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- PDB-8qzb: D-2-hydroxyacid dehydrogenase (D2HDH) from Haloferax mediterranei... -

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Basic information

Entry
Database: PDB / ID: 8qzb
TitleD-2-hydroxyacid dehydrogenase (D2HDH) from Haloferax mediterranei in complex with 2-ketohexanoic acid, NAD+ and chloride (1.16 A resolution)
ComponentsD-2-hydroxyacid dehydrogenase
KeywordsOXIDOREDUCTASE / complex halophilic adaptation substrate specificity mechanism
Function / homology
Function and homology information


NADH binding / carboxylic acid binding / carboxylic acid metabolic process / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / NADPH binding
Similarity search - Function
: / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
2-Ketohexanoic acid / ACETATE ION / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / D-2-hydroxyacid dehydrogenase
Similarity search - Component
Biological speciesHaloferax mediterranei (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.16 Å
AuthorsBaker, P.J. / Barrett, J.R. / Dakhil, A.A.A.B. / Domenech, J. / Bisson, C. / Pramanpol, N. / Ferrer, J. / Rice, D.W.
Funding support United Kingdom, Spain, Thailand, Libya, 5items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/1003703/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/D524975/1 United Kingdom
Other governmentGV05/166 Spain
Other government Thailand
Other governmentLibya
CitationJournal: Commun Biol / Year: 2025
Title: Potassium binding by carbonyl clusters, halophilic adaptation and catalysis of Haloferax mediterranei D-2-hydroxyacid dehydrogenase.
Authors: 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.
History
DepositionOct 26, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 6, 2025Provider: repository / Type: Initial release
Revision 1.1Aug 20, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: D-2-hydroxyacid dehydrogenase
B: D-2-hydroxyacid dehydrogenase
C: D-2-hydroxyacid dehydrogenase
D: D-2-hydroxyacid dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,79751
Polymers133,4724
Non-polymers4,32547
Water29,1661619
1
A: D-2-hydroxyacid dehydrogenase
B: D-2-hydroxyacid dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,95227
Polymers66,7362
Non-polymers2,21625
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10090 Å2
ΔGint-190 kcal/mol
Surface area23740 Å2
MethodPISA
2
C: D-2-hydroxyacid dehydrogenase
D: D-2-hydroxyacid dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,84424
Polymers66,7362
Non-polymers2,10922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9590 Å2
ΔGint-174 kcal/mol
Surface area23570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.182, 74.777, 78.172
Angle α, β, γ (deg.)109.074, 107.882, 95.560
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
D-2-hydroxyacid dehydrogenase


Mass: 33367.992 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haloferax mediterranei (archaea) / Gene: ddh / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2VEQ7

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Non-polymers , 7 types, 1666 molecules

#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical
ChemComp-7N5 / 2-Ketohexanoic acid


Mass: 130.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H10O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1619 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.7 % / Description: blocks
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Protein buffer: 20mM Tris/HCl pH 8.0 2mM EDTA 1M NaCl 50mM 2-ketohexanoic acid 5mM NAD+ Crystallisation conditions: 0.1M Tris/HCl pH 8.0 0.5M Magnesium acetate 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.16→46.633 Å / Num. obs: 427918 / % possible obs: 93.9 % / Redundancy: 3.6 % / CC1/2: 0.94 / Rpim(I) all: 0.042 / Net I/σ(I): 17.1
Reflection shellResolution: 1.16→1.18 Å / Redundancy: 3.3 % / Num. unique obs: 18892 / CC1/2: 0.56 / Rpim(I) all: 0.5 / % possible all: 83.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
xia2data reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.16→46.633 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.975 / WRfactor Rfree: 0.15 / WRfactor Rwork: 0.122 / SU B: 1.258 / SU ML: 0.025 / Average fsc free: 0.9747 / Average fsc work: 0.9817 / Cross valid method: FREE R-VALUE / ESU R: 0.032 / ESU R Free: 0.033
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1651 21342 4.988 %
Rwork0.1346 406541 -
all0.136 --
obs-427883 93.897 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 14.538 Å2
Baniso -1Baniso -2Baniso -3
1-0.041 Å2-0.179 Å2-0.092 Å2
2--0.243 Å20.081 Å2
3----0.159 Å2
Refinement stepCycle: LAST / Resolution: 1.16→46.633 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9396 0 266 1619 11281
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01210069
X-RAY DIFFRACTIONr_bond_other_d0.0030.0169082
X-RAY DIFFRACTIONr_angle_refined_deg1.6891.66413816
X-RAY DIFFRACTIONr_angle_other_deg0.7061.5820942
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.44851296
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.294591
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.06554
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.192101468
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.50910491
X-RAY DIFFRACTIONr_chiral_restr0.0960.21562
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212215
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022253
X-RAY DIFFRACTIONr_nbd_refined0.2280.21925
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1720.28641
X-RAY DIFFRACTIONr_nbtor_refined0.1740.25020
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0730.25062
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.21100
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0520.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1980.260
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2770.228
X-RAY DIFFRACTIONr_nbd_other0.2030.2103
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2360.287
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0050.21
X-RAY DIFFRACTIONr_mcbond_it9.1151.4035006
X-RAY DIFFRACTIONr_mcbond_other9.1111.4035005
X-RAY DIFFRACTIONr_mcangle_it11.4232.5336265
X-RAY DIFFRACTIONr_mcangle_other11.4222.5336266
X-RAY DIFFRACTIONr_scbond_it11.6451.7085063
X-RAY DIFFRACTIONr_scbond_other11.6441.7085064
X-RAY DIFFRACTIONr_scangle_it14.9432.997520
X-RAY DIFFRACTIONr_scangle_other14.9422.997521
X-RAY DIFFRACTIONr_lrange_it20.02220.98211694
X-RAY DIFFRACTIONr_lrange_other18.12418.13911145
X-RAY DIFFRACTIONr_rigid_bond_restr4.983319151
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.16-1.190.27614370.255272770.256337200.9440.9585.15420.247
1.19-1.2230.2516000.231282650.232328770.9520.9690.83860.225
1.223-1.2580.23315010.211278080.213319290.960.96791.79430.203
1.258-1.2970.21714220.198271670.199309880.9670.97292.25830.187
1.297-1.3390.21413520.183265710.185301060.9690.97792.7490.168
1.339-1.3860.20313070.172258460.174291260.9720.9893.2260.154
1.386-1.4390.18913140.147249190.149279960.9760.98593.70270.128
1.439-1.4970.17412520.132241410.134269780.9760.98994.12480.112
1.497-1.5640.15612350.112232660.114258860.9850.99294.64960.094
1.564-1.640.14911790.103223700.105247740.9860.99395.05530.086
1.64-1.7290.14110760.097214320.099235430.9880.99495.60380.081
1.729-1.8330.1410750.1203010.102222510.9880.99496.06760.085
1.833-1.960.14910370.107191270.109208990.9870.99396.48310.094
1.96-2.1160.1459630.109179360.11194870.9880.99396.98260.098
2.116-2.3180.1388510.104165890.106179020.9890.99497.41930.095
2.318-2.5910.1427320.11151410.111162210.9880.99397.85460.101
2.591-2.990.1546830.128133890.129143110.9840.9998.330.122
2.99-3.6580.1546040.136113120.137120640.9860.9998.77320.137
3.658-5.1570.144480.12888020.12993250.9890.99199.19570.139
5.157-46.6330.2072740.18248840.18351810.9780.98499.55610.198

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