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- PDB-2jhf: Structural evidence for a ligand coordination switch in liver alc... -

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Basic information

Entry
Database: PDB / ID: 2jhf
TitleStructural evidence for a ligand coordination switch in liver alcohol dehydrogenase
ComponentsALCOHOL DEHYDROGENASE E CHAIN
KeywordsOXIDOREDUCTASE / METAL COORDINATION / NAD / ZINC / INHIBITION / ACETYLATION / METAL-BINDING / ALCOHOL DEHYDROGENASE
Function / homology
Function and homology information


alcohol dehydrogenase activity, zinc-dependent / ethanol oxidation / NAD-retinol dehydrogenase activity / alcohol dehydrogenase / retinoic acid metabolic process / retinol metabolic process / zinc ion binding / cytosol
Similarity search - Function
Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase ...Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / GroES-like superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Alcohol dehydrogenase E chain
Similarity search - Component
Biological speciesEQUUS CABALLUS (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å
AuthorsMeijers, R. / Adolph, H.W. / Dauter, Z. / Wilson, K.S. / Lamzin, V.S. / Cedergren-Zeppezauer, E.S.
CitationJournal: Biochemistry / Year: 2007
Title: Structural Evidence for a Ligand Coordination Switch in Liver Alcohol Dehydrogenase
Authors: Meijers, R. / Adolph, H.W. / Dauter, Z. / Wilson, K.S. / Lamzin, V.S. / Cedergren-Zeppezauer, E.S.
History
DepositionFeb 22, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ALCOHOL DEHYDROGENASE E CHAIN
B: ALCOHOL DEHYDROGENASE E CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,63910
Polymers79,7072
Non-polymers1,9338
Water22,3571241
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)50.870, 44.460, 94.180
Angle α, β, γ (deg.)104.40, 101.40, 71.10
Int Tables number1
Space group name H-MP1

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Components

#1: Protein ALCOHOL DEHYDROGENASE E CHAIN / LIVER ALCOHOL DEHYDROGENASE


Mass: 39853.273 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: ADDUCT BETWEEN NADH AND A HYDROXIDE ION / Source: (natural) EQUUS CABALLUS (horse) / Organ: LIVER / Variant: HORSE LIVER / References: UniProt: P00327, alcohol dehydrogenase
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1241 / Source method: isolated from a natural source / Formula: H2O

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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: 2.2 Å3/Da / Density % sol: 45 %
Crystal growDetails: DIALYSIS 30 MM TRIS/HCL PH 8.2 25 % MPD

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.84
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.84 Å / Relative weight: 1
ReflectionResolution: 1→25 Å / Num. obs: 323884 / % possible obs: 80 % / Observed criterion σ(I): 0 / Redundancy: 1.7 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 16.7
Reflection shellResolution: 1→1.03 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 1.4 / % possible all: 67.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HEU

1heu


Resolution: 1→20 Å / Cor.coef. Fo:Fc: 0.987 / Cor.coef. Fo:Fc free: 0.979 / SU B: 1.055 / SU ML: 0.022 / Cross valid method: THROUGHOUT / ESU R: 0.023 / ESU R Free: 0.025 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. WATER MOLECULES Y1001 AND Z1001 ARE CLOSE TO THE PYRIDINE RING OF THE NADH MOLECULE AND INTERPRETED AS HYDROXIDE ION ADDUCTS.
RfactorNum. reflection% reflectionSelection details
Rfree0.152 1613 0.5 %RANDOM
Rwork0.125 ---
obs0.125 322228 79.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 12.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å21.49 Å20.15 Å2
2---0.01 Å2-0.05 Å2
3----1.28 Å2
Refinement stepCycle: LAST / Resolution: 1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5570 0 100 1241 6911
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0236111
X-RAY DIFFRACTIONr_bond_other_d00.025730
X-RAY DIFFRACTIONr_angle_refined_deg2.2072.0558327
X-RAY DIFFRACTIONr_angle_other_deg3.293.02213471
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2925803
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.00924.486214
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.66151104
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6581528
X-RAY DIFFRACTIONr_chiral_restr0.3050.2983
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.026682
X-RAY DIFFRACTIONr_gen_planes_other0.0320.021138
X-RAY DIFFRACTIONr_nbd_refined0.2430.21009
X-RAY DIFFRACTIONr_nbd_other0.2250.24916
X-RAY DIFFRACTIONr_nbtor_refined0.1640.22745
X-RAY DIFFRACTIONr_nbtor_other0.0950.22646
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.2648
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2340.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2260.221
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2430.247
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.1361.55005
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.13126337
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.3432578
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.464.51972
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1→1.03 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.32 93
Rwork0.309 20019

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