1HR9 | pdb_00001hr9

Yeast Mitochondrial Processing Peptidase beta-E73Q Mutant Complexed with Malate Dehydrogenase Signal Peptide

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
H	d1hr9h1	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	d1hr9f1	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	d1hr9f3	Artifacts	Tags	Tags	Tags	N-terminal Tags	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
D	d1hr9d1	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	d1hr9b1	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)
G	d1hr9g1	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	d1hr9e1	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	d1hr9c1	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)
A	d1hr9a1	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)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
H	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)
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)
D	SCOP2B Superfamily	LuxS/MPP-like metallohydrolase	8033259	3001831	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	LuxS/MPP-like metallohydrolase	8033258	3001831	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	LuxS/MPP-like metallohydrolase	8033258	3001831	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	LuxS/MPP-like metallohydrolase	8033259	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)
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)
C	SCOP2B Superfamily	LuxS/MPP-like metallohydrolase	8033257	3001831	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	LuxS/MPP-like metallohydrolase	8033255	3001831	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	LuxS/MPP-like metallohydrolase	8033255	3001831	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	LuxS/MPP-like metallohydrolase	8033257	3001831	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)
H	Peptidase_M16_C	e1hr9H1	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	e1hr9H2	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	e1hr9F1	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	e1hr9F2	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	e1hr9D1	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	e1hr9D2	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	e1hr9B1	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	e1hr9B2	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	e1hr9G2	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	e1hr9G1	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	e1hr9E2	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	e1hr9E1	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	e1hr9C2	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	e1hr9C1	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)
A	Peptidase_M16_C	e1hr9A2	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	e1hr9A1	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)
H	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)
D	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)
G	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)
C	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, 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
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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
I [auth O], J [auth P], K [auth Q], L [auth R]	MALATE DEHYDROGENASE	L-malate dehydrogenase (NAD+) activity oxidoreductase activity oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor oxidoreductase activity, acting on CH-OH group of donors malate dehydrogenase activity catalytic activity RNA binding binding nucleic acid binding mRNA binding	aerobic respiration cellular respiration tricarboxylic acid cycle energy derivation by oxidation of organic compounds primary metabolic process metabolic process cellular process generation of precursor metabolites and energy oxoacid metabolic process malate metabolic process dicarboxylic acid metabolic process carboxylic acid metabolic process small molecule metabolic process organic acid 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
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	establishment of protein localization protein targeting primary metabolic process protein processing involved in protein targeting to mitochondrion gene expression establishment of localization macromolecule biosynthetic process protein maturation localization establishment of protein localization to organelle mitochondrial protein processing biosynthetic process proteolysis protein targeting to mitochondrion establishment of protein localization protein targeting primary metabolic process protein processing involved in protein targeting to mitochondrion gene expression establishment of localization macromolecule biosynthetic process protein maturation localization establishment of protein localization to organelle mitochondrial protein processing biosynthetic process proteolysis protein targeting to mitochondrion protein processing metabolic process cellular process protein metabolic process macromolecule metabolic process establishment of protein localization to mitochondrion	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 mitochondrial protein-containing complex protein-containing complex 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 mitochondrial protein-containing complex protein-containing complex catalytic complex peptidase complex mitochondrial processing peptidase complex endopeptidase complex
A, C, E, G	MITOCHONDRIAL PROCESSING PEPTIDASE ALPHA SUBUNIT	peptidase activity catalytic activity, acting on a protein metalloendopeptidase activity hydrolase activity metallopeptidase activity catalytic activity endopeptidase activity endopeptidase activator activity enzyme regulator activity enzyme activator activity peptidase regulator activity molecular function activator activity molecular function regulator activity peptidase activator activity peptidase activity catalytic activity, acting on a protein metalloendopeptidase activity hydrolase activity metallopeptidase activity catalytic activity endopeptidase 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	establishment of protein localization protein targeting primary metabolic process protein processing involved in protein targeting to mitochondrion gene expression establishment of localization macromolecule biosynthetic process protein maturation localization establishment of protein localization to organelle mitochondrial protein processing biosynthetic process proteolysis protein targeting to mitochondrion establishment of protein localization protein targeting primary metabolic process protein processing involved in protein targeting to mitochondrion gene expression establishment of localization macromolecule biosynthetic process protein maturation localization establishment of protein localization to organelle mitochondrial protein processing biosynthetic process proteolysis protein targeting to mitochondrion protein processing metabolic process cellular process protein metabolic process macromolecule metabolic process establishment of protein localization to mitochondrion	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 mitochondrial protein-containing complex protein-containing complex 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 mitochondrial protein-containing complex protein-containing complex catalytic complex peptidase complex mitochondrial processing peptidase complex endopeptidase complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
I [auth O], J [auth P], K [auth Q], L [auth R]	IPR015955	Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal	Homologous Superfamily
I [auth O], J [auth P], K [auth Q], L [auth R]	IPR001252	Malate dehydrogenase, active site	Active Site
I [auth O], J [auth P], K [auth Q], L [auth R]	IPR001557	L-lactate/malate dehydrogenase	Family
I [auth O], J [auth P], K [auth Q], L [auth R]	IPR010097	Malate dehydrogenase, type 1	Family
I [auth O], J [auth P], K [auth Q], L [auth R]	IPR001236	Lactate/malate dehydrogenase, N-terminal	Domain
I [auth O], J [auth P], K [auth Q], L [auth R]	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
I [auth O], J [auth P], K [auth Q], L [auth R]	IPR022383	Lactate/malate dehydrogenase, C-terminal	Domain
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	IPR050361	Mitochondrial Processing Peptidase/Ubiquinol-cytochrome c Reductase Complex	Family
B, D, F, H	IPR001431	Peptidase M16, zinc-binding site	Binding Site
A, C, E, G	IPR007863	Peptidase M16, C-terminal	Domain
A, C, E, G	IPR011249	Metalloenzyme, LuxS/M16 peptidase-like	Homologous Superfamily
A, C, E, G	IPR050361	Mitochondrial Processing Peptidase/Ubiquinol-cytochrome c Reductase Complex	Family
A, C, E, G	IPR011765	Peptidase M16, N-terminal	Domain
A, C, E, G	IPR001431	Peptidase M16, zinc-binding site	Binding Site

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.