4DXH

Horse liver alcohol dehydrogenase complexed with NAD+ and 2,2,2-trifluoroethanol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.12 Å
  • R-Value Free: 0.147 
  • R-Value Work: 0.127 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Atomic-Resolution Structures of Horse Liver Alcohol Dehydrogenase with NAD(+) and Fluoroalcohols Define Strained Michaelis Complexes.

Plapp, B.V.Ramaswamy, S.

(2012) Biochemistry 51: 4035-4048

  • DOI: 10.1021/bi300378n
  • Primary Citation of Related Structures:  
  • Also Cited By: 6OWP, 6OWM, 6O91, 6OA7, 5VN1, 5VL0

  • PubMed Abstract: 
  • Structures of horse liver alcohol dehydrogenase complexed with NAD(+) and unreactive substrate analogues, 2,2,2-trifluoroethanol or 2,3,4,5,6-pentafluorobenzyl alcohol, were determined at 100 K at 1.12 or 1.14 Å resolution, providing estimates of ato ...

    Structures of horse liver alcohol dehydrogenase complexed with NAD(+) and unreactive substrate analogues, 2,2,2-trifluoroethanol or 2,3,4,5,6-pentafluorobenzyl alcohol, were determined at 100 K at 1.12 or 1.14 Å resolution, providing estimates of atomic positions with overall errors of ~0.02 Å, the geometry of ligand binding, descriptions of alternative conformations of amino acid residues and waters, and evidence of a strained nicotinamide ring. The four independent subunits from the two homodimeric structures differ only slightly in the peptide backbone conformation. Alternative conformations for amino acid side chains were identified for 50 of the 748 residues in each complex, and Leu-57 and Leu-116 adopt different conformations to accommodate the different alcohols at the active site. Each fluoroalcohol occupies one position, and the fluorines of the alcohols are well-resolved. These structures closely resemble the expected Michaelis complexes with the pro-R hydrogens of the methylene carbons of the alcohols directed toward the re face of C4N of the nicotinamide rings with a C-C distance of 3.40 Å. The oxygens of the alcohols are ligated to the catalytic zinc at a distance expected for a zinc alkoxide (1.96 Å) and participate in a low-barrier hydrogen bond (2.52 Å) with the hydroxyl group of Ser-48 in a proton relay system. As determined by X-ray refinement with no restraints on bond distances and planarity, the nicotinamide rings in the two complexes are slightly puckered (quasi-boat conformation, with torsion angles of 5.9° for C4N and 4.8° for N1N relative to the plane of the other atoms) and have bond distances that are somewhat different compared to those found for NAD(P)(+). It appears that the nicotinamide ring is strained toward the transition state on the path to alcohol oxidation.


    Related Citations: 
    • Structures of horse liver alcohol dehydrogenase complexed with NAD+ and substituted benzyl alcohols.
      Ramaswamy, S.,Eklund, H.,Plapp, B.V.
      (1994) Biochemistry 33: 5230
    • Formamides mimic aldehydes and inhibit liver alcohol dehydrogenases and ethanol metabolism.
      Venkataramaiah, T.H.,Plapp, B.V.
      (2003) J.Biol.Chem. 278: 36699
    • Amino acid residues in the nicotinamide binding site contribute to catalysis by horse liver alcohol dehydrogenase.
      Rubach, J.K.,Plapp, B.V.
      (2003) Biochemistry 42: 2907


    Organizational Affiliation

    Department of Biochemistry, The University of Iowa, Iowa City, IA 52242, USA. bv-plapp@uiowa.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Alcohol dehydrogenase E chain
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

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ETF
Query on ETF

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Download CCD File 
A, B
TRIFLUOROETHANOL
C2 H3 F3 O
RHQDFWAXVIIEBN-UHFFFAOYSA-N
 Ligand Interaction
NAJ
Query on NAJ

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Download CCD File 
A, B
NICOTINAMIDE-ADENINE-DINUCLEOTIDE (ACIDIC FORM)
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
MRD
Query on MRD

Download SDF File 
Download CCD File 
A, B
(4R)-2-METHYLPENTANE-2,4-DIOL
C6 H14 O2
SVTBMSDMJJWYQN-RXMQYKEDSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ETFKi: 8400 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.12 Å
  • R-Value Free: 0.147 
  • R-Value Work: 0.127 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 44.250α = 91.91
b = 51.160β = 103.02
c = 92.530γ = 109.90
Software Package:
Software NamePurpose
AMoREphasing
REFMACrefinement
d*TREKdata reduction
PDB_EXTRACTdata extraction
ADSCdata collection
d*TREKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-04-11
    Type: Initial release
  • Version 1.1: 2012-05-02
    Type: Structure summary
  • Version 1.2: 2012-05-16
    Type: Database references
  • Version 1.3: 2012-06-27
    Type: Database references