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- PDB-4w6z: YEAST ALCOHOL DEHYDROGENASE I, SACCHAROMYCES CEREVISIAE FERMENTAT... -

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Basic information

Entry
Database: PDB / ID: 4w6z
TitleYEAST ALCOHOL DEHYDROGENASE I, SACCHAROMYCES CEREVISIAE FERMENTATIVE ENZYME
ComponentsAlcohol dehydrogenase 1
KeywordsOXIDOREDUCTASE / TETRAMER OF ASYMMETRIC DIMERS / ZINC COORDINATION / INTRAMOLECULAR DISULFIDE BONDS
Function / homology
Function and homology information


amino acid catabolic process to alcohol via Ehrlich pathway / methylglyoxal reductase (NADH-dependent) activity / glycolytic fermentation to ethanol / replication compartment / NADH oxidation / alcohol dehydrogenase (NAD+) activity / melatonin binding / alcohol dehydrogenase / regulation of viral genome replication / zinc ion binding ...amino acid catabolic process to alcohol via Ehrlich pathway / methylglyoxal reductase (NADH-dependent) activity / glycolytic fermentation to ethanol / 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 / 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-8-IODO-ADENINE-DINUCLEOTIDE / TRIFLUOROETHANOL / Alcohol dehydrogenase 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (baker's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
Authorsplapp, B.v. / savarimuthu, b.r. / ramaswamy, s.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB 918657 United States
National Institutes of Health/National Institute on Alcohol Abuse and Alcoholism (NIH/NIAAA)AA00279 United States
Citation
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.
#1: Journal: J. Mol. Biol. / Year: 1994
Title: Crystallization and preliminary crystallographic studies 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.
#2: Journal: J. Biol. Chem. / Year: 1987
Title: Kinetic characterization of yeast alcohol dehydrogenases. Amino acid residue 294 and substrate specificity.
Authors: Ganzhorn, A.J. / Green, D.W. / Hershey, A.D. / Gould, R.M. / Plapp, B.V.
History
DepositionAug 21, 2014Deposition site: RCSB / Processing site: RCSB
SupersessionSep 3, 2014ID: 2HCY
Revision 1.0Sep 3, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / citation_author ...citation / citation_author / diffrn_source / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_oper_list
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.name / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _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
C: Alcohol dehydrogenase 1
D: Alcohol dehydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,54418
Polymers147,0404
Non-polymers2,50414
Water2,720151
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)149,54418
Polymers147,0404
Non-polymers2,50414
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_556x-y,-y,-z+11
2
C: Alcohol dehydrogenase 1
D: Alcohol dehydrogenase 1
hetero molecules

C: Alcohol dehydrogenase 1
D: Alcohol dehydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,54418
Polymers147,0404
Non-polymers2,50414
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z1
Unit cell
Length a, b, c (Å)144.338, 144.338, 128.204
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11D-509-

HOH

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Components

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


Mass: 36759.906 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (baker's yeast)
Strain: ATCC 204508 / S288c / Gene: ADH1, ADC1, YOL086C, O0947 / Plasmid: YEP13 / Production host: SACCHAROMYCES CEREVISIAE (baker's yeast)
Strain (production host): 302-21#2 (ADH1-11, ADH2, LEU2, TRP2)
References: UniProt: P00330, alcohol dehydrogenase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-8ID / NICOTINAMIDE-8-IODO-ADENINE-DINUCLEOTIDE / 3-(AMINOCARBONYL)-1-[(2R,3R,4S,5R)-5-({[(R)-{[(S)-{[(2R,3S,4R,5R)-5-(6-AMINO-8-IODO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]OXY}METHYL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]PYRIDINIUM


Mass: 790.330 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27IN7O14P2
#4: Chemical
ChemComp-ETF / TRIFLUOROETHANOL / 2,2,2-Trifluoroethanol


Mass: 100.040 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3F3O
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHERE IS AN ERROR IN THE ORIGINAL PUBLISHED DNA SEQUENCE. THE PROTEIN SEQUENCE SHOULD BE TYR AT ...THERE IS AN ERROR IN THE ORIGINAL PUBLISHED DNA SEQUENCE. THE PROTEIN SEQUENCE SHOULD BE TYR AT POSITION 20 (SEE REFERENCE 2 ABOVE).

