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- PDB-1ye3: HORSE LIVER ALCOHOL DEHYDROGENASE APOENZYME -

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Basic information

Entry
Database: PDB / ID: 1ye3
TitleHORSE LIVER ALCOHOL DEHYDROGENASE APOENZYME
ComponentsAlcohol dehydrogenase E chain
KeywordsOXIDOREDUCTASE / DEHYDROGENASE / ALCOHOL / LIVER / APOENZYME / METHYLPENTANEDIOL
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. / 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
Alcohol dehydrogenase E chain
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsPlapp, B.V. / Savarimuthu, B.R. / Ramaswamy, S.
Citation
Journal: To be Published
Title: Horse Liver Alcohol Dehydrogenase Apoenzyme
Authors: Plapp, B.V. / Savarimuthu, B.R. / Ramaswamy, S.
#1: Journal: J.Mol.Biol. / Year: 1976
Title: Three-Dimensional Structure of Horse Liver Alcohol Dehydrogenase at 2.4 Angstroms Resolution
Authors: Eklund, H. / Nordstrom, B. / Zeppezauer, E. / Soderlund, G. / Ohlsson, I. / Boiwe, T. / Soderberg, B.-O. / Tapia, O. / Branden, C.-I. / Akeson, A.
#2: Journal: J.Mol.Biol. / Year: 1981
Title: Structure of a Triclinic Ternary Complex of Horse Liver Alcohol Dehydrogenase at 2.9 Angstroms Resolution
Authors: Eklund, H. / Samama, J.-P. / Wallen, L. / Branden, C.-I. / Akeson, A. / A Jones, T.
#3: Journal: Biochemistry / Year: 1999
Title: Substitutions in the Flexible Loop of Horse Liver Alcohol Dehydrogenase Hinder the Conformational Change and Unmask Hydrogen Transfer
Authors: Ramaswamy, S. / Park, D.H. / Plapp, B.V.
#4: Journal: Biochemistry / Year: 2001
Title: Contributions of Valine-292 in the Nicotinamide Binding Site of Liver Alcohol Dehydrogenase and Dynamics to Catalysis
Authors: Rubach, J.K. / Ramaswamy, S. / Plapp, B.V.
#5: Journal: J.Biol.Chem. / Year: 1982
Title: Binding of Substrate in a Ternary Complex of Horse Liver Alcohol Dehydrogenase
Authors: Eklund, H. / Plapp, B.V. / Samama, J.-P. / Branden, C.-I.
#6: Journal: Biochemistry / Year: 1994
Title: Structures of Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and Substituted Benzyl Alcohols
Authors: Ramaswamy, S. / Eklund, H. / Plapp, B.V.
#7: Journal: Biochemistry / Year: 2002
Title: Mobility of Fluorobenzyl Alcohols Bound to Liver Alcohol Dehydrogenases as Determined by NMR and X-Ray Crystallographic Studies
Authors: Rubach, J.K. / Plapp, B.V.
#8: 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.
#9: Journal: Biochemistry / Year: 1984
Title: Crystallographic Investigations of Nicotinamide Adenine Dinucleotide Binding to Horse Liver Alcohol Dehydrogenase
Authors: Eklund, H. / Samama, J.-P. / Jones, T.A.
#10: Journal: Biochemistry / Year: 1982
Title: Crystal Structure Determinations of Coenzyme Analogue and Substrate Complexes of Liver Alcohol Dehydrogenase. Binding of 1,4,5,6-Tetrahydronicotinamide Adenine Dinucleotide and Trans-4-(N,N- ...Title: Crystal Structure Determinations of Coenzyme Analogue and Substrate Complexes of Liver Alcohol Dehydrogenase. Binding of 1,4,5,6-Tetrahydronicotinamide Adenine Dinucleotide and Trans-4-(N,N-Dimethylamino)Cinnamaldehyde to the Enzyme
Authors: Cedergren-Zeppezauer, E. / Samama, J.-P. / Eklund, H.
History
DepositionDec 27, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alcohol dehydrogenase E chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1024
Polymers39,8531
Non-polymers2493
Water3,603200
1
A: Alcohol dehydrogenase E chain
hetero molecules

A: Alcohol dehydrogenase E chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,2058
Polymers79,7072
Non-polymers4986
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area4350 Å2
ΔGint-126 kcal/mol
Surface area27940 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)55.780, 74.290, 181.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Alcohol dehydrogenase E chain


Mass: 39853.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: liver / Source: (natural) Equus caballus (horse) / References: UniProt: P00327, alcohol dehydrogenase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 2.36 Å3/Da / Density % sol: 47.79 %
Crystal growTemperature: 278 K / Method: microdialysis / pH: 8.4
Details: 50 mM Tris-HCl, 25% methylpentanediol, pH 8.4, MICRODIALYSIS, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 23, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.59→20.2 Å / Num. obs: 36732 / % possible obs: 71.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.66 % / Biso Wilson estimate: 25.468 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 11.5
Reflection shellResolution: 1.59→1.65 Å / Redundancy: 5.74 % / Rmerge(I) obs: 0.211 / Mean I/σ(I) obs: 4.7 / Num. unique all: 2918 / % possible all: 58

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8ADH

8adh


Resolution: 1.59→20.2 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.92 / SU B: 3.926 / SU ML: 0.069 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.2 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: Positions for residues A269-A270 were not well-defined by the electron density. Several residues, including A306, have alternative conformations, but these were not modeled.
RfactorNum. reflection% reflectionSelection details
Rfree0.25593 1143 3.1 %RANDOM
Rwork0.19946 ---
all0.2011 ---
obs0.2011 35539 71.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 35.47 Å2
Baniso -1Baniso -2Baniso -3
1-0.86 Å20 Å20 Å2
2--1.46 Å20 Å2
3----2.32 Å2
Refinement stepCycle: LAST / Resolution: 1.59→20.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2785 0 10 200 2995
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222844
X-RAY DIFFRACTIONr_angle_refined_deg1.5291.9793846
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9085373
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.30424.3397
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.37915498
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0411512
X-RAY DIFFRACTIONr_chiral_restr0.1030.2448
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022072
X-RAY DIFFRACTIONr_nbd_refined0.2070.21284
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21971
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2187
X-RAY DIFFRACTIONr_metal_ion_refined0.0110.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1530.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.10.211
X-RAY DIFFRACTIONr_mcbond_it1.4931.51895
X-RAY DIFFRACTIONr_mcangle_it2.21822996
X-RAY DIFFRACTIONr_scbond_it3.24931043
X-RAY DIFFRACTIONr_scangle_it4.5324.5850
X-RAY DIFFRACTIONr_rigid_bond_restr1.67132931
X-RAY DIFFRACTIONr_sphericity_free17.85852
X-RAY DIFFRACTIONr_sphericity_bonded8.26752785
LS refinement shellResolution: 1.59→1.631 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 71 -
Rwork0.172 2002 -
obs--56.36 %

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