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- PDB-5mh5: D-2-hydroxyacid dehydrogenases (D2-HDH) from Haloferax mediterran... -

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Basic information

Entry
Database: PDB / ID: 5mh5
TitleD-2-hydroxyacid dehydrogenases (D2-HDH) from Haloferax mediterranei in complex with 2-keto-hexanoic acid and NADP+ (1.4 A resolution)
ComponentsD-2-hydroxyacid dehydrogenase
KeywordsOXIDOREDUCTASE / D-2-hydroxyacid dehydrogenase / halophile / chiral specificity / reaction 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 Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2-Ketohexanoic acid / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / D-2-hydroxyacid dehydrogenase
Similarity search - Component
Biological speciesHaloferax mediterranei ATCC 33500 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsBisson, C. / Baker, P.J. / Domenech Perez, J. / Pramanpol, N. / Harding, S.E. / Rice, D.W. / Ferrer, J.
Funding support Spain, United Kingdom, 4items
OrganizationGrant numberCountry
University of AlicanteVIGROB046 Spain
Biotechnology and Biological Sciences Research Council United Kingdom
Wellcome Trust United Kingdom
Wolfson Foundation United Kingdom
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
DepositionNov 23, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 2.0Feb 14, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Aug 20, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)69,18629
Polymers66,7362
Non-polymers2,45027
Water12,178676
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9670 Å2
ΔGint-161 kcal/mol
Surface area24060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.530, 87.400, 66.100
Angle α, β, γ (deg.)90.00, 96.34, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein D-2-hydroxyacid dehydrogenase / D2-HDH / D-specific 2-hydroxyacid dehydrogenase


Mass: 33367.992 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haloferax mediterranei ATCC 33500 (archaea)
Gene: ddh, serA5, HFX_2024 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q2VEQ7, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor

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Non-polymers , 5 types, 703 molecules

#2: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-7N5 / 2-Ketohexanoic acid


Mass: 130.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H10O3
#4: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 676 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.69 Å3/Da / Density % sol: 54.27 % / Description: Plates
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Protein buffer: 20 mM Tris-HCl pH8, 3 mM EDTA and 1 M NaCl Crystallisation condition: 0.1 M Tris-HCl pH8, 0.5 M magnesium acetate and 18 % PEG3350 Ligands: 5 mM NADP+ and 50 mM 2-keto-hexanoic acid

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9507 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 6, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9507 Å / Relative weight: 1
ReflectionResolution: 1.4→52.51 Å / Num. obs: 132820 / % possible obs: 95.5 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.036 / Net I/σ(I): 15.4
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 8 % / Rmerge(I) obs: 0.377 / Mean I/σ(I) obs: 2.4 / Num. unique all: 6288 / % possible all: 91.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
iMOSFLMdata reduction
Aimlessdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MH6

5mh6


Resolution: 1.4→52.51 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.863 / SU ML: 0.032 / Cross valid method: THROUGHOUT / ESU R: 0.054 / ESU R Free: 0.051 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16701 6675 5.1 %RANDOM
Rwork0.13587 ---
obs0.13746 125480 95.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 20.538 Å2
Baniso -1Baniso -2Baniso -3
1--0.88 Å20 Å20.1 Å2
2---0.31 Å20 Å2
3---1.14 Å2
Refinement stepCycle: 1 / Resolution: 1.4→52.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4698 0 145 676 5519
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0195023
X-RAY DIFFRACTIONr_bond_other_d0.0030.024582
X-RAY DIFFRACTIONr_angle_refined_deg1.5881.986879
X-RAY DIFFRACTIONr_angle_other_deg1.315310543
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1985624
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.91823.566244
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.03515737
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.891545
X-RAY DIFFRACTIONr_chiral_restr0.0870.2777
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215722
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021135
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it6.5731.5572478
X-RAY DIFFRACTIONr_mcbond_other6.5731.5572477
X-RAY DIFFRACTIONr_mcangle_it6.3112.3353095
X-RAY DIFFRACTIONr_mcangle_other6.312.3363096
X-RAY DIFFRACTIONr_scbond_it9.5282.0372545
X-RAY DIFFRACTIONr_scbond_other9.4932.0322538
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.9632.8213766
X-RAY DIFFRACTIONr_long_range_B_refined7.94721.1965795
X-RAY DIFFRACTIONr_long_range_B_other7.94621.1945796
X-RAY DIFFRACTIONr_rigid_bond_restr12.36139605
X-RAY DIFFRACTIONr_sphericity_free26.8665428
X-RAY DIFFRACTIONr_sphericity_bonded27.57459759
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 443 -
Rwork0.273 8929 -
obs--91.23 %

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