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- PDB-5env: YEAST ALCOHOL DEHYDROGENASE WITH BOUND COENZYME -

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Basic information

Entry
Database: PDB / ID: 5env
TitleYEAST ALCOHOL DEHYDROGENASE WITH BOUND COENZYME
ComponentsAlcohol dehydrogenase 1
KeywordsOXIDOREDUCTASE / TETRAMER / ROSSMANN / NAD / ALCOHOL
Function / homology
Function and homology information


methylglyoxal reductase (NADH-dependent) activity / glycolytic fermentation to ethanol => GO:0019655 / amino acid catabolic process to alcohol via Ehrlich pathway / replication compartment / NADH oxidation / alcohol dehydrogenase (NAD+) activity / melatonin binding / alcohol dehydrogenase / regulation of viral genome replication / zinc ion binding ...methylglyoxal reductase (NADH-dependent) activity / glycolytic fermentation to ethanol => GO:0019655 / amino acid catabolic process to alcohol via Ehrlich pathway / replication compartment / NADH oxidation / alcohol dehydrogenase (NAD+) activity / melatonin binding / alcohol dehydrogenase / regulation of viral genome replication / zinc ion binding / identical protein binding / plasma membrane / cytoplasm
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 / Zinc-binding dehydrogenase / Alcohol dehydrogenase-like, C-terminal / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Enoylreductase / Polyketide synthase, enoylreductase domain ...Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Zinc-binding dehydrogenase / Alcohol dehydrogenase-like, C-terminal / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Enoylreductase / Polyketide synthase, enoylreductase domain / 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
TRIFLUOROETHANOL / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Alcohol dehydrogenase 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (baker's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsPlapp, B.V. / Charlier Jr., H.A. / Ramaswamy, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB 95-06831 United States
Citation
Journal: Arch.Biochem.Biophys. / Year: 2015
Title: Mechanistic implications from structures of yeast alcohol dehydrogenase complexed with coenzyme and an alcohol.
Authors: Plapp, B.V. / Charlier, H.A. / Ramaswamy, S.
#1: Journal: Biochemistry / Year: 2014
Title: Yeast alcohol dehydrogenase structure and catalysis.
Authors: Savarimuthu Baskar Raj / S Ramaswamy / Bryce V Plapp /
Abstract: Yeast (Saccharomyces cerevisiae) alcohol dehydrogenase I (ADH1) is the constitutive enzyme that reduces acetaldehyde to ethanol during the fermentation of glucose. ADH1 is a homotetramer of subunits ...Yeast (Saccharomyces cerevisiae) alcohol dehydrogenase I (ADH1) is the constitutive enzyme that reduces acetaldehyde to ethanol during the fermentation of glucose. ADH1 is a homotetramer of subunits with 347 amino acid residues. A structure for ADH1 was determined by X-ray crystallography at 2.4 Å resolution. The asymmetric unit contains four different subunits, arranged as similar dimers named AB and CD. The unit cell contains two different tetramers made up of "back-to-back" dimers, AB:AB and CD:CD. The A and C subunits in each dimer are structurally similar, with a closed conformation, bound coenzyme, and the oxygen of 2,2,2-trifluoroethanol ligated to the catalytic zinc in the classical tetrahedral coordination with Cys-43, Cys-153, and His-66. In contrast, the B and D subunits have an open conformation with no bound coenzyme, and the catalytic zinc has an alternative, inverted coordination with Cys-43, Cys-153, His-66, and the carboxylate of Glu-67. The asymmetry in the dimeric subunits of the tetramer provides two structures that appear to be relevant for the catalytic mechanism. The alternative coordination of the zinc may represent an intermediate in the mechanism of displacement of the zinc-bound water with alcohol or aldehyde substrates. Substitution of Glu-67 with Gln-67 decreases the catalytic efficiency by 100-fold. Previous studies of structural modeling, evolutionary relationships, substrate specificity, chemical modification, and site-directed mutagenesis are interpreted more fully with the three-dimensional structure.
#2: Journal: J.Mol.Biol. / Year: 1994
Title: Crystallization And Preliminary Crystallographic Of Saccharomyces Cerevisiae Alcohol Dehydrogenase I
Authors: Ramaswamy, S. / Kratzer, D.A. / Hershey, A.D. / Rogers, P.H. / Arnone, A. / Eklund, H. / Plapp, B.V.
History
DepositionNov 9, 2015Deposition site: RCSB / Processing site: RCSB
SupersessionNov 25, 2015ID: 5C1K
Revision 1.0Nov 25, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations
Category: citation / diffrn_detector ...citation / diffrn_detector / diffrn_source / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_detector.detector ..._citation.journal_id_CSD / _diffrn_detector.detector / _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Data collection / Category: diffrn_source / pdbx_audit_support
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alcohol dehydrogenase 1
B: Alcohol dehydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,30810
Polymers73,5202
Non-polymers1,7898
Water36020
1
A: Alcohol dehydrogenase 1
B: Alcohol dehydrogenase 1
hetero molecules

