1HR6

Yeast Mitochondrial Processing Peptidase

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Structure Motif: Primary M-CSA Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1hr6a1	Alpha and beta proteins (a+b)	LuxS/MPP-like metallohydrolase	LuxS/MPP-like metallohydrolase	MPP-like	Mitochondrial processing peptidase (MPP) alpha chain	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
C	d1hr6c1	Alpha and beta proteins (a+b)	LuxS/MPP-like metallohydrolase	LuxS/MPP-like metallohydrolase	MPP-like	Mitochondrial processing peptidase (MPP) alpha chain	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
E	d1hr6e1	Alpha and beta proteins (a+b)	LuxS/MPP-like metallohydrolase	LuxS/MPP-like metallohydrolase	MPP-like	Mitochondrial processing peptidase (MPP) alpha chain	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
G	d1hr6g1	Alpha and beta proteins (a+b)	LuxS/MPP-like metallohydrolase	LuxS/MPP-like metallohydrolase	MPP-like	Mitochondrial processing peptidase (MPP) alpha chain	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
D	d1hr6d1	Alpha and beta proteins (a+b)	LuxS/MPP-like metallohydrolase	LuxS/MPP-like metallohydrolase	MPP-like	Mitochondrial processing peptidase (MPP) beta chain	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
D	d1hr6d3	Artifacts	Tags	Tags	Tags	N-terminal Tags	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
F	d1hr6f1	Alpha and beta proteins (a+b)	LuxS/MPP-like metallohydrolase	LuxS/MPP-like metallohydrolase	MPP-like	Mitochondrial processing peptidase (MPP) beta chain	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
F	d1hr6f3	Artifacts	Tags	Tags	Tags	N-terminal Tags	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
H	d1hr6h1	Alpha and beta proteins (a+b)	LuxS/MPP-like metallohydrolase	LuxS/MPP-like metallohydrolase	MPP-like	Mitochondrial processing peptidase (MPP) beta chain	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
B	d1hr6b1	Alpha and beta proteins (a+b)	LuxS/MPP-like metallohydrolase	LuxS/MPP-like metallohydrolase	MPP-like	Mitochondrial processing peptidase (MPP) beta chain	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	MPP-like	8020875	4002871	SCOP2 (2022-06-29)
A	SCOP2 Family	MPP-like	8020877	4002871	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	LuxS/MPP-like metallohydrolase	8033255	3001831	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	LuxS/MPP-like metallohydrolase	8033257	3001831	SCOP2 (2022-06-29)
C	SCOP2B Superfamily	LuxS/MPP-like metallohydrolase	8033255	3001831	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	LuxS/MPP-like metallohydrolase	8033257	3001831	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	LuxS/MPP-like metallohydrolase	8033255	3001831	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	LuxS/MPP-like metallohydrolase	8033257	3001831	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	LuxS/MPP-like metallohydrolase	8033257	3001831	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	LuxS/MPP-like metallohydrolase	8033255	3001831	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	LuxS/MPP-like metallohydrolase	8033258	3001831	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	LuxS/MPP-like metallohydrolase	8033259	3001831	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	LuxS/MPP-like metallohydrolase	8033259	3001831	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	LuxS/MPP-like metallohydrolase	8033258	3001831	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	LuxS/MPP-like metallohydrolase	8033259	3001831	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	LuxS/MPP-like metallohydrolase	8033258	3001831	SCOP2B (2022-06-29)
B	SCOP2 Family	MPP-like	8020878	4002871	SCOP2 (2022-06-29)
B	SCOP2 Family	MPP-like	8020879	4002871	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	LuxS/MPP-like metallohydrolase	8033258	3001831	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	LuxS/MPP-like metallohydrolase	8033259	3001831	SCOP2 (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	Peptidase_M16_C	e1hr6A2	A: a+b two layers	X: LuxS, MPP, ThrRS/AlaRS common domain	H: LuxS, MPP, ThrRS/AlaRS common domain	T: LuxS/MPP-like metallohydrolase	F: Peptidase_M16_C	ECOD (1.6)
A	Peptidase_M16	e1hr6A1	A: a+b two layers	X: LuxS, MPP, ThrRS/AlaRS common domain	H: LuxS, MPP, ThrRS/AlaRS common domain	T: LuxS/MPP-like metallohydrolase	F: Peptidase_M16	ECOD (1.6)
C	Peptidase_M16_C	e1hr6C2	A: a+b two layers	X: LuxS, MPP, ThrRS/AlaRS common domain	H: LuxS, MPP, ThrRS/AlaRS common domain	T: LuxS/MPP-like metallohydrolase	F: Peptidase_M16_C	ECOD (1.6)
C	Peptidase_M16	e1hr6C1	A: a+b two layers	X: LuxS, MPP, ThrRS/AlaRS common domain	H: LuxS, MPP, ThrRS/AlaRS common domain	T: LuxS/MPP-like metallohydrolase	F: Peptidase_M16	ECOD (1.6)
