1J49

INSIGHTS INTO DOMAIN CLOSURE, SUBSTRATE SPECIFICITY AND CATALYSIS OF D-LACTATE DEHYDROGENASE FROM LACTOBACILLUS BULGARICUS

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
Structure Motif: Primary M-CSA Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1j49a1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Formate/glycerate dehydrogenases, NAD-domain	D-lactate dehydrogenase	(Lactobacillus delbrueckii subsp. bulgaricus ) [TaxId: 1585 ],	SCOPe (2.08)
A	d1j49a2	Alpha and beta proteins (a/b)	Flavodoxin-like	Formate/glycerate dehydrogenase catalytic domain-like	Formate/glycerate dehydrogenases, substrate-binding domain	D-lactate dehydrogenase	(Lactobacillus delbrueckii subsp. bulgaricus ) [TaxId: 1585 ],	SCOPe (2.08)
B	d1j49b1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Formate/glycerate dehydrogenases, NAD-domain	D-lactate dehydrogenase	(Lactobacillus delbrueckii subsp. bulgaricus ) [TaxId: 1585 ],	SCOPe (2.08)
B	d1j49b2	Alpha and beta proteins (a/b)	Flavodoxin-like	Formate/glycerate dehydrogenase catalytic domain-like	Formate/glycerate dehydrogenases, substrate-binding domain	D-lactate dehydrogenase	(Lactobacillus delbrueckii subsp. bulgaricus ) [TaxId: 1585 ],	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	8056166	4000099	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	D-2-hydroxyacid dehydrogenase-like	8056167	3000044	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	D-2-hydroxyacid dehydrogenase-like	8056167	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	2-Hacid_dh_C	e1j49A1	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	e1j49A2	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	2-Hacid_dh_C	e1j49B1	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	e1j49B2	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)
B	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	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	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	D-LACTATE 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 lactate dehydrogenase activity D-lactate 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 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 lactate dehydrogenase activity D-lactate 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	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
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	IPR029753	D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site	Conserved Site
A, B	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
A	D-lactate dehydrogenase M-CSA #576	D -Lactate dehydrogenase from Lactobacillus bulgaricus, a homodimer with 332 amino acid, acts at the last step of the glycolytic pathway under anaerobic conditions, allowing re-oxidation of NAD, which is necessary for glycolysis. The enzyme catalyses the NAD-dependent conversion of pyruvate into the D -isomer of lactic acid. The reaction is reversible: pyruvate reduction (the forward reaction) shows a maximum rate at pH 7.5 and D-lactate oxidation (the inverse reaction) at pH 8.0. The reaction leading to the other enantiomer, L-lactic acid, is catalysed by another enzyme, L-lactate dehydrogenase (L-LDH). While L-LDH has a wide occurrence in nature, D-LDH is found only in invertebrates, lower fungi and prokaryotic organisms. Lactic bacteria possess either one or both enzymes. In Lactobacillus bulgaricus, commonly used in the dairy industry for the production of yoghurt, more than 90% of the pyruvate is converted into D-lactate.	Defined by 4 residues: ARG:A-236ASP:A-260GLU:A-265HIS:A-297 \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 1.1.1.28 (PDB Primary Data) Search M-CSA Motif + EC 1.1.1.28

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.