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InterPro: IPR006140 D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding

Protein matches Help

UniProtKB

Matches:

8572 proteins

Overview:	sorted by AC,	sorted by name,	of known structure,	proteins with splice variants
Detailed:	sorted by AC,	sorted by name,	of known structure	proteins with splice variants
Table:	For all matching proteins,	of known structure
Architectures
Accession List
Matches in BioMart

Accession

IPR006140 D-isomer_2_OHA_DH_NAD-bd

Secondary

IPR002162

Type

Domain

Signatures Help

Database	ID	Name	Proteins
Pfam	PF02826	2-Hacid_dh_C	7904
PROSITE pattern	PS00065	D_2_HYDROXYACID_DH_1	4536
PROSITE pattern	PS00670	D_2_HYDROXYACID_DH_2	2786
PROSITE pattern	PS00671	D_2_HYDROXYACID_DH_3	4513
Signatures in BioMart

InterPro Relationships Help

Parent

IPR016040 NAD(P)-binding domain

Found in

IPR006236 D-3-phosphoglycerate dehydrogenase
IPR015508 D-3-phosphogylcerate Dehydrogenase
IPR020921 Erythronate-4-phosphate dehydrogenase

GO Term annotation Help

Function

GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
GO:0048037 cofactor binding

InterPro annotation

Entry Details in BioMart

Abstract

A number of NAD-dependent 2-hydroxyacid dehydrogenases which seem to be specific for the D-isomer of their substrate have been shown to be functionally and structurally related. All contain a glycine-rich region located in the central section of these enzymes, this region corresponds to the NAD-binding domain. The catalytic domain is described in IPR006139

