5M4G | pdb_00005m4g

Crystal Structure of Wild-Type Human Prolidase with Mn ions

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Structure Motif: Primary M-CSA Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A		e5m4gA1	A: gH main domain	X: gH main domain	H: gH main domain	T: Tubulin_C	F:	ECOD (20:10:01)
B		e5m4gB1	A: gH main domain	X: gH main domain	H: gH main domain	T: Tubulin_C	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.350.10	Alpha Beta	3-Layer(aba) Sandwich	Creatine Amidinohydrolase	Chain A, domain 1	CATH (4.3.0)
A	3.90.230.10	Alpha Beta	Alpha-Beta Complex	Creatine Amidinohydrolase	Creatinase/methionine aminopeptidase superfamily	CATH (4.3.0)
B	3.40.350.10	Alpha Beta	3-Layer(aba) Sandwich	Creatine Amidinohydrolase	Chain A, domain 1	CATH (4.3.0)
B	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, B	PF05195	Aminopeptidase P, N-terminal domain (AMP_N)	Aminopeptidase P, N-terminal domain	This domain is structurally very similar [1] to the creatinase N-terminal domain (Pfam:PF01321). However, little or no sequence similarity exists between the two families.	Domain
A, B	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Xaa-Pro dipeptidase	peptidase activity catalytic activity, acting on a protein metallocarboxypeptidase activity hydrolase activity metallopeptidase activity exopeptidase activity catalytic activity metalloexopeptidase activity carboxypeptidase activity proline dipeptidase activity dipeptidase activity cation binding manganese ion binding transition metal ion binding peptidase activity catalytic activity, acting on a protein metallocarboxypeptidase activity hydrolase activity metallopeptidase activity exopeptidase activity catalytic activity metalloexopeptidase activity carboxypeptidase activity proline dipeptidase activity dipeptidase activity cation binding manganese ion binding transition metal ion binding ion binding binding metal ion binding small molecule binding aminopeptidase activity metalloaminopeptidase activity	collagen catabolic process catabolic process metabolic process cellular process collagen metabolic process proteolysis primary metabolic process protein metabolic process macromolecule metabolic process regulation of biological process regulation of cellular process negative regulation of programmed cell death biological regulation negative regulation of cellular process collagen catabolic process catabolic process metabolic process cellular process collagen metabolic process proteolysis primary metabolic process protein metabolic process macromolecule metabolic process regulation of biological process regulation of cellular process negative regulation of programmed cell death biological regulation negative regulation of cellular process negative regulation of biological process regulation of programmed cell death cell death programmed cell death amino acid metabolic process	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR001131	Peptidase M24B, X-Pro dipeptidase/aminopeptidase P, conserved site	Conserved Site
A, B	IPR007865	Aminopeptidase P, N-terminal	Domain
A, B	IPR029149	Creatinase/Aminopeptidase P/Spt16, N-terminal	Homologous Superfamily
A, B	IPR052433	Xaa-Pro dipeptidase-like	Family
A, B	IPR036005	Creatinase/aminopeptidase-like	Homologous Superfamily
A, B	IPR000994	Peptidase M24	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: P12955	prolidase deficiency Skin Ulcer type 2 diabetes mellitus astrocytic tumor glioblastoma intellectual disability pancreatic intraductal papillary-mucinous carcinoma respiratory system disease diabetes mellitus maturity-onset diabetes of the young ovarian cancer pancreatic intraductal papillary-mucinous neoplasm tuberculosis non-alcoholic fatty liver disease pancreatic ductal adenocarcinoma

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A	Prolidase (Xaa-Pro dipeptidase) M-CSA #1001	Prolidase is a ubiquitously distributed dipeptidase and the only known metalloenzyme in humans capable of cleaving the peptide bond preceding the amino acids proline (Pro) or hydroxyproline (Hyp) in Xaa-Pro (Xaa: any hydrophobic amino acid) dipeptides. Prolidase plays an important role in the degradation of dietary and endogenous proteins to recycle Pro for protein synthesis. Moreover, it's also involved in hydrolysis of Pro- and hydroxyproline-containing dipeptides in the last step of collagen catabolism. Diminished or absent prolidase activity is related to a rare autosomal disease, referred to as prolidase deficiency.	Defined by 8 residues: HIS:A-250 [auth A-255]ASP:A-271 [auth A-276]ASP:A-282 [auth A-287]HIS:A-365 [auth A-370]HIS:A-372 [auth A-377]ARG:A-393 [auth A-398]GLU:A-407 [auth A-412]GLU:A-447 [auth A-452] \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 3.4.13.9 (PDB Primary Data) Search M-CSA Motif + EC 3.4.13.9

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.