1YGY

Crystal Structure of D-3-Phosphoglycerate dehydrogenase From Mycobacterium tuberculosis

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)
A	d1ygya1	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	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
A	d1ygya2	Alpha and beta proteins (a/b)	Flavodoxin-like	Formate/glycerate dehydrogenase catalytic domain-like	Formate/glycerate dehydrogenases, substrate-binding domain	Phosphoglycerate dehydrogenase	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
A	d1ygya3	Alpha and beta proteins (a+b)	Ferredoxin-like	ACT-like	Phosphoglycerate dehydrogenase, regulatory (C-terminal) domain	Phosphoglycerate dehydrogenase, regulatory (C-terminal) domain	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
A	d1ygya4	Alpha and beta proteins (a+b)	FwdE/GAPDH domain-like	Serine metabolism enzymes domain	SerA intervening domain-like	D-3-phosphoglycerate dehydrogenase SerA	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
B	d1ygyb1	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	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
B	d1ygyb2	Alpha and beta proteins (a/b)	Flavodoxin-like	Formate/glycerate dehydrogenase catalytic domain-like	Formate/glycerate dehydrogenases, substrate-binding domain	Phosphoglycerate dehydrogenase	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
B	d1ygyb3	Alpha and beta proteins (a+b)	Ferredoxin-like	ACT-like	Phosphoglycerate dehydrogenase, regulatory (C-terminal) domain	Phosphoglycerate dehydrogenase, regulatory (C-terminal) domain	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
B	d1ygyb4	Alpha and beta proteins (a+b)	FwdE/GAPDH domain-like	Serine metabolism enzymes domain	SerA intervening domain-like	D-3-phosphoglycerate dehydrogenase SerA	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	D-lactate/D-glycerate dehydrogenase-like	8001025	4000099	SCOP2 (2022-06-29)
A	SCOP2 Family	Phosphoglycerate dehydrogenase, regulatory (C-terminal) domain	8001026	4000051	SCOP2 (2022-06-29)
A	SCOP2 Family	SerA intervening domain-like	8001027	4000037	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	D-2-hydroxyacid dehydrogenase-like	8017543	3000044	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	ACT-like	8017540	3000006	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Serine metabolism enzymes domain	8001028	3000019	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	ACT-like	8017540	3000006	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Serine metabolism enzymes domain	8001028	3000019	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	D-2-hydroxyacid dehydrogenase-like	8017543	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)
A	PRK13581	e1ygyA2	A: a+b two layers	X: FwdE/GAPDH domain-like	H: Serine dehydratase beta chain-like (From Topology)	T: Serine dehydratase beta chain-like	F: PRK13581	ECOD (1.6)
A	ACT	e1ygyA1	A: a+b two layers	X: Alpha-beta plaits	H: ACT-like (From Topology)	T: ACT-like	F: ACT	ECOD (1.6)
A	2-Hacid_dh_C	e1ygyA3	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	e1ygyA4	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)
B	PRK13581	e1ygyB2	A: a+b two layers	X: FwdE/GAPDH domain-like	H: Serine dehydratase beta chain-like (From Topology)	T: Serine dehydratase beta chain-like	F: PRK13581	ECOD (1.6)
B	ACT	e1ygyB1	A: a+b two layers	X: Alpha-beta plaits	H: ACT-like (From Topology)	T: ACT-like	F: ACT	ECOD (1.6)
B	2-Hacid_dh_C	e1ygyB3	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	e1ygyB4	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)
A	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
A	3.30.1330.90	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
A	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	3.30.1330.90	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