Structural links Help

PDB - click here

SCOP: c.2.1.1 , c.2.1.4

CATH: 3.40.50.720

Database links Help

PDBe-motif: PS00065 , PS00670 , PS00671

Enzyme: EC:1.1.1

PROSITE doc: PDOC00063

PANDIT: PF02826

Blocks: IPB006140

Pfam Clan: CL0063.21

AC	CL0063.21
ID	NADP_Rossmann
DE	FAD/NAD(P)-binding Rossmann fold Superfamily
PF00044	IPR020828	Glyceraldehyde 3-phosphate dehydrogenase, NAD(P) binding domain
PF00056	IPR001236	Lactate/malate dehydrogenase
PF00070	IPR001327	Pyridine nucleotide-disulphide oxidoreductase, NAD-binding region
PF00106	IPR002198	Short-chain dehydrogenase/reductase SDR
PF00107	IPR013149	Alcohol dehydrogenase, zinc-binding
PF00208	IPR006096	Glutamate/phenylalanine/leucine/valine dehydrogenase, C-terminal
PF00479	IPR001282	Glucose-6-phosphate dehydrogenase
PF00670	IPR015878	S-adenosyl-L-homocysteine hydrolase, NAD binding
PF00732	IPR000172	Glucose-methanol-choline oxidoreductase, N-terminal
PF00743	IPR000960	Flavin-containing monooxygenase FMO
PF00890	IPR003953	Fumarate reductase/succinate dehydrogenase flavoprotein, N-terminal
PF00899	IPR000594	UBA/THIF-type NAD/FAD binding fold
PF00996	IPR018203	GDP dissociation inhibitor
PF01073	IPR002225	3-beta hydroxysteroid dehydrogenase/isomerase
PF01113	IPR000846	Dihydrodipicolinate reductase
PF01118	IPR000534	Semialdehyde dehydrogenase, NAD-binding
PF01134	IPR002218	Glucose-inhibited division protein A-related
PF01210	IPR011128	NAD-dependent glycerol-3-phosphate dehydrogenase, N-terminal
PF01225	IPR000713	Mur ligase, N-terminal
PF01232	IPR013131	Mannitol dehydrogenase, N-terminal
PF01262	IPR007698	Alanine dehydrogenase/PNT, C-terminal
PF01266	IPR006076	FAD dependent oxidoreductase
PF01370	IPR001509	NAD-dependent epimerase/dehydratase
PF01408	IPR000683	Oxidoreductase, N-terminal
PF01488	IPR006151	Quinate/shikimate 5-dehydrogenase/glutamyl-tRNA reductase
PF01494	IPR002938	Monooxygenase, FAD-binding
PF01593	IPR002937	Amine oxidase
PF01946	IPR002922	Thiamine biosynthesis Thi4 protein
PF02153	IPR003099	Prephenate dehydrogenase
PF02254	IPR003148	Regulator of K+ conductance, N-terminal
PF02423	IPR003462	Ornithine cyclodeaminase/mu-crystallin
PF02558	IPR013332	Ketopantoate reductase ApbA/PanE, N-terminal
PF02629	IPR003781	CoA-binding
PF02670	IPR013512	1-deoxy-D-xylulose 5-phosphate reductoisomerase, N-terminal
PF02719	IPR003869	Polysaccharide biosynthesis protein CapD-like
PF02737	IPR006176	3-hydroxyacyl-CoA dehydrogenase, NAD binding
PF02826	IPR006140	D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding
PF02882	IPR020631	Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain
PF03435	IPR005097	Saccharopine dehydrogenase
PF03446	IPR006115	6-phosphogluconate dehydrogenase, NAD-binding
PF03447	IPR005106	Aspartate/homoserine dehydrogenase, NAD-binding
PF03486	IPR004792	HI0933-like protein
PF03721	IPR001732	UDP-glucose/GDP-mannose dehydrogenase, N-terminal
PF03807	IPR004455	NADP oxidoreductase, coenzyme F420-dependent
PF03949	IPR012302	Malic enzyme, NAD-binding
PF04321	IPR005913	dTDP-4-dehydrorhamnose reductase
PF04723	IPR006812	Glycine reductase complex selenoprotein A
PF04820	IPR006905	Tryptophan halogenase
PF05368	IPR008030	NmrA-like
PF05834	IPR008671	Lycopene beta/epsilon cyclase
PF06039	IPR006231	Malate:quinone-oxidoreductase
PF07157	IPR009826	DNA circulation, N-terminal
PF07991	IPR013116	Acetohydroxy acid isomeroreductase, catalytic
PF07992	IPR013027	FAD-dependent pyridine nucleotide-disulphide oxidoreductase
PF07993	IPR013120	Male sterility, NAD-binding
PF07994	IPR002587	Myo-inositol-1-phosphate synthase
PF08491	IPR013698	Squalene epoxidase
PF08659	IPR013968	Polyketide synthase, KR
PF10727	IPR019665	Putative oxidoreductase/dehydrogenase, Rossmann-like domain

Taxonomic coverage Help

Overlapping InterPro entries Help

IPR006140

Numbers of overlapping proteins

Average numbers of overlapping amino acids

Example proteins Help

O04130 D-3-phosphoglycerate dehydrogenase, chloroplastic

O43175 D-3-phosphoglycerate dehydrogenase

O46036 C-terminal-binding protein

O88712 C-terminal-binding protein 1

P25377 NADP-dependent alcohol dehydrogenase 7

More proteins

Example Proteins Key

InterPro entry accession number/name and structure databases		Colour code
IPR006236	D-3-phosphoglycerate dehydrogenase
IPR013149	Alcohol dehydrogenase, zinc-binding
IPR013154	Alcohol dehydrogenase GroES-like
IPR002912	Amino acid-binding ACT
IPR002085	Alcohol dehydrogenase superfamily, zinc-containing
IPR015508	D-3-phosphogylcerate Dehydrogenase
IPR002328	Alcohol dehydrogenase, zinc-containing, conserved site
IPR011032	GroES-like
IPR016040	NAD(P)-binding domain
IPR006140	D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding
IPR006139	D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain
	PDB Chain
	ModBase
	SWISS-MODEL

