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- PDB-8g2x: Horse liver alcohol dehydrogense His-51-Gln form complexed with N... -

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Basic information

Entry
Database: PDB / ID: 8g2x
TitleHorse liver alcohol dehydrogense His-51-Gln form complexed with NAD+ and pyrazole
ComponentsAlcohol dehydrogenase E chain
KeywordsOXIDOREDUCTASE / alcohol dehydrogenase horse liver His-48 Gln substitution complex with NAD+ and pyrazole
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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE (ACIDIC FORM) / PYRAZOLE / Alcohol dehydrogenase E chain
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.47 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.
#6: Journal: Biochemistry / Year: 2003
Title: Amino acid residues in the nicotinamide binding site contribute to catalysis by horse liver alcohol dehydrogenase.
Authors: Rubach, J.K. / Plapp, B.V.
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)81,64812
Polymers79,6872
Non-polymers1,96110
Water12,538696
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7030 Å2
ΔGint-113 kcal/mol
Surface area26460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.130, 50.800, 92.410
Angle α, β, γ (deg.)92.09, 102.96, 109.68
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, 706 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-PZO / PYRAZOLE


Mass: 68.077 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4N2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / 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.: 696 / 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: 2.24 Å3/Da / Density % sol: 45 % / 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 15 mM pyrazole, 13 % 2-methyl-2,4-pentanediol, raised to 25% MPD ...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 15 mM pyrazole, 13 % 2-methyl-2,4-pentanediol, raised to 25% MPD 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: Apr 4, 2003 / 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: 1.47→19.98 Å / Num. obs: 112102 / % possible obs: 90.1 % / Redundancy: 1.95 % / Rmerge(I) obs: 0.029 / Rrim(I) all: 0.041 / Χ2: 1.24 / Net I/σ(I): 14.3 / Num. measured all: 219812
Reflection shell

Diffraction-ID: 1

Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsRrim(I) allΧ2Net I/σ(I) obs
1.47-1.5283.11.920.24820072103780.3511.32.5
1.52-1.5884.31.920.18120284104780.2571.253.2
1.58-1.6686.11.910.14220548106670.2011.234.1
1.66-1.7487.61.910.10921012108830.1541.255.4
1.74-1.8589.51.920.07921654111510.1111.247.7
1.85-1.9990.91.950.05722246113070.081.2210.8
1.99-2.292.41.970.04922875115200.071.2213.1
2.2-2.5194.11.980.03623177116600.0511.1617.8
2.51-3.1695.71.980.02723737119290.0381.225.1
3.16-19.9897.61.980.01524207121290.0221.2946

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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: 1N92

1n92


Resolution: 1.47→19.99 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.269 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19092 1659 1.5 %RANDOM
Rwork0.17317 ---
obs0.17343 110430 90.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.302 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å2-0.85 Å20.21 Å2
2--1.05 Å20.26 Å2
3----0.88 Å2
Refinement stepCycle: 1 / Resolution: 1.47→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5568 0 118 696 6382
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0135992
X-RAY DIFFRACTIONr_bond_other_d0.0010.0155851
X-RAY DIFFRACTIONr_angle_refined_deg1.8781.6828144
X-RAY DIFFRACTIONr_angle_other_deg1.4931.59413617
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8185787
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.49523.233232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.017151075
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.3331524
X-RAY DIFFRACTIONr_chiral_restr0.0960.2821
X-RAY DIFFRACTIONr_gen_planes_refined0.010.026605
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021201
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_it1.411.7093049
X-RAY DIFFRACTIONr_mcbond_other1.4091.7083048
X-RAY DIFFRACTIONr_mcangle_it1.932.5653818
X-RAY DIFFRACTIONr_mcangle_other1.932.5653819
X-RAY DIFFRACTIONr_scbond_it2.3951.9672943
X-RAY DIFFRACTIONr_scbond_other2.3951.9682944
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5492.8424306
X-RAY DIFFRACTIONr_long_range_B_refined4.67721.6736707
X-RAY DIFFRACTIONr_long_range_B_other4.45720.9566507
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.47→1.508 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.459 108 -
Rwork0.497 7485 -
obs--82.9 %

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