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Structure paper

TitlePotassium binding by carbonyl clusters, halophilic adaptation and catalysis of Haloferax mediterranei D-2-hydroxyacid dehydrogenase.
Journal, issue, pagesCommun Biol, Vol. 8, Page 1170-1170, Year 2025
Publish dateNov 23, 2016 (structure data deposition date)
AuthorsDomenech, J. / Pramanpol, N. / Bisson, C. / Sedelnikova, S.E. / Barrett, J.R. / Dakhil, A.A.A.B. / Mykhaylyk, V. / Abdelhameed, A.S. / Harding, S.E. / Rice, D.W. ...Domenech, J. / Pramanpol, N. / Bisson, C. / Sedelnikova, S.E. / Barrett, J.R. / Dakhil, A.A.A.B. / Mykhaylyk, V. / Abdelhameed, A.S. / Harding, S.E. / Rice, D.W. / Baker, P.J. / Ferrer, J.
External linksCommun Biol / PubMed:40770045
MethodsX-ray diffraction
Resolution1.16 - 2.252 Å
Structure data

PDB-5mh5:
D-2-hydroxyacid dehydrogenases (D2-HDH) from Haloferax mediterranei in complex with 2-keto-hexanoic acid and NADP+ (1.4 A resolution)
Method: X-RAY DIFFRACTION / Resolution: 1.4 Å

PDB-5mh6:
D-2-hydroxyacid dehydrogenases (D2-HDH) from Haloferax mediterranei in complex with 2-ketohexanoic acid and NAD+ (1.35 A resolution)
Method: X-RAY DIFFRACTION / Resolution: 1.35 Å

PDB-5mha:
D-2-hydroxyacid dehydrogenases (D2-HDH) from Haloferax mediterranei in complex with a mixture of 2-ketohexanoic acid and 2-hydroxyhexanoic acid, and NADPH (1.57 A resolution)
Method: X-RAY DIFFRACTION / Resolution: 1.57 Å

PDB-8qza:
D-2-hydroxyacid dehydrogenase (D2-HDH) from Haloferax mediterranei apo-enzyme (2.25 A resolution)
Method: X-RAY DIFFRACTION / Resolution: 2.252 Å

PDB-8qzb:
D-2-hydroxyacid dehydrogenase (D2HDH) from Haloferax mediterranei in complex with 2-ketohexanoic acid, NAD+ and chloride (1.16 A resolution)
Method: X-RAY DIFFRACTION / Resolution: 1.16 Å

PDB-9ibe:
D-2-hydroxyacid dehydrogenase (D2HDH) from Haloferax mediterranei in complex with potassium, 2-ketohexanoic acid, NADP+ and chloride
Method: X-RAY DIFFRACTION / Resolution: 1.26 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-7N5:
2-Ketohexanoic acid

ChemComp-NAP:
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

ChemComp-SO4:
SULFATE ION

ChemComp-HOH:
WATER

ChemComp-EDO:
1,2-ETHANEDIOL

ChemComp-NAD:
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD*YM

ChemComp-NA:
Unknown entry

ChemComp-NDP:
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

ChemComp-7N6:
(2R)-2-hydroxyhexanoic acid

ChemComp-ACT:
ACETATE ION

ChemComp-CL:
Unknown entry

ChemComp-K:
Unknown entry

Source
  • haloferax mediterranei atcc 33500 (archaea)
  • haloferax mediterranei (archaea)
KeywordsOXIDOREDUCTASE / D-2-hydroxyacid dehydrogenase / halophile / chiral specificity / reaction mechanism / halophilic adaptation domain closure mechanism / complex halophilic adaptation substrate specificity mechanism / halophilic adaptation / potassium binding / complex / substrate specificity

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