	SCOP2B Superfamily	Peptidase M24 C-terminal domain-like	8054215	3002284	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A [auth P]	Peptidase_M24	e4s2tP2	A: a+b duplicates or obligate multimers	X: Creatinase/aminopeptidase-like	H: Creatinase/aminopeptidase (From Topology)	T: Creatinase/aminopeptidase	F: Peptidase_M24	ECOD (1.6)
A [auth P]	Creatinase_N	e4s2tP3	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Creatinase/prolidase N-terminal domain (From Topology)	T: Creatinase/prolidase N-terminal domain	F: Creatinase_N	ECOD (1.6)
A [auth P]	Creatinase_N_2	e4s2tP1	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Creatinase/prolidase N-terminal domain (From Topology)	T: Creatinase/prolidase N-terminal domain	F: Creatinase_N_2	ECOD (1.6)
B [auth Q]	Peptidase_M24	e4s2tQ3	A: a+b duplicates or obligate multimers	X: Creatinase/aminopeptidase-like	H: Creatinase/aminopeptidase (From Topology)	T: Creatinase/aminopeptidase	F: Peptidase_M24	ECOD (1.6)
B [auth Q]	Creatinase_N	e4s2tQ1	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Creatinase/prolidase N-terminal domain (From Topology)	T: Creatinase/prolidase N-terminal domain	F: Creatinase_N	ECOD (1.6)
B [auth Q]	Creatinase_N_2	e4s2tQ2	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Creatinase/prolidase N-terminal domain (From Topology)	T: Creatinase/prolidase N-terminal domain	F: Creatinase_N_2	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth P]	3.40.350.10	Alpha Beta	3-Layer(aba) Sandwich	Creatine Amidinohydrolase	Chain A, domain 1	CATH (4.3.0)
A [auth P]	3.90.230.10	Alpha Beta	Alpha-Beta Complex	Creatine Amidinohydrolase	Creatinase/methionine aminopeptidase superfamily	CATH (4.3.0)
B [auth Q]	3.40.350.10	Alpha Beta	3-Layer(aba) Sandwich	Creatine Amidinohydrolase	Chain A, domain 1	CATH (4.3.0)
B [auth Q]	3.90.230.10	Alpha Beta	Alpha-Beta Complex	Creatine Amidinohydrolase	Creatinase/methionine aminopeptidase superfamily	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth P], B [auth Q]	PF00557	Metallopeptidase family M24 (Peptidase_M24)	Metallopeptidase family M24	This family contains metallopeptidases. It also contains non-peptidase homologues such as the N terminal domain of Spt16 which is a histone H3-H4 binding module [3].	Domain
A [auth P], B [auth Q]	PF16189	Creatinase/Prolidase N-terminal domain (Creatinase_N_2)	Creatinase/Prolidase N-terminal domain	-	Domain
A [auth P], B [auth Q]	PF16188	C-terminal region of peptidase_M24 (Peptidase_M24_C)	C-terminal region of peptidase_M24	This is a short region at the C-terminus of a number of metallo-peptidases of the M24 family.	Domain
A [auth P], B [auth Q]	PF01321	Creatinase/Prolidase N-terminal domain (Creatinase_N)	Creatinase/Prolidase N-terminal domain	This family includes the N-terminal non-catalytic domains from creatinase and prolidase. The exact function of this domain is uncertain.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth P], B [auth Q]	Protein APP-1	identical protein binding protein binding binding protein homodimerization activity protein dimerization activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding peptidase activity catalytic activity, acting on a protein hydrolase activity identical protein binding protein binding binding protein homodimerization activity protein dimerization activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding peptidase activity catalytic activity, acting on a protein hydrolase activity metallopeptidase activity aminopeptidase activity metalloaminopeptidase activity exopeptidase activity catalytic activity metalloexopeptidase activity	organonitrogen compound catabolic process organonitrogen compound metabolic process catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process organic substance metabolic process proteolysis metabolic process protein metabolic process macromolecule metabolic process organic substance catabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity
C [auth A], D [auth B]	apstatin	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth P], B [auth Q]	IPR000587	Creatinase, N-terminal	Domain
A [auth P], B [auth Q]	IPR029149	Creatinase/Aminopeptidase P/Spt16, N-terminal	Homologous Superfamily
A [auth P], B [auth Q]	IPR033740	Aminopeptidase P	Domain
A [auth P], B [auth Q]	IPR032416	Peptidase M24, C-terminal domain	Domain
A [auth P], B [auth Q]	IPR036005	Creatinase/aminopeptidase-like	Homologous Superfamily
A [auth P], B [auth Q]	IPR000994	Peptidase M24	Domain

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
C [auth A], D [auth B]	01B
C [auth A], D [auth B]	NH2	RESID: AA0081 , AA0083 , AA0084 , AA0086 , AA0087 , AA0088 , AA0090 , AA0091 , AA0092 , AA0093 , AA0095 , AA0096 , AA0097 , AA0098 , AA0099 , AA0100 PSI-MOD : L-alanine amide MOD:00090 , L-asparagine amide MOD:00092 , L-aspartic acid 1-amide MOD:00093 , L-glutamine amide MOD:00095 , L-glutamic acid 1-amide MOD:00096 , glycine amide MOD:00097 , L-isoleucine amide MOD:00099 , L-leucine amide MOD:00100 , L-lysine amide MOD:00101 , L-methionine amide MOD:00102 , L-proline amide MOD:00104 , L-serine amide MOD:00105 , L-threonine amide MOD:00106 , L-tryptophan amide MOD:00107 , L-tyrosine amide MOD:00108 , L-valine amide MOD:00109

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.