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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: 2.62 Å3/Da / Density % sol: 53.07 % / Description: plate
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 8.4
Details: 125 MM SODIUM N-TRIS(HYDROXYMETHYL) METHYL-3-AMINOPROPANE SULFONIC ACID, 1.7 MM NICOTINAMIDE 8- IODOADENINE DINUCLEOTIDE, 0.1 M 2,2,2-TRIFLUOROETHANOL, 0.16 MM EDTA, 10 MG/ML PROTEIN, 6% ...Details: 125 MM SODIUM N-TRIS(HYDROXYMETHYL) METHYL-3-AMINOPROPANE SULFONIC ACID, 1.7 MM NICOTINAMIDE 8- IODOADENINE DINUCLEOTIDE, 0.1 M 2,2,2-TRIFLUOROETHANOL, 0.16 MM EDTA, 10 MG/ML PROTEIN, 6% INITIAL POLYETHYLENE GLYCOL 5000 MONOMETHYL ETHER (FLUKA MPEG5000) IN DROP HANGING OVER 22-26% MPEG5000 AND 0.1 M 2,2,2-TRIFLUOROETHANOL. CRYSTALS WERE SOAKED IN SAME BUFFER WITH 30% W/V MPEG5000 WITH 0.5 M 2,2,2- TRIFLUOROETHANOL FOR FIVE DAYS BEFORE FREEZING AT 100 K., PH 8.4, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 278K, PH 8.40
PH range: 8.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.857 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jul 28, 1995 / Details: MULTIPOLE WIGGLER
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.8571
20.8571
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.713
11-h,-k,l20.287
ReflectionResolution: 2.4→40.4 Å / Num. obs: 59662 / % possible obs: 98.5 % / Redundancy: 3.85 % / Rmerge(I) obs: 0.116 / Rsym value: 0.116 / Net I/σ(I): 8
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.71 % / Rmerge(I) obs: 0.418 / Mean I/σ(I) obs: 3.5 / Rsym value: 0.418 / % possible all: 93.3

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Processing

Software
NameVersionClassification
d*TREKdata scaling
AMoREphasing
REFMAC5.7.0032refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LLU.PDB
Resolution: 2.4→28.09 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.915 / SU B: 11.881 / SU ML: 0.15 / Cross valid method: THROUGHOUT / ESU R: 0.075 / ESU R Free: 0.049 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22177 1473 2.5 %RANDOM
Rwork0.17652 ---
obs0.17767 58104 98.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.195 Å2
Baniso -1Baniso -2Baniso -3
1--8.39 Å2-0 Å2-0 Å2
2---8.39 Å2-0 Å2
3---16.79 Å2
Refinement stepCycle: 1 / Resolution: 2.4→28.09 Å / Total: 10601
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01910664
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210154
X-RAY DIFFRACTIONr_angle_refined_deg1.8611.96814474
X-RAY DIFFRACTIONr_angle_other_deg0.847323416
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2551384
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.23924.752404
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.884151716
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.521532
X-RAY DIFFRACTIONr_chiral_restr0.0940.21612
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02112140
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022310
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_it1.3412.0445548
X-RAY DIFFRACTIONr_mcbond_other1.3412.0445547
X-RAY DIFFRACTIONr_mcangle_it2.1833.0636928
X-RAY DIFFRACTIONr_mcangle_other2.1833.0636929
X-RAY DIFFRACTIONr_scbond_it1.362.2065112
X-RAY DIFFRACTIONr_scbond_other1.3592.2065112
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.1513.2637547
X-RAY DIFFRACTIONr_long_range_B_refined4.14716.73812189
X-RAY DIFFRACTIONr_long_range_B_other4.12616.71712168
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 76 -
Rwork0.335 3860 -
obs--90.57 %
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)Origin x (Å)Origin y (Å)Origin z (Å)
11.3942-0.3814-0.2012.00140.12661.18450.09410.18360.0404-0.0762-0.032-0.31490.05150.1467-0.06220.20930.06540.02660.20340.01060.054197.271-15.34950.391
22.588-0.24440.15711.6879-0.16520.87570.06860.2384-0.0643-0.2366-0.13450.04530.0972-0.14130.06580.23440.04820.01030.1841-0.00690.011171.079-15.2147.536
31.5442-0.37210.52822.0802-0.38830.88070.08150.3322-0.0283-0.4245-0.02620.31250.0169-0.0644-0.05520.32230.0373-0.030.2658-0.04010.078745.21513.67850.5
42.4867-0.0662-0.78032.93450.7572.00750.03520.33620.2898-0.3147-0.03160.0643-0.1264-0.0714-0.00370.23240.0625-0.00630.20590.05450.0473.21813.77546.514
51.5423-0.6958-0.00661.90190.04720.90250.05020.09450.0166-0.0212-0.0073-0.34460.03670.0978-0.04280.17480.0272-0.0040.1412-0.00830.073196.585-16.062-12.573
61.4739-0.22160.26690.93940.31721.27030.08550.0838-0.1622-0.0218-0.13460.15760.1173-0.13180.04920.17360.0143-0.01380.1327-0.03030.038370.398-16.154-15.437
72.1478-0.53850.71911.9646-0.0580.92130.05990.4655-0.0151-0.4995-0.02560.18820.0002-0.0698-0.03420.33540.0374-0.02790.26890.01440.035944.32412.801-14.487
81.9266-0.5749-0.85922.79090.29270.54610.11340.3550.2654-0.4502-0.03480.0727-0.1426-0.0618-0.07860.29020.0229-0.03030.23350.06710.054772.4512.672-18.601
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 154
2X-RAY DIFFRACTION1A294 - 347
3X-RAY DIFFRACTION2A155 - 293
4X-RAY DIFFRACTION3B1 - 154
5X-RAY DIFFRACTION3B294 - 347
6X-RAY DIFFRACTION4B155 - 293
7X-RAY DIFFRACTION5C1 - 154
8X-RAY DIFFRACTION5C294 - 347
9X-RAY DIFFRACTION6C155 - 293
10X-RAY DIFFRACTION7D1 - 154
11X-RAY DIFFRACTION7D294 - 347
12X-RAY DIFFRACTION8D155 - 293

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