1PJ3

Crystal structure of human mitochondrial NAD(P)+-dependent malic enzyme in a pentary complex with natural substrate pyruvate, cofactor NAD+, Mn++, and allosteric activator fumarate.

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
Pharos: Disease Associations

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1pj3a1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Aminoacid dehydrogenase-like, C-terminal domain	Mitochondrial NAD(P)-dependent malic enzyme	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d1pj3a2	Alpha and beta proteins (a/b)	Aminoacid dehydrogenase-like, N-terminal domain	Aminoacid dehydrogenase-like, N-terminal domain	Malic enzyme N-domain	Mitochondrial NAD(P)-dependent malic enzyme	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d1pj3b1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Aminoacid dehydrogenase-like, C-terminal domain	Mitochondrial NAD(P)-dependent malic enzyme	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d1pj3b2	Alpha and beta proteins (a/b)	Aminoacid dehydrogenase-like, N-terminal domain	Aminoacid dehydrogenase-like, N-terminal domain	Malic enzyme N-domain	Mitochondrial NAD(P)-dependent malic enzyme	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d1pj3c1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Aminoacid dehydrogenase-like, C-terminal domain	Mitochondrial NAD(P)-dependent malic enzyme	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d1pj3c2	Alpha and beta proteins (a/b)	Aminoacid dehydrogenase-like, N-terminal domain	Aminoacid dehydrogenase-like, N-terminal domain	Malic enzyme N-domain	Mitochondrial NAD(P)-dependent malic enzyme	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d1pj3d1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Aminoacid dehydrogenase-like, C-terminal domain	Mitochondrial NAD(P)-dependent malic enzyme	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d1pj3d2	Alpha and beta proteins (a/b)	Aminoacid dehydrogenase-like, N-terminal domain	Aminoacid dehydrogenase-like, N-terminal domain	Malic enzyme N-domain	Mitochondrial NAD(P)-dependent malic enzyme	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Malate oxidoreductase-like	8056186	4000103	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	MtdA-like	8056187	3000046	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	MtdA-like	8056187	3000046	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	MtdA-like	8056187	3000046	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	MtdA-like	8056187	3000046	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	Malic_M	e1pj3A1	A: alpha arrays	X: C-terminal domain of Malic enzyme (From Topology)	H: C-terminal domain of Malic enzyme (From Topology)	T: C-terminal domain of Malic enzyme	F: Malic_M	ECOD (1.6)
A	Malic_M	e1pj3A2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: Malic_M	ECOD (1.6)
A	malic	e1pj3A3	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Aminoacid dehydrogenase-like, N-terminal domain	F: malic	ECOD (1.6)
B	Malic_M	e1pj3B3	A: alpha arrays	X: C-terminal domain of Malic enzyme (From Topology)	H: C-terminal domain of Malic enzyme (From Topology)	T: C-terminal domain of Malic enzyme	F: Malic_M	ECOD (1.6)
B	Malic_M	e1pj3B1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: Malic_M	ECOD (1.6)
B	malic	e1pj3B2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Aminoacid dehydrogenase-like, N-terminal domain	F: malic	ECOD (1.6)
C	Malic_M	e1pj3C3	A: alpha arrays	X: C-terminal domain of Malic enzyme (From Topology)	H: C-terminal domain of Malic enzyme (From Topology)	T: C-terminal domain of Malic enzyme	F: Malic_M	ECOD (1.6)
C	Malic_M	e1pj3C1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: Malic_M	ECOD (1.6)
C	malic	e1pj3C2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Aminoacid dehydrogenase-like, N-terminal domain	F: malic	ECOD (1.6)
D	Malic_M	e1pj3D3	A: alpha arrays	X: C-terminal domain of Malic enzyme (From Topology)	H: C-terminal domain of Malic enzyme (From Topology)	T: C-terminal domain of Malic enzyme	F: Malic_M	ECOD (1.6)
D	Malic_M	e1pj3D1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: Malic_M	ECOD (1.6)
D	malic	e1pj3D2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Aminoacid dehydrogenase-like, N-terminal domain	F: malic	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.10380	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Malic enzyme, N-terminal domain	CATH (4.3.0)
A	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
