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- PDB-8g2s: Horse liver alcohol dehydrogense His-51-Gln form complexed with N... -

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Basic information

Entry
Database: PDB / ID: 8g2s
TitleHorse liver alcohol dehydrogense His-51-Gln form complexed with NAD+ and capric acid
ComponentsAlcohol dehydrogenase E chain
KeywordsOXIDOREDUCTASE / alcohol dehydrogenase horse liver His-51 Gln substitution complex with NAD+ and capric acid
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
DECANOIC ACID / NICOTINAMIDE-ADENINE-DINUCLEOTIDE (ACIDIC FORM) / Alcohol dehydrogenase E chain
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.45 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 deprotonation of the zinc-bound ligand during catalysis by horse liver alcohol dehydrogenase
Authors: Plapp, B.V. / Kovaleva, E.G.
#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.
History
DepositionFeb 6, 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)81,97413
Polymers79,6872
Non-polymers2,28811
Water13,529751
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8040 Å2
ΔGint-115 kcal/mol
Surface area26410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.240, 51.250, 92.460
Angle α, β, γ (deg.)92.01, 102.87, 109.91
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 , 6 types, 762 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-NAJ / NICOTINAMIDE-ADENINE-DINUCLEOTIDE (ACIDIC FORM)


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-DKA / DECANOIC ACID


Mass: 172.265 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H20O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: 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
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 751 / 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: 46 % / Description: block
Crystal growTemperature: 278 K / Method: batch mode / 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 1 mM sodium caprate, 13 % 2-methyl-2,4-pentanediol, raised to ...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 1 mM sodium caprate, 13 % 2-methyl-2,4-pentanediol, raised to 25% MPD, then crystals soaked with 1 mM acetaldehyde at 278 K for 70 min and then with 100 mM sodium caprate for 2 h before pliunging into liquid N2.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 18, 2004 / Details: confocal
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.45→19.98 Å / Num. obs: 114498 / % possible obs: 87.4 % / Redundancy: 3.79 % / Rmerge(I) obs: 0.033 / Rrim(I) all: 0.039 / Χ2: 1.14 / Net I/σ(I): 23.8 / Num. measured all: 437190
Reflection shell

Diffraction-ID: 1

Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsRrim(I) allΧ2Net I/σ(I) obs
1.45-1.552.13.550.212494468110.2481.54.3
1.5-1.5685.13.740.11142222111780.130.97.1
1.56-1.6387.23.820.07843734114270.0910.7810.1
1.63-1.7288.53.820.06444389115720.0740.8213.2
1.72-1.8389.83.820.05545258117970.0640.8816.3
1.83-1.9791.13.820.04845592118990.0560.9319.9
1.97-2.1792.73.830.04246408121120.0490.9723.4
2.17-2.4894.13.830.03947382123630.0451.0627.3
2.48-3.1295.93.820.03348101125550.0391.2534.9
3.12-19.9897.73.740.02449160127840.0292.3466.9

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Processing

Software
NameVersionClassification
d*TREK9.9.9.8Ldata scaling
REFMAC5.8.0267refinement
d*TREKdata reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1n8k

1n8k


Resolution: 1.45→19.98 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.063 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18912 2272 2 %RANDOM
Rwork0.15624 ---
obs0.15689 112223 87.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.575 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å2-0.52 Å20.18 Å2
2--0.46 Å2-0.02 Å2
3----0.7 Å2
Refinement stepCycle: 1 / Resolution: 1.45→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5568 0 140 751 6459
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0136099
X-RAY DIFFRACTIONr_bond_other_d0.0010.0156007
X-RAY DIFFRACTIONr_angle_refined_deg1.9891.6888279
X-RAY DIFFRACTIONr_angle_other_deg1.4991.61314013
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7435790
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.89623.458240
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.332151112
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.2351524
X-RAY DIFFRACTIONr_chiral_restr0.1010.2835
X-RAY DIFFRACTIONr_gen_planes_refined0.010.026674
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021204
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_it1.191.313060
X-RAY DIFFRACTIONr_mcbond_other1.1891.3093059
X-RAY DIFFRACTIONr_mcangle_it1.6861.9683837
X-RAY DIFFRACTIONr_mcangle_other1.6861.9683838
X-RAY DIFFRACTIONr_scbond_it2.041.5563039
X-RAY DIFFRACTIONr_scbond_other2.0391.5563040
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0182.2354425
X-RAY DIFFRACTIONr_long_range_B_refined4.20817.0176792
X-RAY DIFFRACTIONr_long_range_B_other3.96416.3216584
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.45→1.487 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.95 92 -
Rwork0.711 4516 -
obs--47.63 %

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