1YBA | pdb_00001yba

The active form of phosphoglycerate dehydrogenase

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)
D	d1ybad1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Formate/glycerate dehydrogenases, NAD-domain	Phosphoglycerate dehydrogenase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D	d1ybad2	Alpha and beta proteins (a/b)	Flavodoxin-like	Formate/glycerate dehydrogenase catalytic domain-like	Formate/glycerate dehydrogenases, substrate-binding domain	Phosphoglycerate dehydrogenase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D	d1ybad3	Alpha and beta proteins (a+b)	Ferredoxin-like	ACT-like	Phosphoglycerate dehydrogenase, regulatory (C-terminal) domain	Phosphoglycerate dehydrogenase, regulatory (C-terminal) domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d1ybac1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Formate/glycerate dehydrogenases, NAD-domain	Phosphoglycerate dehydrogenase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d1ybac2	Alpha and beta proteins (a/b)	Flavodoxin-like	Formate/glycerate dehydrogenase catalytic domain-like	Formate/glycerate dehydrogenases, substrate-binding domain	Phosphoglycerate dehydrogenase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d1ybac3	Alpha and beta proteins (a+b)	Ferredoxin-like	ACT-like	Phosphoglycerate dehydrogenase, regulatory (C-terminal) domain	Phosphoglycerate dehydrogenase, regulatory (C-terminal) domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1ybab1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Formate/glycerate dehydrogenases, NAD-domain	Phosphoglycerate dehydrogenase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1ybab2	Alpha and beta proteins (a/b)	Flavodoxin-like	Formate/glycerate dehydrogenase catalytic domain-like	Formate/glycerate dehydrogenases, substrate-binding domain	Phosphoglycerate dehydrogenase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1ybab3	Alpha and beta proteins (a+b)	Ferredoxin-like	ACT-like	Phosphoglycerate dehydrogenase, regulatory (C-terminal) domain	Phosphoglycerate dehydrogenase, regulatory (C-terminal) domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d1ybaa1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Formate/glycerate dehydrogenases, NAD-domain	Phosphoglycerate dehydrogenase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d1ybaa2	Alpha and beta proteins (a/b)	Flavodoxin-like	Formate/glycerate dehydrogenase catalytic domain-like	Formate/glycerate dehydrogenases, substrate-binding domain	Phosphoglycerate dehydrogenase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d1ybaa3	Alpha and beta proteins (a+b)	Ferredoxin-like	ACT-like	Phosphoglycerate dehydrogenase, regulatory (C-terminal) domain	Phosphoglycerate dehydrogenase, regulatory (C-terminal) domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	ACT-like	8001021	3000006	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	D-2-hydroxyacid dehydrogenase-like	8017558	3000044	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	D-2-hydroxyacid dehydrogenase-like	8017558	3000044	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	ACT-like	8001021	3000006	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	ACT-like	8001021	3000006	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	D-2-hydroxyacid dehydrogenase-like	8017558	3000044	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	D-2-hydroxyacid dehydrogenase-like	8017558	3000044	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	ACT-like	8001021	3000006	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)
D	ACT_6	e1ybaD1	A: alpha bundles	X: EGF-like	H: Rpp14/Pop5-like	T: Rpp14/Pop5-like	F: ACT_6	ECOD (develop294)
D	FAD_binding_3	e1ybaD2	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: FAD_binding_3	ECOD (develop294)
D	NAD_binding_1	e1ybaD3	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: NAD_binding_1	ECOD (develop294)
C	ACT_6	e1ybaC1	A: alpha bundles	X: EGF-like	H: Rpp14/Pop5-like	T: Rpp14/Pop5-like	F: ACT_6	ECOD (develop294)
C	FAD_binding_3	e1ybaC2	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: FAD_binding_3	ECOD (develop294)
C	NAD_binding_1	e1ybaC3	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: NAD_binding_1	ECOD (develop294)
B	ACT_6	e1ybaB1	A: alpha bundles	X: EGF-like	H: Rpp14/Pop5-like	T: Rpp14/Pop5-like	F: ACT_6	ECOD (develop294)
B	FAD_binding_3	e1ybaB2	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: FAD_binding_3	ECOD (develop294)
B	NAD_binding_1	e1ybaB3	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: NAD_binding_1	ECOD (develop294)
A	ACT_6	e1ybaA1	A: alpha bundles	X: EGF-like	H: Rpp14/Pop5-like	T: Rpp14/Pop5-like	F: ACT_6	ECOD (develop294)
A	FAD_binding_3	e1ybaA2	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: FAD_binding_3	ECOD (develop294)
A	NAD_binding_1	e1ybaA3	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: NAD_binding_1	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
D	3.30.70.260	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	ACT 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)
C	3.30.70.260	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	ACT 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)
B	3.30.70.260	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	ACT 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)
A	3.30.70.260	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	ACT 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	PF22629	AHAS small subunit-like ACT domain (ACT_AHAS_ss)	AHAS small subunit-like ACT domain	This entry represents the ACT domain found at the N-terminal of acetolactate synthase small subunit from Escherichia coli and similar sequences. This domain is also found at the C-terminal of D-3-phosphoglycerate dehydrogenase, which are closely rela ...	This entry represents the ACT domain found at the N-terminal of acetolactate synthase small subunit from Escherichia coli and similar sequences. This domain is also found at the C-terminal of D-3-phosphoglycerate dehydrogenase, which are closely related [4-7]. Acetolactate synthase small subunit (ILVH) is the regulatory subunit of acetohydroxyacid synthase (AHAS), an enzyme hat catalyses the first step in the biosynthesis of the three branched-chain amino acids [4-7].	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	D-3-phosphoglycerate dehydrogenase	NAD+ binding NAD binding binding nucleotide binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding heterocyclic compound binding small molecule binding NADH binding cation binding organic acid binding NAD+ binding NAD binding binding nucleotide binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding heterocyclic compound binding small molecule binding NADH binding cation binding organic acid binding serine binding amino acid binding carboxylic acid binding 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 phosphoglycerate dehydrogenase activity catalytic activity (S)-2-hydroxyglutarate dehydrogenase activity identical protein binding protein binding	oxoacid metabolic process small molecule biosynthetic process carboxylic acid metabolic process L-amino acid biosynthetic process amino acid metabolic process primary metabolic process organic acid metabolic process organic acid biosynthetic process alpha-amino acid metabolic process L-serine metabolic process L-serine biosynthetic process L-amino acid metabolic process carboxylic acid biosynthetic process proteinogenic amino acid metabolic process amino acid biosynthetic process oxoacid metabolic process small molecule biosynthetic process carboxylic acid metabolic process L-amino acid biosynthetic process amino acid metabolic process primary metabolic process organic acid metabolic process organic acid biosynthetic process alpha-amino acid metabolic process L-serine metabolic process L-serine biosynthetic process L-amino acid metabolic process carboxylic acid biosynthetic process proteinogenic amino acid metabolic process amino acid biosynthetic process biosynthetic process proteinogenic amino acid biosynthetic process metabolic process cellular process small molecule metabolic process serine family amino acid biosynthetic process alpha-amino acid biosynthetic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR050223	D-isomer specific 2-hydroxyacid dehydrogenase	Family
A, B, C, D	IPR045865	ACT-like domain	Homologous Superfamily
A, B, C, D	IPR002912	ACT domain	Domain
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	IPR054480	Acetolactate synthase small subunit-like, ACT domain	Domain
A, B, C, D	IPR029752	D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1	Conserved Site
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

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.