4E5K | pdb_00004e5k

Thermostable phosphite dehydrogenase in complex with NAD and sulfite

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	D-2-hydroxyacid dehydrogenase-like	8079258	3000044	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	D-2-hydroxyacid dehydrogenase-like	8079258	3000044	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	D-2-hydroxyacid dehydrogenase-like	8079258	3000044	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	D-2-hydroxyacid dehydrogenase-like	8079258	3000044	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)
B	2-Hacid_dh_C	e4e5kB1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: 2-Hacid_dh_C	ECOD (1.6)
B	2-Hacid_dh	e4e5kB2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: Formate/glycerate dehydrogenase catalytic domain-like	F: 2-Hacid_dh	ECOD (1.6)
A	2-Hacid_dh_C	e4e5kA1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: 2-Hacid_dh_C	ECOD (1.6)
A	2-Hacid_dh	e4e5kA2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: Formate/glycerate dehydrogenase catalytic domain-like	F: 2-Hacid_dh	ECOD (1.6)
C	2-Hacid_dh_C	e4e5kC1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: 2-Hacid_dh_C	ECOD (1.6)
C	2-Hacid_dh	e4e5kC2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: Formate/glycerate dehydrogenase catalytic domain-like	F: 2-Hacid_dh	ECOD (1.6)
D	2-Hacid_dh_C	e4e5kD1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: 2-Hacid_dh_C	ECOD (1.6)
D	2-Hacid_dh	e4e5kD2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: Formate/glycerate dehydrogenase catalytic domain-like	F: 2-Hacid_dh	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like 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)
C	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
D	3.40.50.720	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	PF02826	D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain (2-Hacid_dh_C)	D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain	This domain is inserted into the catalytic domain, the large dehydrogenase and D-lactate dehydrogenase families in SCOP. N-terminal portion of which is represented by family Pfam:PF00389.	Domain
A, B, C, D	PF00389	D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain (2-Hacid_dh)	D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain	This family represents the largest portion of the catalytic domain of 2-hydroxyacid dehydrogenases as the NAD binding domain is inserted within the structural domain.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Phosphite dehydrogenase (thermostable variant)	glyoxylate reductase activity oxidoreductase activity glyoxylate reductase (NADPH) 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 catalytic activity oxidoreductase activity, acting on phosphorus or arsenic in donors, with NAD(P)+ as acceptor phosphonate dehydrogenase activity oxidoreductase activity, acting on phosphorus or arsenic in donors NAD binding binding nucleoside phosphate binding purine nucleotide binding adenyl nucleotide binding glyoxylate reductase activity oxidoreductase activity glyoxylate reductase (NADPH) 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 catalytic activity oxidoreductase activity, acting on phosphorus or arsenic in donors, with NAD(P)+ as acceptor phosphonate dehydrogenase activity oxidoreductase activity, acting on phosphorus or arsenic in donors NAD binding binding nucleoside phosphate binding purine nucleotide binding adenyl nucleotide binding nucleotide binding heterocyclic compound binding small molecule binding hydroxypyruvate reductase (NADH) activity hydroxypyruvate reductase [NAD(P)H] activity	-	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR006139	D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain	Domain
A, B, C, D	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
A, B, C, D	IPR050223	D-isomer specific 2-hydroxyacid dehydrogenase	Family
A, B, C, D	IPR029753	D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site	Conserved Site
A, B, C, D	IPR006140	D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain	Domain

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

Chains	Enzyme Name	Description	Catalytic Residues
B	phosphonate dehydrogenase M-CSA #984	Phosphonate dehydrogenase, originally isolated from the Gram-negative bacterium Pseudomonas stutzeri (strain WM88), was the first protein known to catalyze redox chemistry on inorganic phosphorus compounds. Phosphonate dehydrogenase catalyzes the oxidation of phosphonate to phosphate with the concurrent reduction of NAD+ to NADH. Due to the strong exergonic nature of the reaction, phosphonate dehydrogenase has gained a particularly high interest for use as a cofactor regeneration enzyme.	Defined by 3 residues: MET:B-53ARG:B-237HIS:B-292 \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 1.20.1.1 (UniProt) Search M-CSA Motif + EC 1.20.1.1

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.