2OXI

REFINED CRYSTAL STRUCTURE OF CU-SUBSTITUTED ALCOHOL DEHYDROGENASE AT 2.1 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Work: 0.160 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Refined structure of Cu-substituted alcohol dehydrogenase at 2.1 A resolution.

Al-Karadaghi, S.Cedergren-Zeppezauer, E.S.Dauter, Z.Wilson, K.S.

(1995) Acta Crystallogr.,Sect.D 51: 805-813

  • DOI: 10.1107/S090744499500045X
  • Also Cited By: 1HET

  • PubMed Abstract: 
  • Liver alcohol dehydrogenase (LADH) is a Zn(II)-dependent dimeric enzyme. LADH with the active-site Zn(II) substituted by Cu(II) resembles blue (type I) copper proteins by its spectroscopic characteristics. In this work we present the X-ray structure ...

    Liver alcohol dehydrogenase (LADH) is a Zn(II)-dependent dimeric enzyme. LADH with the active-site Zn(II) substituted by Cu(II) resembles blue (type I) copper proteins by its spectroscopic characteristics. In this work we present the X-ray structure of the active site Cu(II)-substituted LADH complex with NADH and dimethyl sulfoxide (DMSO). The structure was solved by molecular replacement. The space group is P2(1) with cell dimensions a = 44.4, b = 180.6, c = 50.8 A and beta = 108 degrees. There is one dimer of the enzyme in the asymmetric unit. The refinement was carried out to a crystallographic R-factor of 16.1% for 41 119 unique reflections in the resolution range 12.0 to 2.1 A. The coordination geometry of Cu(II) in LADH is compared with the active-site metal coordination in the Zn-LADH-NADH-DMSO complex and blue-copper proteins. The distances from the metal to the protein ligands (Cys46, His67 and Cys174) are similar for the Zn(II) and Cu(II) ions. The distances of the O atom of the inhibitor DMSO to the Cu(II) ion in the two subunits of the dimer are 3.19 and 3.45 A. These are considerably longer than the corresponding distances for the Zn(II) enzyme, 2.19 and 2.15 A. The Cu(II) ion is positioned nearly in the plane of the three protein ligands (NS(2)) with a geometry similar to the trigonal arrangement of the three strongly bound ligands (N(2)S) in blue-copper proteins. This coordination probably accounts for the similarity of the spectral characteristics of Cu(II)-LADH and type I copper proteins.


    Related Citations: 
    • An Epr Study of the Blue Copper Center in Horse Liver Alcohol Dehydrogenase
      Maret, W.,Zeppezauer, M.,Desideri, A.,Morpurgo, L.,Rotilio, G.
      (1983) Biochim.Biophys.Acta 743: 200
    • Resonance Raman Spectra of Copper(II)-Substituted Liver Alcohol Dehydrogenase: A Type 1 Copper Analogue
      Maret, W.,Zeppezauer, M.,Sanders-Loehr, J.,Loehr, T.M.
      (1983) Biochemistry 22: 3202
    • Electronic Absorption and Epr Spectroscopy of Copper Alcohol Dehydrogenase: Pink, Violet and Green Forms of a Type 1 Copper Center Analog
      Maret, W.,Kozlowski, H.
      (1987) Biochim.Biophys.Acta 912: 329
    • Resonance Raman Spectroscopy of Blue Copper Proteins: Ligand and Coenzyme Effects in Copper(II)-Substituted Liver Alcohol Dehydrogenase
      Maret, W.,Shiemke, A.K.,Wheeler, W.D.,Loehr, T.M.,Sanders-Loehr, J.
      (1986) J.Am.Chem.Soc. 108: 6351
    • Active Site-Specific Reconstituted Copper(II) Horse Liver Alcohol Dehydrogenase: A Biological Model for Type 1 Cu and its Changes Upon Ligand Binding and Conformational Transitions
      Maret, W.,Dietrich, H.,Ruf, H.-H.,Zeppezauer, M.
      (1980) J.Inorg.Biochem. 12: 241
    • Copper(II)-Substituted Horse Liver Alcohol Dehydrogenase: Structure of the Minor Species
      Formicka, G.,Zeppezauer, M.,Fey, F.,Huettermann, J.
      (1992) FEBS Lett. 309: 92
    • Ligand Binding to the Blue Copper Center of Horse Liver Alcohol Dehydrogenase
      Maret, W.,Zeppezauer, M.,Desideri, A.,Morpurgo, L.,Rotilio, G.
      (1981) FEBS Lett. 136: 72


    Organizational Affiliation

    Department of Structural Chemistry, Arrhenius Laboratories for Natural Sciences, Stockholm University, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ALCOHOL DEHYDROGENASE
A, B
374Equus caballusMutation(s): 0 
EC: 1.1.1.1
Find proteins for P00327 (Equus caballus)
Go to UniProtKB:  P00327
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
NAD
Query on NAD

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Download CCD File 
A, B
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
CU
Query on CU

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Download CCD File 
A, B
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

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Download CCD File 
A, B
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Work: 0.160 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 44.400α = 90.00
b = 180.600β = 108.00
c = 50.800γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
X-PLORmodel building
X-PLORrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-01-31
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-11-29
    Type: Advisory, Derived calculations, Other