1F0X | pdb_00001f0x

CRYSTAL STRUCTURE OF D-LACTATE DEHYDROGENASE, A PERIPHERAL MEMBRANE RESPIRATORY ENZYME.

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)
B	d1f0xb1	Alpha and beta proteins (a+b)	Ferredoxin-like	FAD-linked oxidases, C-terminal domain	D-lactate dehydrogenase	D-lactate dehydrogenase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1f0xb2	Alpha and beta proteins (a+b)	FAD-binding/transporter-associated domain-like	FAD-binding/transporter-associated domain-like	FAD-linked oxidases, N-terminal domain	D-lactate dehydrogenase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d1f0xa1	Alpha and beta proteins (a+b)	Ferredoxin-like	FAD-linked oxidases, C-terminal domain	D-lactate dehydrogenase	D-lactate dehydrogenase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d1f0xa2	Alpha and beta proteins (a+b)	FAD-binding/transporter-associated domain-like	FAD-binding/transporter-associated domain-like	FAD-linked oxidases, N-terminal domain	D-lactate dehydrogenase	(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)
B	SCOP2B Superfamily	FAD-binding/transporter-associated domain-like	8036703	3000913	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	FAD-linked oxidases C-terminal domain-like	8035652	3001317	SCOP2B (2022-06-29)
A	SCOP2 Family	D-lactate dehydrogenase	8023272	4001341	SCOP2 (2022-06-29)
A	SCOP2 Family	FAD-linked oxidases, N-terminal domain	8024324	4002178	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	FAD-linked oxidases C-terminal domain-like	8035652	3001317	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	FAD-binding/transporter-associated domain-like	8036703	3000913	SCOP2 (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		e1f0xB1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: Propep_M14	F:	ECOD (20:10:01)
B		e1f0xB2	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: Hexapep,Acetyltransf_11	F:	ECOD (20:10:01)
A		e1f0xA1	A: Alpha-beta plaits	X: FAD-linked oxidases, C-terminal domain	H: FAD-linked oxidases, C-terminal domain	T: Lact-deh-memb	F:	ECOD (20:10:01)
A		e1f0xA2	A: FAD-binding domain-like	X: FAD-binding domain	H: FAD-binding domain	T: FAD_binding_4	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.30.70.610	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	D-lactate dehydrogenase, cap domain, subdomain 1	CATH (4.3.0)
B	3.30.43.10	Alpha Beta	2-Layer Sandwich	Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase	domain 2	CATH (4.3.0)
B	3.30.465.10	Alpha Beta	2-Layer Sandwich	Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase	domain 3	CATH (4.3.0)
B	3.30.1370.20	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S8	Chain: A, domain 1	CATH (4.3.0)
A	3.30.70.610	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	D-lactate dehydrogenase, cap domain, subdomain 1	CATH (4.3.0)
A	3.30.43.10	Alpha Beta	2-Layer Sandwich	Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase	domain 2	CATH (4.3.0)
A	3.30.465.10	Alpha Beta	2-Layer Sandwich	Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase	domain 3	CATH (4.3.0)
A	3.30.1370.20	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S8	Chain: A, domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF09330	D-lactate dehydrogenase, membrane binding (Lact-deh-memb)	D-lactate dehydrogenase, membrane binding	Members of this family are predominantly found in prokaryotic D-lactate dehydrogenase, forming the cap-membrane-binding domain, which consists of a large seven-stranded antiparallel beta-sheet flanked on both sides by alpha-helices. They allow for me ...	Members of this family are predominantly found in prokaryotic D-lactate dehydrogenase, forming the cap-membrane-binding domain, which consists of a large seven-stranded antiparallel beta-sheet flanked on both sides by alpha-helices. They allow for membrane association [1].	Domain