Publications Help

Additional Reading Open in usermanual
	Levin EJ, Kondrashov DA, Wesenberg GE, Phillips GN Jr. Ensemble refinement of protein crystal structures: validation and application. Structure 15 2007 1040-52 [PubMed: 17850744] http://dx.doi.org/10.1016/j.str.2007.06.019
	Grant GA. A new family of 2-hydroxyacid dehydrogenases. Biochem. Biophys. Res. Commun. 165 1989 1371-4 [PubMed: 2692566] http://dx.doi.org/10.1016/0006-291X(89)92755-1
	Taguchi H, Ohta T. D-lactate dehydrogenase is a member of the D-isomer-specific 2-hydroxyacid dehydrogenase family. Cloning, sequencing, and expression in Escherichia coli of the D-lactate dehydrogenase gene of Lactobacillus plantarum. J. Biol. Chem. 266 1991 12588-94 [PubMed: 1840590] http://intl.jbc.org/cgi/reprint/266/19/12588.pdf
	Popov VO, Lamzin VS. NAD(+)-dependent formate dehydrogenase. Biochem. J. 301 ( Pt 3) 1994 625-43 [PubMed: 8053888] http://www.pubmedcentral.nih.gov/picrender.fcgi?tool=EBI&pubmedid=8053888&action=stream&blobtype=pdf
	Quinlan KG, Nardini M, Verger A, Francescato P, Yaswen P, Corda D, Bolognesi M, Crossley M. Specific recognition of ZNF217 and other zinc finger proteins at a surface groove of C-terminal binding proteins. Mol. Cell. Biol. 26 2006 8159-72 [PubMed: 16940172] http://dx.doi.org/10.1128/MCB.00680-06
	Goldberg JD, Yoshida T, Brick P. Crystal structure of a NAD-dependent D-glycerate dehydrogenase at 2.4 A resolution. J. Mol. Biol. 236 1994 1123-40 [PubMed: 8120891] http://dx.doi.org/10.1016/0022-2836(94)90016-7
	Kochhar S, Hunziker PE, Leong-Morgenthaler P, Hottinger H. Evolutionary relationship of NAD(+)-dependent D-lactate dehydrogenase: comparison of primary structure of 2-hydroxy acid dehydrogenases. Biochem. Biophys. Res. Commun. 184 1992 60-6 [PubMed: 1567457] http://dx.doi.org/10.1016/0006-291X(92)91157-L
	Dey S, Hu Z, Xu XL, Sacchettini JC, Grant GA. The effect of hinge mutations on effector binding and domain rotation in Escherichia coli D-3-phosphoglycerate dehydrogenase. J. Biol. Chem. 282 2007 18418-26 [PubMed: 17459882] http://dx.doi.org/10.1074/jbc.M701174200
	Dey S, Grant GA, Sacchettini JC. Crystal structure of Mycobacterium tuberculosis D-3-phosphoglycerate dehydrogenase: extreme asymmetry in a tetramer of identical subunits. J. Biol. Chem. 280 2005 14892-9 [PubMed: 15668249] http://dx.doi.org/10.1074/jbc.M414489200
	Dengler U, Niefind K, Kiess M, Schomburg D. Crystal structure of a ternary complex of D-2-hydroxyisocaproate dehydrogenase from Lactobacillus casei, NAD+ and 2-oxoisocaproate at 1.9 A resolution. J. Mol. Biol. 267 1997 640-60 [PubMed: 9126843] http://dx.doi.org/10.1006/jmbi.1996.0864
	Booth MP, Conners R, Rumsby G, Brady RL. Structural basis of substrate specificity in human glyoxylate reductase/hydroxypyruvate reductase. J. Mol. Biol. 360 2006 178-89 [PubMed: 16756993] http://dx.doi.org/10.1016/j.jmb.2006.05.018

InterPro 23.1