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- PDB-8g41: Horse liver alcohol dehydrogense His-51-Gln form complexed with NADH -

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Basic information

Entry
Database: PDB / ID: 8g41
TitleHorse liver alcohol dehydrogense His-51-Gln form complexed with NADH
ComponentsAlcohol dehydrogenase E chain
KeywordsOXIDOREDUCTASE / alcohol dehydrogenase horse liver His-51-Gln substitution complex with NADH
Function / homology
Function and homology information


all-trans-retinol dehydrogenase (NAD+) 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. / 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 ...Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / 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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Alcohol dehydrogenase E chain
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsPlapp, B.V.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Alcohol Abuse and Alcoholism (NIH/NIAAA)AA00279 United States
Citation
Journal: To Be Published
Title: Histidine-51 facilitates deprotonatation of the zinc-bound ligand during catalysis by horse liver alcohol dehydrogenase
Authors: Plapp, B.V.
#1: Journal: Chem.Biol.Interact. / Year: 2024
Title: Solvent isotope and mutagenesis studies on the proton relay system in yeast alcohol dehydrogenase 1.
Authors: Plapp, B.V.
#2: Journal: Biochemistry / Year: 2012
Title: Atomic-resolution structures of horse liver alcohol dehydrogenase with NAD(+) and fluoroalcohols define strained Michaelis complexes.
Authors: Plapp, B.V. / Ramaswamy, S.
#3: Journal: Biochemistry / Year: 2004
Title: Participation of histidine-51 in catalysis by horse liver alcohol dehydrogenase.
Authors: LeBrun, L.A. / Park, D.H. / Ramaswamy, S. / Plapp, B.V.
#4: Journal: Ph.D. Thesis / Year: 2004
Title: Proton Transfer In The Mechanism Of Horse Liver Alcohol Dehydrogenase
Authors: Kovaleva, E.G.
#5: Journal: Biochemistry / Year: 1999
Title: Control of coenzyme binding to horse liver alcohol dehydrogenase.
Authors: Plapp, B.V. / LeBrun, L.A.
#6: Journal: Biochemistry / Year: 2017
Title: Horse Liver Alcohol Dehydrogenase: Zinc Coordination and Catalysis.
Authors: Plapp, B.V. / Savarimuthu, B.R. / Ferraro, D.J. / Rubach, J.K. / Brown, E.N. / Ramaswamy, S.
History
DepositionFeb 8, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.2Sep 4, 2024Group: Database references / Category: citation / citation_author

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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)81,75212
Polymers79,6872
Non-polymers2,06510
Water11,944663
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7280 Å2
ΔGint-142 kcal/mol
Surface area26640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.060, 51.320, 92.750
Angle α, β, γ (deg.)91.90, 103.08, 109.89
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Alcohol dehydrogenase E chain


Mass: 39843.258 Da / Num. of mol.: 2 / Mutation: H51Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equus caballus (horse) / Organ: liver / Production host: Escherichia coli (E. coli) / Variant (production host): XL1-Blue / References: UniProt: P00327, alcohol dehydrogenase

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Non-polymers , 5 types, 673 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H29N7O14P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#5: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 663 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.26 Å3/Da / Density % sol: 47 % / Description: block
Crystal growTemperature: 278 K / Method: microdialysis / pH: 7
Details: 10 mg/ml protein in 50 mM ammonium N-[tris(hydroxymethyl)methyl]-2-aminoethanesulfate buffer with 0.25 mM EDTA, 2 mM NAD+ and 0.1 mM 2,2,2-trifluoroetanol, crystals formed at 13 % 2-methyl- ...Details: 10 mg/ml protein in 50 mM ammonium N-[tris(hydroxymethyl)methyl]-2-aminoethanesulfate buffer with 0.25 mM EDTA, 2 mM NAD+ and 0.1 mM 2,2,2-trifluoroetanol, crystals formed at 13 % 2-methyl-2,4-pentanediol, raised to 25% MPD before crystal pliunged into liquid N2.
Temp details: pH 6.7 at 298

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU R-AXIS IV / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 24, 2004 / Details: confocal
RadiationMonochromator: grafite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.5→19.91 Å / Num. obs: 107864 / % possible obs: 91.2 % / Redundancy: 3.84 % / Rmerge(I) obs: 0.031 / Rrim(I) all: 0.036 / Χ2: 1.13 / Net I/σ(I): 25
Reflection shell

Diffraction-ID: 1

Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsRrim(I) allΧ2Net I/σ(I) obs
1.5-1.5584.93.750.1738068100370.1991.545.7
1.55-1.62873.810.09639630102920.1120.998.5
1.62-1.69883.820.07540171104020.0870.9210.6
1.69-1.7889.23.820.06240962105900.0720.9213.4
1.78-1.8990.23.830.05141250106440.0590.8517.1
1.89-2.0491.63.860.04341909108330.050.8520.8
2.04-2.2493.13.860.03742622110230.0420.9527.1
2.24-2.5694.43.870.03343386111800.0381.0532.2
2.56-3.2395.93.880.02744132113360.0321.2140.7
3.23-19.997.53.870.02345049115270.0261.9565.6

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Processing

Software
NameVersionClassification
d*TREK9.9.9.8Ldata scaling
REFMAC5.8.0267refinement
O14model building
REFMAC5.8.0267phasing
d*TREKdata processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8g2l

8g2l


Resolution: 1.5→19.91 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.123 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.07 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17722 2114 2 %RANDOM
Rwork0.15508 ---
obs0.15551 105749 91.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.969 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å2-0.42 Å20.23 Å2
2--0.5 Å20.1 Å2
3----0.8 Å2
Refinement stepCycle: 1 / Resolution: 1.5→19.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5568 0 124 663 6355
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0136053
X-RAY DIFFRACTIONr_bond_other_d0.0010.0155948
X-RAY DIFFRACTIONr_angle_refined_deg1.9391.6828235
X-RAY DIFFRACTIONr_angle_other_deg1.511.59713861
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9145793
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.71123.403238
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.511151109
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.5751524
X-RAY DIFFRACTIONr_chiral_restr0.0990.2833
X-RAY DIFFRACTIONr_gen_planes_refined0.010.026651
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021203
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_it1.291.3633056
X-RAY DIFFRACTIONr_mcbond_other1.291.3623055
X-RAY DIFFRACTIONr_mcangle_it1.772.0463831
X-RAY DIFFRACTIONr_mcangle_other1.772.0463832
X-RAY DIFFRACTIONr_scbond_it2.1541.6182997
X-RAY DIFFRACTIONr_scbond_other2.1531.6182998
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1842.3234383
X-RAY DIFFRACTIONr_long_range_B_refined4.11317.2086675
X-RAY DIFFRACTIONr_long_range_B_other3.9616.7486530
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 153 -
Rwork0.366 7176 -
obs--84.32 %

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