A: Alcohol dehydrogenase 1
B: Alcohol dehydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,61720
Polymers147,0404
Non-polymers3,57716
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area17200 Å2
ΔGint-166 kcal/mol
Surface area49550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.256, 146.256, 65.980
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

#1: Protein Alcohol dehydrogenase 1 / / Alcohol dehydrogenase I / YADH-1


Mass: 36759.906 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: ADH1, ADC1, YOL086C, O0947 / Plasmid: YEP13 / Production host: SACCHAROMYCES CEREVISIAE (baker's yeast) / Strain (production host): ATC 204508 / References: UniProt: P00330, alcohol dehydrogenase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#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-ETF / TRIFLUOROETHANOL / 2,2,2-Trifluoroethanol


Mass: 100.040 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3F3O
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.77 Å3/Da / Density % sol: 55.61 % / Description: hexagonal plates
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.4
Details: 100 MM SODIUM N-TRIS(HYDROXYMETHYL)METHYL-3-AMINOPROPANESULFONATE, 0.25 MM EDTA, 2 MM NAD+, 0.2 M 2,2,2-TRIFLUOROETHANOL, 1 MM YBCL3, 16 % POLYETHYETHYLENE GLYCOL 5000 MONOMETHYL ETHER, PH 8.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 1.39 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: May 18, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.39 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.714
11-h,-k,l20.286
ReflectionResolution: 3→20 Å / Num. all: 74630 / Num. obs: 15427 / % possible obs: 98.1 % / Redundancy: 4.8 % / Biso Wilson estimate: 60 Å2 / Rsym value: 0.064 / Net I/σ(I): 18
Reflection shellResolution: 3→3.08 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.326 / Mean I/σ(I) obs: 2.8 / Rsym value: 0.326 / % possible all: 84.41

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4W6Z
Resolution: 3→19.99 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.913 / SU B: 33.393 / SU ML: 0.282 / Cross valid method: THROUGHOUT / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19653 733 4.5 %RANDOM
Rwork0.13166 ---
obs0.13462 15427 98.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.1 Å2
Baniso -1Baniso -2Baniso -3
1--4.91 Å2-0 Å2-0 Å2
2---4.91 Å2-0 Å2
3---9.81 Å2
Refinement stepCycle: LAST / Resolution: 3→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5164 0 104 20 5288
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0195399
X-RAY DIFFRACTIONr_bond_other_d0.0020.025116
X-RAY DIFFRACTIONr_angle_refined_deg1.7551.9797327
X-RAY DIFFRACTIONr_angle_other_deg13.00211786
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3345692
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.62224.752202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.24315861
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5591516
X-RAY DIFFRACTIONr_chiral_restr0.0860.2815
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026088
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021168
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_it0.3971.7822774
X-RAY DIFFRACTIONr_mcbond_other0.3971.7822773
X-RAY DIFFRACTIONr_mcangle_it0.7062.6723464
X-RAY DIFFRACTIONr_mcangle_other0.7052.6713465
X-RAY DIFFRACTIONr_scbond_it0.3651.8532625
X-RAY DIFFRACTIONr_scbond_other0.3651.8532625
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.6132.7683864
X-RAY DIFFRACTIONr_long_range_B_refined1.79614.3665863
X-RAY DIFFRACTIONr_long_range_B_other1.79614.3675864
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.076 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 59 -
Rwork0.252 937 -
obs--84.41 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)DetailsOrigin x (Å)Origin y (Å)Origin z (Å)
12.39380.966-0.29172.73210.12141.6674-0.08870.3556-0.8185-0.55360.1719-0.32840.4596-0.0313-0.08330.4224-0.1166-0.00150.2655-0.0950.4679Chain A catalytic domain-37.89833.5838-13.24761
22.72470.9506-0.61552.8435-0.54162.0528-0.30830.46190.0108-0.66420.21520.49280.1317-0.21280.0930.3036-0.1923-0.09840.27480.0040.1113CHAIN A COENZYME DOMAIN-50.879256.2406-16.3257
33.62860.9170.72153.9099-0.67640.9171-0.1980.99680.754-0.93860.16110.2671-0.1923-0.01890.03690.5856-0.0102-0.00010.53050.15480.4123B CHAIN CATALYTIC DOMAIN-38.63193.7395-14.3801
44.33471.28060.02242.55621.27661.8476-0.26060.71910.3059-0.78670.2698-0.2986-0.14040.1945-0.00920.4153-0.15940.15730.34370.07220.1341CHAIN B COENZYME DOMAIN-24.941469.5485-18.6768
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 154
2X-RAY DIFFRACTION1A294 - 347
3X-RAY DIFFRACTION1A401 - 402
4X-RAY DIFFRACTION1A404
5X-RAY DIFFRACTION2A155 - 293
6X-RAY DIFFRACTION2A403
7X-RAY DIFFRACTION3B1 - 154
8X-RAY DIFFRACTION3B294 - 347
9X-RAY DIFFRACTION3B401 - 402
10X-RAY DIFFRACTION3B404
11X-RAY DIFFRACTION4B155 - 293
12X-RAY DIFFRACTION4B403

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