1J4A | pdb_00001j4a

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D	d1j4ad1	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)
D	d1j4ad2	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)
C	d1j4ac1	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)
C	d1j4ac2	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	d1j4ab1	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	d1j4ab2	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)
A	d1j4aa1	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	d1j4aa2	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)
D	SCOP2B Superfamily	D-2-hydroxyacid dehydrogenase-like	8056167	3000044	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	D-2-hydroxyacid dehydrogenase-like	8056167	3000044	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	D-2-hydroxyacid dehydrogenase-like	8056167	3000044	SCOP2B (2022-06-29)
A	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)
D	FAD_binding_3	e1j4aD1	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: FAD_binding_3	ECOD (v294.1)
D	NAD_binding_1	e1j4aD2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: NAD_binding_1	ECOD (v294.1)
C	FAD_binding_3	e1j4aC1	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: FAD_binding_3	ECOD (v294.1)
C	NAD_binding_1	e1j4aC2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: NAD_binding_1	ECOD (v294.1)
B	FAD_binding_3	e1j4aB1	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: FAD_binding_3	ECOD (v294.1)
B	NAD_binding_1	e1j4aB2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: NAD_binding_1	ECOD (v294.1)
A	2-Hacid_dh	e1j4aA2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Rossmann-related	T: Formate/glycerate dehydrogenase catalytic domain-like	F: 2-Hacid_dh	ECOD (v294.1)
A	FAD_binding_3	e1j4aA1	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: FAD_binding_3	ECOD (v294.1)

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)
C	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)
A	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	D-LACTATE DEHYDROGENASE	NAD binding binding nucleoside phosphate binding purine nucleotide binding adenyl nucleotide binding nucleotide binding heterocyclic compound binding small molecule binding oxidoreductase activity (2R)-oxo-acid reductase activity (2R)-2-hydroxyacid dehydrogenase (NAD+) 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 D-lactate dehydrogenase (NAD+) activity NAD binding binding nucleoside phosphate binding purine nucleotide binding adenyl nucleotide binding nucleotide binding heterocyclic compound binding small molecule binding oxidoreductase activity (2R)-oxo-acid reductase activity (2R)-2-hydroxyacid dehydrogenase (NAD+) 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 D-lactate dehydrogenase (NAD+) activity lactate dehydrogenase activity D-lactate dehydrogenase activity catalytic activity	oxoacid metabolic process carboxylic acid metabolic process small molecule metabolic process metabolic process cellular process monocarboxylic acid metabolic process organic acid metabolic process lactate metabolic process	-

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	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	IPR058205	D-lactate dehydrogenase-like	Family
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.