5JCM | pdb_00005jcm

Structure and catalytic mechanism of monodehydroascorbate reductase, MDHAR, from Oryza sativa L. japonica

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	KOG1336	e5jcmA1	A: a+b two layers	X: FAD-linked reductases, C-terminal domain-like	H: FAD/NAD-linked reduatases, dimerisation (C-terminal) domain (From Topology)	T: FAD/NAD-linked reduatases, dimerisation (C-terminal) domain	F: KOG1336	ECOD (1.6)
A	Pyr_redox_2_1	e5jcmA2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: FAD/NAD(P)-binding domain	F: Pyr_redox_2_1	ECOD (1.6)
A	Pyr_redox_2	e5jcmA3	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: FAD/NAD(P)-binding domain	F: Pyr_redox_2	ECOD (1.6)
B	KOG1336	e5jcmB1	A: a+b two layers	X: FAD-linked reductases, C-terminal domain-like	H: FAD/NAD-linked reduatases, dimerisation (C-terminal) domain (From Topology)	T: FAD/NAD-linked reduatases, dimerisation (C-terminal) domain	F: KOG1336	ECOD (1.6)
B	Pyr_redox_2_1	e5jcmB2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: FAD/NAD(P)-binding domain	F: Pyr_redox_2_1	ECOD (1.6)
B	Pyr_redox_2	e5jcmB3	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: FAD/NAD(P)-binding domain	F: Pyr_redox_2	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.50.50.60	Alpha Beta	3-Layer(bba) Sandwich	FAD/NAD(P)-binding domain	FAD/NAD(P)-binding domain	CATH (4.3.0)
A	3.30.390.30	Alpha Beta	2-Layer Sandwich	Enolase-like	domain 1	CATH (4.3.0)
B	3.50.50.60	Alpha Beta	3-Layer(bba) Sandwich	FAD/NAD(P)-binding domain	FAD/NAD(P)-binding domain	CATH (4.3.0)
B	3.30.390.30	Alpha Beta	2-Layer Sandwich	Enolase-like	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF07992	Pyridine nucleotide-disulphide oxidoreductase (Pyr_redox_2)	Pyridine nucleotide-disulphide oxidoreductase	This family includes both class I and class II oxidoreductases and also NADH oxidases and peroxidases. This domain is actually a small NADH binding domain within a larger FAD binding domain.	Domain
A, B	PF21791	Monodehydroascorbate reductase 3-like, C-terminal domain (MDHAR3-like_C)	Monodehydroascorbate reductase 3-like, C-terminal domain	This domain is found at the C-terminal end of Monodehydroascorbate reductase 3 (MDHAR3) from Oryza sativa and similar plant sequences. MDHAR3 transfers an electron directly to its substrate, monodehydroascorbate (MDHA), which binds to its active site ...	This domain is found at the C-terminal end of Monodehydroascorbate reductase 3 (MDHAR3) from Oryza sativa and similar plant sequences. MDHAR3 transfers an electron directly to its substrate, monodehydroascorbate (MDHA), which binds to its active site pocket. It consists of three domains: an NAD(P)-binding domain, an FAD-binding domain, and a C-terminal domain (this entry) [1]. This domain shows an alpha-beta structure.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Os09g0567300 protein	RNA binding binding nucleic acid binding mRNA binding oxidoreductase activity oxidoreductase activity, acting on NAD(P)H catalytic activity nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding monodehydroascorbate reductase (NADH) activity oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor	cellular response to stimulus cellular detoxification cellular response to chemical stimulus response to stimulus response to chemical detoxification cellular process cellular oxidant detoxification cellular response to toxic substance response to toxic substance	cellular anatomical structure intracellular anatomical structure cytoplasm peroxisomal matrix membrane-bounded organelle peroxisome membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle organelle lumen organelle microbody lumen microbody

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR048618	Monodehydroascorbate reductase 3-like, C-terminal domain	Domain
A, B	IPR023753	FAD/NAD(P)-binding domain	Domain
A, B	IPR016156	FAD/NAD-linked reductase, dimerisation domain superfamily	Homologous Superfamily
A, B	IPR036188	FAD/NAD(P)-binding domain superfamily	Homologous Superfamily
A, B	IPR050446	FAD-dependent Oxidoreductases and Apoptosis Regulators	Family

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.