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- PDB-6o91: Horse liver L57F alcohol dehydrogenase complexed with NAD and pen... -

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Basic information

Entry
Database: PDB / ID: 6o91
TitleHorse liver L57F alcohol dehydrogenase complexed with NAD and pentafluorobenzyl alcohol
ComponentsAlcohol dehydrogenase E chain
KeywordsOXIDOREDUCTASE / alcohol dehydrogenase / NAD / pentafluorobenzyl alcohol / Leu57 to Phe57 substitution / Horse liver E enzyme
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 (ACIDIC FORM) / 2,3,4,5,6-PENTAFLUOROBENZYL ALCOHOL / Alcohol dehydrogenase E chain
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsPlapp, B.V.
Funding support United States, 2items
OrganizationGrant numberCountry
Department of Health & Human Services (HHS)AA00279 United States
Department of Health & Human Services (HHS)GM078446 United States
Citation
Journal: Biochemistry / Year: 2020
Title: Substitutions of Amino Acid Residues in the Substrate Binding Site of Horse Liver Alcohol Dehydrogenase Have Small Effects on the Structures but Significantly Affect Catalysis of Hydrogen Transfer.
Authors: Kim, K. / Plapp, B.V.
#1: Journal: Biochemistry / Year: 1993
Title: Unmasking of hydrogen tunneling in the horse liver alcohol dehydrogenase reaction by site-directed mutagenesis.
Authors: Bahnson, B.J. / Park, D.H. / Kim, K. / Plapp, B.V. / Klinman, J.P.
#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: Isotope Effects in Chemistry and Biology / Year: 2006
Title: Catalysis by Alcohol Dehydrogenases
Authors: Plapp, B.V.
#4: Journal: Chem. Biol. Interact. / Year: 2017
Title: Inversion of substrate stereoselectivity of horse liver alcohol dehydrogenase by substitutions of Ser-48 and Phe-93.
Authors: Kim, K. / Plapp, B.V.
History
DepositionMar 12, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Feb 12, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Mar 11, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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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)82,35015
Polymers79,7752
Non-polymers2,57613
Water19,9071105
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation, The unit cell contains on homodimeric molecule.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7820 Å2
ΔGint-111 kcal/mol
Surface area27030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.500, 51.520, 92.540
Angle α, β, γ (deg.)91.800, 103.070, 110.420
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: 39887.289 Da / Num. of mol.: 2 / Mutation: L57F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equus caballus (horse) / Organ: liver / Plasmid: PBPP/EQADH / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blue / References: UniProt: P00327, alcohol dehydrogenase

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Non-polymers , 5 types, 1118 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) / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2
#4: Chemical ChemComp-PFB / 2,3,4,5,6-PENTAFLUOROBENZYL ALCOHOL


Mass: 198.090 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H3F5O
#5: Chemical
ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1105 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsNAJ is the dianionic form of NAD, refined with relaxed restraints on the nicotinamide ring

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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: 2.41 Å3/Da / Density % sol: 48.96 % / Description: block
Crystal growTemperature: 278 K / Method: microdialysis / pH: 7
Details: 50 MM AMMONIUM N-[TRIS(HYDROXYMETHYL) METHYL]-2-AMINOETHANE SULFONATE, PH 6.7 (AT 25 C), 0.25 MM EDTA, 10 MG/ML PROTEIN, 1 MM NAD+, 10 MM 2,3,4,5,6-PENTAFLUOROBENZYL ALCOHOL, 12 TO 25 % 2-METHYL-2,4-PENTANEDIOL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 16, 2007 / Details: ADJUSTABLE FOCUS K-B PAIR SIPLUS PT, RH COATINGS
RadiationMonochromator: DOUBLE CRYSTAL CRYOCOOLED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.09→19.89 Å / Num. obs: 273671 / % possible obs: 88 % / Redundancy: 5.52 % / Rmerge(I) obs: 0.103 / Rrim(I) all: 0.113 / Χ2: 1.17 / Net I/σ(I): 10 / Num. measured all: 1521595 / Scaling rejects: 11412
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRrim(I) allΧ2Rejects% possible all
1.09-1.133.510.2423.454729156120.2850.97450.2
1.13-1.173.50.21489815256920.2480.991782.4
1.17-1.233.920.1784.9108797277820.20612889.5
1.23-1.293.940.1625.7110730280970.1871.024390.5
1.29-1.374.350.185.4123795284220.2031.0313391.5
1.37-1.485.180.1935.7149653288460.2120.9815492.6
1.48-1.636.710.2086.7195216290700.2241.0526193.8
1.63-1.867.840.14510.4232878296390.1551.0556395.1
1.86-2.357.770.116.5236485300410.1071.29304396.6
2.35-19.896.970.09420219497304700.1031.73716698

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
d*TREK9.9.9.8Ldata scaling
PDB_EXTRACT3.24data extraction
d*TREKdata reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DWV
Resolution: 1.1→19.9 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.984 / SU B: 0.74 / SU ML: 0.016 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.026 / ESU R Free: 0.025 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1324 2639 1 %RANDOM
Rwork0.1183 ---
obs0.1184 267504 89.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 66.83 Å2 / Biso mean: 15.169 Å2 / Biso min: 7.58 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å2-0.77 Å20.19 Å2
2--0.63 Å2-0.01 Å2
Refinement stepCycle: final / Resolution: 1.1→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5576 0 174 1138 6888
Biso mean--19.3 29.19 -
Num. residues----748
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0136272
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176086
X-RAY DIFFRACTIONr_angle_refined_deg1.8361.698542
X-RAY DIFFRACTIONr_angle_other_deg1.5411.59114240
X-RAY DIFFRACTIONr_dihedral_angle_1_deg17.6495.38829
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.78823.067238
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.187151124
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4221524
X-RAY DIFFRACTIONr_chiral_restr0.1060.2867
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.027569
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021152
X-RAY DIFFRACTIONr_rigid_bond_restr2.327312356
LS refinement shellResolution: 1.1→1.128 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.188 106 -
Rwork0.179 11746 -
all-11852 -
obs--53.12 %

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