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- PDB-1p1r: Horse liver alcohol dehydrogenase complexed with NADH and R-N-1-m... -

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Basic information

Entry
Database: PDB / ID: 1p1r
TitleHorse liver alcohol dehydrogenase complexed with NADH and R-N-1-methylhexylformamide
ComponentsAlcohol dehydrogenase E chain
KeywordsOXIDOREDUCTASE / puckered reduced nicotinamide ring / Michaelis complex analogue / formamide
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
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / (R)-N-(1-METHYL-HEXYL)-FORMAMIDE / Alcohol dehydrogenase E chain
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsVenkataramaiah, T.H. / Plapp, B.V.
Citation
Journal: J.Biol.Chem. / Year: 2003
Title: Formamides mimic aldehydes and inhibit liver alcohol dehydrogenases and ethanol metabolism
Authors: Venkataramaiah, T.H. / Plapp, B.V.
#1: Journal: Biochemistry / Year: 1997
Title: Flexibility of liver alcohol dehydrogenase in stereoselective binding of 3-butylthiolane 1-oxides
Authors: Cho, H. / Ramaswamy, S. / Plapp, B.V.
#2: 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.
#3: Journal: Biochemistry / Year: 1999
Title: SUBSTITUTIONS IN A 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: Acta Crystallogr.,Sect.D / Year: 1994
Title: Refined crystal structure of liver alcohol dehydrogenase-NADH complex at 1.8 angstrom resolution
Authors: Al-Karadaghi, S. / Cedergren-Zeppezauer, E.S. / Hovmoller, S. / Petratos, K. / Terry, H. / Wilson, K.S.
#5: Journal: J.Mol.Biol. / Year: 1981
Title: STRUCTURE OF A TRICLINIC TERNARY COMPLEX OF HORSE LIVER ALCOHOL DEHYDROGENASE AT 2.9 A RESOLUTION
Authors: Eklund, H. / Samama, J.P. / Wallen, L. / Branden, C.I. / Akeson, A. / Jones, T.A.
#6: Journal: J.Mol.Biol. / Year: 1976
Title: Three-dimensional structure of horse liver alcohol dehydrogenase at 2.4 A resolution
Authors: Eklund, H. / Nordstrom, B. / Zeppezauer, E. / Soderlund, G. / Ohlsson, I. / Boiwe, T. / Soderberg, B.O. / Tapia, O. / Branden, C.I. / Akeson, A.
#7: 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.
#8: Journal: J.Biol.Chem. / Year: 2001
Title: On the enzymatic activation of NADH
Authors: Meijers, R. / Morris, R.J. / Adolph, H.W. / Merli, A. / Lamzin, V.S. / Cedergren-Zeppezauer, E.S.
#9: 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.
#10: Journal: Biochemistry / Year: 1997
Title: Binding of formamides to liver alcohol dehydrogenase
Authors: Ramaswamy, S. / Scholze, M. / Plapp, B.V.
History
DepositionApr 13, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_remark / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_remark.text / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 600Heterogen THE STRUCTURE DETERMINED IN THIS ENTRY CONTAINS THE HETEROATOM MOLECULE NAI, WHICH IS 1,4- ...Heterogen THE STRUCTURE DETERMINED IN THIS ENTRY CONTAINS THE HETEROATOM MOLECULE NAI, WHICH IS 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE. BUT THE RESTRAINTS ON THE PLANARITY OF THE NICOTINAMIDE RING WERE REMOVED DURING REFINEMENT WITH THE RESULT THAT THE RING IS PUCKERED. THE COMPLEX ALSO HAS THE R ISOMER OF THE N-1-METHYLHEXYLFORMAMIDE BOUND TO THE CATALYTIC ZINC, RESIDUE 376 IN CHAINS A, B, C, AND D.

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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
C: Alcohol dehydrogenase E chain
D: Alcohol dehydrogenase E chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,28921
Polymers159,4134
Non-polymers3,87617
Water22,3571241
1
A: Alcohol dehydrogenase E chain
B: Alcohol dehydrogenase E chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,70411
Polymers79,7072
Non-polymers1,9979
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7050 Å2
ΔGint-111 kcal/mol
Surface area26510 Å2
MethodPISA
2
C: Alcohol dehydrogenase E chain
D: Alcohol dehydrogenase E chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,58610
Polymers79,7072
Non-polymers1,8798
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7240 Å2
ΔGint-116 kcal/mol
Surface area26600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.095, 180.340, 87.000
Angle α, β, γ (deg.)90.00, 106.36, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Alcohol dehydrogenase E chain


Mass: 39853.273 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / Organ: liver / References: UniProt: P00327, alcohol dehydrogenase

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Non-polymers , 5 types, 1258 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#4: Chemical
ChemComp-NMH / (R)-N-(1-METHYL-HEXYL)-FORMAMIDE


Mass: 143.227 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H17NO
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1241 / 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: 2.14 Å3/Da / Density % sol: 41.95 %
Crystal growTemperature: 277 K / pH: 7
Details: MPD, 50 mM ammonium tris-[(hydroxymethyl)methyl]-2-aminosulfonate buffer, 0.25 mM EDTA, pH 7.0, dialysis, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6.7 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
19.4 mg/mlprotein1drop
250 mMammonium TES1reservoirpH6.7
31 mMNADH1reservoir
45 mM(R)-N-1-methyl hexyl formamide1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 9, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.57→20 Å / Num. all: 191371 / Num. obs: 191371 / % possible obs: 94.29 % / Observed criterion σ(F): 1 / Redundancy: 3.3 % / Biso Wilson estimate: 24.3 Å2 / Rmerge(I) obs: 0.047 / Rsym value: 0.047 / Net I/σ(I): 32.9
Reflection shellResolution: 1.57→1.63 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 5.2 / Num. unique all: 16092 / Rsym value: 0.2 / % possible all: 79
Reflection
*PLUS
Num. obs: 192617 / % possible obs: 94.3 % / Num. measured all: 636860
Reflection shell
*PLUS
% possible obs: 79 % / Rmerge(I) obs: 0.2

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Processing

Software
NameVersionClassification
REFMAC5.1.27refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HLD

1hld


Resolution: 1.57→20 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.305 / SU ML: 0.047 / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(I): 1 / ESU R: 0.095 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19991 1159 0.6 %RANDOM
Rwork0.15243 ---
obs0.1527 191371 94.29 %-
all-191371 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.166 Å2
Baniso -1Baniso -2Baniso -3
1-1.96 Å20 Å20.08 Å2
2---1.75 Å20 Å2
3----0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.57→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11140 0 224 1249 12613
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02211583
X-RAY DIFFRACTIONr_angle_refined_deg1.4692.01415678
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.93251492
X-RAY DIFFRACTIONr_chiral_restr0.0960.21829
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028344
X-RAY DIFFRACTIONr_nbd_refined0.1980.25724
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.10.2
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.180.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1410.231
X-RAY DIFFRACTIONr_mcbond_it1.3191.57420
X-RAY DIFFRACTIONr_mcangle_it2.094211996
X-RAY DIFFRACTIONr_scbond_it3.34434163
X-RAY DIFFRACTIONr_scangle_it5.0094.53682
X-RAY DIFFRACTIONr_rigid_bond_restr1.301211576
X-RAY DIFFRACTIONr_sphericity_free5.82458
X-RAY DIFFRACTIONr_sphericity_bonded6.339511356
LS refinement shellResolution: 1.57→1.614 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 71 -
Rwork0.157 11496 -
obs-16092 79 %
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor Rfree: 0.2 / Rfactor Rwork: 0.153
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.014
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.47

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