E	Peptidase_M16_C	e1hr6E2	A: a+b two layers	X: LuxS, MPP, ThrRS/AlaRS common domain	H: LuxS, MPP, ThrRS/AlaRS common domain	T: LuxS/MPP-like metallohydrolase	F: Peptidase_M16_C	ECOD (1.6)
E	Peptidase_M16	e1hr6E1	A: a+b two layers	X: LuxS, MPP, ThrRS/AlaRS common domain	H: LuxS, MPP, ThrRS/AlaRS common domain	T: LuxS/MPP-like metallohydrolase	F: Peptidase_M16	ECOD (1.6)
G	Peptidase_M16_C	e1hr6G2	A: a+b two layers	X: LuxS, MPP, ThrRS/AlaRS common domain	H: LuxS, MPP, ThrRS/AlaRS common domain	T: LuxS/MPP-like metallohydrolase	F: Peptidase_M16_C	ECOD (1.6)
G	Peptidase_M16	e1hr6G1	A: a+b two layers	X: LuxS, MPP, ThrRS/AlaRS common domain	H: LuxS, MPP, ThrRS/AlaRS common domain	T: LuxS/MPP-like metallohydrolase	F: Peptidase_M16	ECOD (1.6)
D	Peptidase_M16_C	e1hr6D1	A: a+b two layers	X: LuxS, MPP, ThrRS/AlaRS common domain	H: LuxS, MPP, ThrRS/AlaRS common domain	T: LuxS/MPP-like metallohydrolase	F: Peptidase_M16_C	ECOD (1.6)
D	Peptidase_M16	e1hr6D2	A: a+b two layers	X: LuxS, MPP, ThrRS/AlaRS common domain	H: LuxS, MPP, ThrRS/AlaRS common domain	T: LuxS/MPP-like metallohydrolase	F: Peptidase_M16	ECOD (1.6)
F	Peptidase_M16_C	e1hr6F1	A: a+b two layers	X: LuxS, MPP, ThrRS/AlaRS common domain	H: LuxS, MPP, ThrRS/AlaRS common domain	T: LuxS/MPP-like metallohydrolase	F: Peptidase_M16_C	ECOD (1.6)
F	Peptidase_M16	e1hr6F2	A: a+b two layers	X: LuxS, MPP, ThrRS/AlaRS common domain	H: LuxS, MPP, ThrRS/AlaRS common domain	T: LuxS/MPP-like metallohydrolase	F: Peptidase_M16	ECOD (1.6)
H	Peptidase_M16_C	e1hr6H1	A: a+b two layers	X: LuxS, MPP, ThrRS/AlaRS common domain	H: LuxS, MPP, ThrRS/AlaRS common domain	T: LuxS/MPP-like metallohydrolase	F: Peptidase_M16_C	ECOD (1.6)
H	Peptidase_M16	e1hr6H2	A: a+b two layers	X: LuxS, MPP, ThrRS/AlaRS common domain	H: LuxS, MPP, ThrRS/AlaRS common domain	T: LuxS/MPP-like metallohydrolase	F: Peptidase_M16	ECOD (1.6)
B	Peptidase_M16_C	e1hr6B1	A: a+b two layers	X: LuxS, MPP, ThrRS/AlaRS common domain	H: LuxS, MPP, ThrRS/AlaRS common domain	T: LuxS/MPP-like metallohydrolase	F: Peptidase_M16_C	ECOD (1.6)
B	Peptidase_M16	e1hr6B2	A: a+b two layers	X: LuxS, MPP, ThrRS/AlaRS common domain	H: LuxS, MPP, ThrRS/AlaRS common domain	T: LuxS/MPP-like metallohydrolase	F: Peptidase_M16	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.830.10	Alpha Beta	2-Layer Sandwich	Cytochrome Bc1 Complex	Chain A, domain 1	CATH (4.3.0)
C	3.30.830.10	Alpha Beta	2-Layer Sandwich	Cytochrome Bc1 Complex	Chain A, domain 1	CATH (4.3.0)
E	3.30.830.10	Alpha Beta	2-Layer Sandwich	Cytochrome Bc1 Complex	Chain A, domain 1	CATH (4.3.0)
G	3.30.830.10	Alpha Beta	2-Layer Sandwich	Cytochrome Bc1 Complex	Chain A, domain 1	CATH (4.3.0)
D	3.30.830.10	Alpha Beta	2-Layer Sandwich	Cytochrome Bc1 Complex	Chain A, domain 1	CATH (4.3.0)
F	3.30.830.10	Alpha Beta	2-Layer Sandwich	Cytochrome Bc1 Complex	Chain A, domain 1	CATH (4.3.0)
H	3.30.830.10	Alpha Beta	2-Layer Sandwich	Cytochrome Bc1 Complex	Chain A, domain 1	CATH (4.3.0)
B	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
A, C, E, G	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, C, E, G	PF00675	Insulinase (Peptidase family M16) (Peptidase_M16)	Insulinase (Peptidase family M16)	-	Family
B, D, F, H	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, D, F, H	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
A, C, E, G	MITOCHONDRIAL PROCESSING PEPTIDASE ALPHA SUBUNIT	endopeptidase activator activity enzyme regulator activity enzyme activator activity peptidase regulator activity molecular function activator activity molecular function regulator activity peptidase activator activity endopeptidase regulator activity cation binding ion binding binding metal ion binding small molecule binding peptidase activity endopeptidase activator activity enzyme regulator activity enzyme activator activity peptidase regulator activity molecular function activator activity molecular function regulator activity peptidase activator activity endopeptidase regulator activity cation binding ion binding binding metal ion binding small molecule binding peptidase activity catalytic activity, acting on a protein metalloendopeptidase activity hydrolase activity metallopeptidase activity catalytic activity endopeptidase activity	protein localization establishment of protein localization cellular localization cellular biosynthetic process protein targeting protein processing involved in protein targeting to mitochondrion protein maturation localization organic substance metabolic process proteolysis cellular macromolecule localization organic substance biosynthetic process protein metabolic process organonitrogen compound metabolic process protein localization establishment of protein localization cellular localization cellular biosynthetic process protein targeting protein processing involved in protein targeting to mitochondrion