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Information on EC 1.1.1.345 - D-2-hydroxyacid dehydrogenase (NAD+)

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IUBMB Comments
The enzymes, characterized from bacteria (Peptoclostridium difficile, Enterococcus faecalis and from lactic acid bacteria) prefer substrates with a main chain of 5 carbons (such as 4-methyl-2-oxopentanoate) to those with a shorter chain. It also utilizes phenylpyruvate. The enzyme from the halophilic archaeon Haloferax mediterranei prefers substrates with a main chain of 3-4 carbons (pyruvate and 2-oxobutanoate). cf. EC 1.1.1.272, (D)-2-hydroxyacid dehydrogenase (NADP+).
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UNIPROT: Q1GAA2
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The expected taxonomic range for this enzyme is: Bacteria, Archaea, Eukaryota
Synonyms
d-mandelate dehydrogenase, d-2-hydroxyisocaproate dehydrogenase, d-isomer-specific 2-hydroxyacid dehydrogenase, d-hicdh, mandh2, d-mdh, nad-dependent d-2-hydroxyacid dehydrogenase, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
D-isomer specific 2-hydroxyacid dehydrogenase
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PATHWAY SOURCE
PATHWAYS
-
-
SYSTEMATIC NAME
IUBMB Comments
(R)-2-hydroxycarboxylate:NAD+ oxidoreductase
The enzymes, characterized from bacteria (Peptoclostridium difficile, Enterococcus faecalis and from lactic acid bacteria) prefer substrates with a main chain of 5 carbons (such as 4-methyl-2-oxopentanoate) to those with a shorter chain. It also utilizes phenylpyruvate. The enzyme from the halophilic archaeon Haloferax mediterranei prefers substrates with a main chain of 3-4 carbons (pyruvate and 2-oxobutanoate). cf. EC 1.1.1.272, (D)-2-hydroxyacid dehydrogenase (NADP+).
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
(R)-2-hydroxycarboxylate + NAD+
a 2-oxocarboxylate + NADH + H+
show the reaction diagram
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-
-
r
phenylpyruvate + NADH + H+
phenyl-D-lactate + NAD+
show the reaction diagram
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-
-
r
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
(R)-2-hydroxycarboxylate + NAD+
a 2-oxocarboxylate + NADH + H+
show the reaction diagram
-
-
-
r
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
NAD+
enzyme binding structure analysis, overview
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0591
phenylpyruvate
recombinant His-tagged enzyme, pH and temperature not specified in the publication
additional information
additional information
Michaelis-Menten kinetics, recombinant enzyme
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
8.48
phenylpyruvate
recombinant His-tagged enzyme, pH and temperature not specified in the publication
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
evolution
the enzyme belongs to the the NAD-dependent dehydrogenase family. Comparison with closely related members of the NAD-dependent dehydrogenase family reveals that whilst the D2-HDH core fold is structurally conserved, the substrate-binding site has a number of non-canonical features that may influence substrate selection and thus dictate the physiological function of the enzyme. The protein, 2-hydroxyisocaproate dehydrogenase (HO-HxoDH), is virtually identical to the D2-HDH, with only three amino-acid differences between the two proteins, all at sites not known to be biologically relevant
physiological function
the substrate-binding site has a number of non-canonical features that may influence substrate selection and thus dictate the physiological function of the enzyme
additional information
enzyme three-dimensional structure analysis, active site and cofactor binding site structures, overview
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION?
Q1GAA2_LACDA
Lactobacillus delbrueckii subsp. bulgaricus (strain ATCC 11842 / DSM 20081 / BCRC 10696 / JCM 1002 / NBRC 13953 / NCIMB 11778 / NCTC 12712 / WDCM 00102 / Lb 14)
333
0
36849
TrEMBL
-
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
enzyme three-dimensional structure analysis, overview
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
purified enzyme in apoform and complexed with coenzyme NAD+, hanging drop vapor diffusion method, mixing of 400 nl of 10 mg/ml protein in 40 mM HEPES, pH 7.4, 300 mM NaCl, and 0.02% v/v monothioglycerol, with 400 nl reservoir solution containing 25% PEG 3350, 200 mM MgCl2, 100 mM HEPES, pH 7.5, and equilibration against 0.1 ml of reservoir solution at 19°C, crystals are supplemented with 10 mM NAD+ for the enzyme complex crystals, X-ray diffraction structure determination at 3.45 A and 2.75 A resolution, respectively, molecular replacement and modeling using the monomer structure of D-2-hydroxyisocaproate dehydrogenase (D-HicDH) from Lactobacillus casei, PDB ID 1DXY
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant His-tagged D2-HDH from Escherichia coli BL21(DE3) pLysS by nickel affinity chromatography and gel filtration
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
gene Ldb1010, recombinant expression of His-tagged D2-HDH in Escherichia coli BL21(DE3) pLysS. The enzyme containing the non-native C-terminal hexahistidine tag and a 4-residue linker (Thr Ala Ser Gly linker) is enzymatically active
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Holton, S.; Anandhakrishnan, M.; Geerlof, A.; Wilmanns, M.
Structural characterization of a D-isomer specific 2-hydroxyacid dehydrogenase from Lactobacillus delbrueckii ssp. bulgaricus
J. Struct. Biol.
181
179-184
2013
Lactobacillus delbrueckii subsp. bulgaricus (Q1GAA2), Lactobacillus delbrueckii subsp. bulgaricus ATCC 11842 (Q1GAA2)
Manually annotated by BRENDA team