A, B	PF01565	FAD binding domain (FAD_binding_4)	FAD binding domain	This family consists of various enzymes that use FAD as a co-factor, most of the enzymes are similar to oxygen oxidoreductase. One of the enzymes Vanillyl-alcohol oxidase (VAO) has a solved structure, the alignment includes the FAD binding site, call ...	This family consists of various enzymes that use FAD as a co-factor, most of the enzymes are similar to oxygen oxidoreductase. One of the enzymes Vanillyl-alcohol oxidase (VAO) has a solved structure, the alignment includes the FAD binding site, called the PP-loop, between residues 99-110 [1]. The FAD molecule is covalently bound in the known structure, however the residue that links to the FAD is not in the alignment. VAO catalyses the oxidation of a wide variety of substrates, ranging form aromatic amines to 4-alkylphenols. Other members of this family include D-lactate dehydrogenase, this enzyme catalyses the conversion of D-lactate to pyruvate using FAD as a co-factor; mitomycin radical oxidase, this enzyme oxidises the reduced form of mitomycins and is involved in mitomycin resistance. This family includes MurB an UDP-N-acetylenolpyruvoylglucosamine reductase enzyme EC:1.1.1.158. This enzyme is involved in the biosynthesis of peptidoglycan [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	D-LACTATE DEHYDROGENASE	D-lactate dehydrogenase (cytochrome) activity oxidoreductase activity, acting on the CH-OH group of donors, cytochrome as acceptor oxidoreductase activity (2R)-oxo-acid reductase activity oxidoreductase activity, acting on CH-OH group of donors lactate dehydrogenase activity catalytic activity D-lactate dehydrogenase activity FAD binding flavin adenine dinucleotide binding binding nucleoside phosphate binding ion binding anion binding D-lactate dehydrogenase (cytochrome) activity oxidoreductase activity, acting on the CH-OH group of donors, cytochrome as acceptor oxidoreductase activity (2R)-oxo-acid reductase activity oxidoreductase activity, acting on CH-OH group of donors lactate dehydrogenase activity catalytic activity D-lactate dehydrogenase activity FAD binding flavin adenine dinucleotide binding binding nucleoside phosphate binding ion binding anion binding nucleotide binding heterocyclic compound binding small molecule binding electron transfer activity D-lactate dehydrogenase (quinone) activity (2R)-hydroxyacid dehydrogenase (quinone) activity oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor quinone binding	aerobic respiration cellular respiration energy derivation by oxidation of organic compounds metabolic process cellular process generation of precursor metabolites and energy oxoacid metabolic process carboxylic acid metabolic process small molecule metabolic process monocarboxylic acid metabolic process organic acid metabolic process lactate metabolic process anaerobic respiration transmembrane transport aerobic respiration cellular respiration energy derivation by oxidation of organic compounds metabolic process cellular process generation of precursor metabolites and energy oxoacid metabolic process carboxylic acid metabolic process small molecule metabolic process monocarboxylic acid metabolic process organic acid metabolic process lactate metabolic process anaerobic respiration transmembrane transport localization transport establishment of localization respiratory electron transport chain electron transport chain	cell periphery cellular anatomical structure plasma membrane membrane extrinsic component of plasma membrane cytoplasmic side of plasma membrane cytoplasmic side of membrane extrinsic component of membrane extrinsic component of cytoplasmic side of plasma membrane side of membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR016167	FAD-binding, type PCMH, subdomain 1	Homologous Superfamily
A, B	IPR051264	FAD-binding Oxidoreductase/Transferase Type 4	Family
A, B	IPR036318	FAD-binding, type PCMH-like superfamily	Homologous Superfamily
A, B	IPR015409	D-lactate dehydrogenase, membrane binding, C-terminal	Domain
A, B	IPR012256	D-lactate dehydrogenase	Family
A, B	IPR016164	FAD-linked oxidase-like, C-terminal	Homologous Superfamily
A, B	IPR006094	FAD linked oxidase, N-terminal	Domain
A, B	IPR016166	FAD-binding domain, PCMH-type	Domain
A, B	IPR016172	D-lactate dehydrogenase, cap domain, subdomain 1	Homologous Superfamily
A, B	IPR016173	D-lactate dehydrogenase, cap domain, subdomain 2	Homologous Superfamily
A, B	IPR016169	FAD-binding, type PCMH, subdomain 2	Homologous Superfamily

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.