protein maturation localization organic substance metabolic process proteolysis cellular macromolecule localization organic substance biosynthetic process protein metabolic process organonitrogen compound metabolic process cellular metabolic process primary metabolic process gene expression establishment of localization macromolecule biosynthetic process establishment of protein localization to organelle mitochondrial protein processing biosynthetic process macromolecule localization protein localization to organelle protein localization to mitochondrion protein targeting to mitochondrion protein processing cellular process metabolic process macromolecule metabolic process establishment of protein localization to mitochondrion	membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle membrane-enclosed lumen mitochondrial matrix intracellular organelle lumen organelle lumen mitochondrial protein-containing complex protein-containing complex membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle membrane-enclosed lumen mitochondrial matrix intracellular organelle lumen organelle lumen mitochondrial protein-containing complex protein-containing complex catalytic complex mitochondrial processing peptidase complex
B, D, F, H	MITOCHONDRIAL PROCESSING PEPTIDASE BETA SUBUNIT	cation binding ion binding binding metal ion binding small molecule binding peptidase activity catalytic activity, acting on a protein metalloendopeptidase activity hydrolase activity metallopeptidase activity catalytic activity endopeptidase activity	protein localization establishment of protein localization cellular localization cellular biosynthetic process protein targeting protein processing involved in protein targeting to mitochondrion protein maturation localization organic substance metabolic process proteolysis cellular macromolecule localization organic substance biosynthetic process protein metabolic process organonitrogen compound metabolic process protein localization establishment of protein localization cellular localization cellular biosynthetic process protein targeting protein processing involved in protein targeting to mitochondrion protein maturation localization organic substance metabolic process proteolysis cellular macromolecule localization organic substance biosynthetic process protein metabolic process organonitrogen compound metabolic process cellular metabolic process primary metabolic process gene expression establishment of localization macromolecule biosynthetic process establishment of protein localization to organelle mitochondrial protein processing biosynthetic process macromolecule localization protein localization to organelle protein localization to mitochondrion protein targeting to mitochondrion protein processing cellular process metabolic process macromolecule metabolic process establishment of protein localization to mitochondrion	membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle membrane-enclosed lumen mitochondrial matrix intracellular organelle lumen organelle lumen mitochondrial protein-containing complex protein-containing complex membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle membrane-enclosed lumen mitochondrial matrix intracellular organelle lumen organelle lumen mitochondrial protein-containing complex protein-containing complex catalytic complex mitochondrial processing peptidase complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C, E, G	IPR007863	Peptidase M16, C-terminal	Domain
A, C, E, G	IPR011765	Peptidase M16, N-terminal	Domain
A, C, E, G	IPR011249	Metalloenzyme, LuxS/M16 peptidase-like	Homologous Superfamily
A, C, E, G	IPR001431	Peptidase M16, zinc-binding site	Binding Site
B, D, F, H	IPR007863	Peptidase M16, C-terminal	Domain
B, D, F, H	IPR011765	Peptidase M16, N-terminal	Domain
B, D, F, H	IPR011249	Metalloenzyme, LuxS/M16 peptidase-like	Homologous Superfamily
B, D, F, H	IPR001431	Peptidase M16, zinc-binding site	Binding Site

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

Chains	Enzyme Name	Description	Catalytic Residues
B	mitochondrial processing peptidase M-CSA #657	Mitochondrial processing peptidase is a metalloendopeptidase that cleaves N-terminal signal sequences of proteins produced from nuclear information, transported from the cytosol to mitochondria. Cleavage of the signal sequence occurs at a single specific site. The enzyme shows functional and structural convergent evolution of this protease family with that of thermolysin, which has a very similar active site.	Defined by 5 residues: HIS:B-51 [auth B-70]GLU:B-54 [auth B-73]HIS:B-55 [auth B-74]GLU:B-124 [auth B-143]GLU:B-131 [auth B-150] \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 3.4.24.64 (PDB Primary Data) Search M-CSA Motif + EC 3.4.24.64