B	3.40.50.10380	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Malic enzyme, N-terminal domain	CATH (4.3.0)
B	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
C	3.40.50.10380	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Malic enzyme, N-terminal domain	CATH (4.3.0)
C	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
D	3.40.50.10380	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Malic enzyme, N-terminal domain	CATH (4.3.0)
D	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF00390	Malic enzyme, N-terminal domain (malic)	Malic enzyme, N-terminal domain	-	Domain
A, B, C, D	PF03949	Malic enzyme, NAD binding domain (Malic_M)	Malic enzyme, NAD binding domain	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	NAD-dependent malic enzyme, mitochondrial	oxidoreductase activity malate dehydrogenase (decarboxylating) (NADP+) 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 malic enzyme activity malate dehydrogenase activity catalytic activity malate dehydrogenase (decarboxylating) (NAD+) activity oxaloacetate decarboxylase activity carboxy-lyase activity lyase activity carbon-carbon lyase activity NAD binding binding oxidoreductase activity malate dehydrogenase (decarboxylating) (NADP+) 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 malic enzyme activity malate dehydrogenase activity catalytic activity malate dehydrogenase (decarboxylating) (NAD+) activity oxaloacetate decarboxylase activity carboxy-lyase activity lyase activity carbon-carbon lyase activity NAD binding binding nucleoside phosphate binding purine nucleotide binding organic cyclic compound binding adenyl nucleotide binding nucleotide binding heterocyclic compound binding small molecule binding electron transfer activity cation binding ion binding metal ion binding	oxoacid metabolic process malate metabolic process cellular metabolic process dicarboxylic acid metabolic process carboxylic acid metabolic process small molecule metabolic process metabolic process cellular process organic acid metabolic process pyruvate metabolic process monocarboxylic acid metabolic process regulation of cellular process regulation of primary metabolic process nucleobase-containing compound metabolic process oxoacid metabolic process malate metabolic process cellular metabolic process dicarboxylic acid metabolic process carboxylic acid metabolic process small molecule metabolic process metabolic process cellular process organic acid metabolic process pyruvate metabolic process monocarboxylic acid metabolic process regulation of cellular process regulation of primary metabolic process nucleobase-containing compound metabolic process purine nucleotide metabolic process regulation of small molecule metabolic process nucleobase-containing small molecule metabolic process regulation of nucleotide metabolic process regulation of phosphate metabolic process phosphate-containing compound metabolic process pyridine-containing compound metabolic process regulation of NADP metabolic process regulation of nucleobase-containing compound metabolic process phosphorus metabolic process pyridine nucleotide metabolic process nucleoside phosphate metabolic process nicotinamide nucleotide metabolic process regulation of biological process biological regulation primary metabolic process regulation of cellular metabolic process nucleotide metabolic process regulation of purine nucleotide metabolic process purine-containing compound metabolic process NADP metabolic process organophosphate metabolic process regulation of phosphorus metabolic process regulation of metabolic process	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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR012302	Malic enzyme, NAD-binding	Domain
A, B, C, D	IPR012301	Malic enzyme, N-terminal domain	Domain
A, B, C, D	IPR046346	Aminoacid dehydrogenase-like, N-terminal domain superfamily	Homologous Superfamily
A, B, C, D	IPR015884	Malic enzyme, conserved site	Conserved Site
A, B, C, D	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
A, B, C, D	IPR037062	Malic enzyme, N-terminal domain superfamily	Homologous Superfamily
A, B, C, D	IPR001891	Malic oxidoreductase	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: P23368	adenoma breast cancer large cell medulloblastoma Manic Disorder osteosarcoma atypical teratoid rhabdoid tumor glioblastoma lymphoplasmacytic lymphoma medulloblastoma ovarian cancer schizophrenia bipolar disorder IgA glomerulonephritis plasma cell myeloma Sjogren syndrome

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.