4L3T | pdb_00004l3t

Crystal Structure of Substrate-free Human Presequence Protease

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
Protein Modification Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	Peptidase_C30	e4l3tB1	A: alpha bundles	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Peptidase_C30	ECOD (develop294)
B	PRDM2_PR	e4l3tB5	A: alpha bundles	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: PRDM2_PR	ECOD (develop294)
A	CBS	e4l3tA1	A: alpha bundles	X: Thioredoxin-like	H: ClpP/crotonase	T: ClpP/crotonase	F: CBS	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.30.830.10	Alpha Beta	2-Layer Sandwich	Cytochrome Bc1 Complex	Chain A, domain 1	CATH (4.3.0)
A	3.30.830.10	Alpha Beta	2-Layer Sandwich	Cytochrome Bc1 Complex	Chain A, domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B	PF05193	Peptidase M16 inactive domain (Peptidase_M16_C)	Peptidase M16 inactive domain	Peptidase M16 consists of two structurally related domains. One is the active peptidase, whereas the other is inactive. The two domains hold the substrate like a clamp [1].	Domain
B	PF08367	Peptidase M16C associated (M16C_assoc)	Peptidase M16C associated	-	Family
B	PF22516	PreP C-terminal domain (PreP_C)	PreP C-terminal domain	PreP is a protease that degrades targeting peptides as well as other unstructured peptides in both mitochondria and chloroplasts. This entry represents the C-terminal domain of PreP and related proteins.	Domain
B	PF00675	Insulinase (Peptidase family M16) (Peptidase_M16)	Insulinase (Peptidase family M16)	-	Family
A	PF05193	Peptidase M16 inactive domain (Peptidase_M16_C)	Peptidase M16 inactive domain	Peptidase M16 consists of two structurally related domains. One is the active peptidase, whereas the other is inactive. The two domains hold the substrate like a clamp [1].	Domain
A	PF08367	Peptidase M16C associated (M16C_assoc)	Peptidase M16C associated	-	Family
A	PF22516	PreP C-terminal domain (PreP_C)	PreP C-terminal domain	PreP is a protease that degrades targeting peptides as well as other unstructured peptides in both mitochondria and chloroplasts. This entry represents the C-terminal domain of PreP and related proteins.	Domain
A	PF00675	Insulinase (Peptidase family M16) (Peptidase_M16)	Insulinase (Peptidase family M16)	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	Presequence protease, mitochondrial	peptidase activity catalytic activity, acting on a protein metallopeptidase activity hydrolase activity catalytic activity enzyme regulator activity enzyme activator activity molecular function activator activity molecular function regulator activity metalloendopeptidase activity endopeptidase activity cation binding transition metal ion binding zinc ion binding peptidase activity catalytic activity, acting on a protein metallopeptidase activity hydrolase activity catalytic activity enzyme regulator activity enzyme activator activity molecular function activator activity molecular function regulator activity metalloendopeptidase activity endopeptidase activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding	primary metabolic process gene expression macromolecule biosynthetic process protein maturation biosynthetic process proteolysis protein processing metabolic process cellular process protein metabolic process macromolecule metabolic process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle membrane-enclosed lumen mitochondrial matrix intracellular organelle lumen organelle lumen
A	Presequence protease, mitochondrial	peptidase activity catalytic activity, acting on a protein metallopeptidase activity hydrolase activity catalytic activity enzyme regulator activity enzyme activator activity molecular function activator activity molecular function regulator activity metalloendopeptidase activity endopeptidase activity cation binding transition metal ion binding zinc ion binding peptidase activity catalytic activity, acting on a protein metallopeptidase activity hydrolase activity catalytic activity enzyme regulator activity enzyme activator activity molecular function activator activity molecular function regulator activity metalloendopeptidase activity endopeptidase activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding	primary metabolic process gene expression macromolecule biosynthetic process protein maturation biosynthetic process proteolysis protein processing metabolic process cellular process protein metabolic process macromolecule metabolic process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle membrane-enclosed lumen mitochondrial matrix intracellular organelle lumen organelle lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR007863	Peptidase M16, C-terminal	Domain
B	IPR013578	Peptidase M16C associated	Domain
B	IPR011249	Metalloenzyme, LuxS/M16 peptidase-like	Homologous Superfamily
B	IPR055130	Presequence protease, mitochondrial-type, C-terminal domain	Domain
B	IPR011765	Peptidase M16, N-terminal	Domain
A	IPR007863	Peptidase M16, C-terminal	Domain
A	IPR013578	Peptidase M16C associated	Domain
A	IPR011249	Metalloenzyme, LuxS/M16 peptidase-like	Homologous Superfamily
A	IPR055130	Presequence protease, mitochondrial-type, C-terminal domain	Domain
A	IPR011765	Peptidase M16, N-terminal	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B	Pharos: Q5JRX3	malignant glioma osteosarcoma Mitochondrial Diseases ovarian cancer neurodegenerative disease Pick disease
A	Pharos: Q5JRX3	malignant glioma osteosarcoma Mitochondrial Diseases ovarian cancer neurodegenerative disease Pick disease

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B	CAS	Parent Component: CYS
B	MLY	Parent Component: LYS RESID: AA0075 PSI-MOD : N6,N6-dimethyl-L-lysine MOD:00084
B	MLZ	Parent Component: LYS RESID: AA0075 , AA0076 PSI-MOD : N6,N6-dimethyl-L-lysine MOD:00084 , N6-methyl-L-lysine MOD:00085
A	CAS	Parent Component: CYS RESID: AA0075 , AA0076
A	MLY	Parent Component: LYS RESID: AA0075 , AA0076 , AA0075 PSI-MOD : N6,N6-dimethyl-L-lysine MOD:00084 , N6-methyl-L-lysine MOD:00085 , N6,N6-dimethyl-L-lysine MOD:00084
A	MLZ	Parent Component: LYS RESID: AA0075 , AA0076 , AA0075 , AA0076 PSI-MOD : N6,N6-dimethyl-L-lysine MOD:00084 , N6-methyl-L-lysine MOD:00085 , N6,N6-dimethyl-L-lysine MOD:00084 , N6-methyl-L-lysine MOD:00085

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.