B	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	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	PF19304	D-3-phosphoglycerate dehydrogenase intervening domain (PGDH_inter)	D-3-phosphoglycerate dehydrogenase intervening domain	This domain is found in the D-3-phosphoglycerate dehydrogenase enzyme. In the structure of the Mycobacterium tuberculosis enzyme this domain was described as the intervening domain, also known as the allosteric substrate binding domain (ASB) [1,2,3]. ...	This domain is found in the D-3-phosphoglycerate dehydrogenase enzyme. In the structure of the Mycobacterium tuberculosis enzyme this domain was described as the intervening domain, also known as the allosteric substrate binding domain (ASB) [1,2,3]. The intervening domain between the substrate-binding and regulatory domains is not present in E. coli PGDH. This domain is closely related to Pfam:PF03315. It serves as an anion-binding site and may function as an allosteric site for the control of enzyme activity [3].	Domain
A, B	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
A, B	PF01842	ACT domain (ACT)	ACT domain	This family of domains generally have a regulatory role. ACT domains are linked to a wide range of metabolic enzymes that are regulated by amino acid concentration. Pairs of ACT domains bind specifically to a particular amino acid leading to regulati ...	This family of domains generally have a regulatory role. ACT domains are linked to a wide range of metabolic enzymes that are regulated by amino acid concentration. Pairs of ACT domains bind specifically to a particular amino acid leading to regulation of the linked enzyme. The ACT domain is found in: D-3-phosphoglycerate dehydrogenase EC:1.1.1.95 Swiss:P08328, which is inhibited by serine [1]. Aspartokinase EC:2.7.2.4 Swiss:P53553, which is regulated by lysine. Acetolactate synthase small regulatory subunit Swiss:P00894, which is inhibited by valine. Phenylalanine-4-hydroxylase EC:1.14.16.1 Swiss:P00439, which is regulated by phenylalanine. Prephenate dehydrogenase EC:4.2.1.51 Swiss:P21203. formyltetrahydrofolate deformylase EC:3.5.1.10, Swiss:P37051, which is activated by methionine and inhibited by glycine. GTP pyrophosphokinase EC:2.7.6.5 Swiss:P11585	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	D-3-phosphoglycerate dehydrogenase	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 NAD binding binding nucleoside phosphate binding purine nucleotide binding organic cyclic compound binding adenyl nucleotide binding nucleotide binding heterocyclic compound binding small molecule binding	serine family amino acid metabolic process oxoacid metabolic process cellular biosynthetic process amino acid metabolic process organic acid metabolic process organic acid biosynthetic process alpha-amino acid metabolic process carboxylic acid biosynthetic process small molecule metabolic process small molecule biosynthetic process cellular metabolic process carboxylic acid metabolic process primary metabolic process L-amino acid biosynthetic process serine family amino acid metabolic process oxoacid metabolic process cellular biosynthetic process amino acid metabolic process organic acid metabolic process organic acid biosynthetic process alpha-amino acid metabolic process carboxylic acid biosynthetic process small molecule metabolic process small molecule biosynthetic process cellular metabolic process carboxylic acid metabolic process primary metabolic process L-amino acid biosynthetic process L-serine metabolic process L-serine biosynthetic process L-amino acid metabolic process proteinogenic amino acid metabolic process amino acid biosynthetic process biosynthetic process proteinogenic amino acid biosynthetic process metabolic process cellular process serine family amino acid biosynthetic process alpha-amino acid biosynthetic process	cell periphery plasma membrane membrane cellular anatomical entity external encapsulating structure cell wall peptidoglycan-based cell wall

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR029009	Allosteric substrate binding domain superfamily	Homologous Superfamily
A, B	IPR050857	D-isomer specific 2-hydroxyacid dehydrogenases	Family
A, B	IPR045865	ACT-like domain	Homologous Superfamily
A, B	IPR002912	ACT domain	Domain
A, B	IPR006139	D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain	Domain
A, B	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
A, B	IPR029752	D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1	Conserved Site
A, B	IPR006236	D-3-phosphoglycerate dehydrogenase	Family
A, B	IPR029753	D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site	Conserved Site
A, B	IPR045626	D-3-phosphoglycerate dehydrogenase, ASB domain	Domain
A, B	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.