5KJ6

V197I Horse liver alcohol dehydrogenase complexed with NAD+ and pentafluorobenzyl alcohol

  • Classification: OXIDOREDUCTASE
  • Organism(s): Equus caballus
  • Expression System: Escherichia coli
  • Mutation(s): 

  • Deposited: 2016-06-17 Released: 2016-07-06 
  • Deposition Author(s): Plapp, B.V.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.14 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.136 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Contribution of buried distal amino acid residues in horse liver alcohol dehydrogenase to structure and catalysis.

Shanmuganatham, K.K.Wallace, R.S.Ting-I Lee, A.Plapp, B.V.

(2018) Protein Sci. 27: 750-768

  • DOI: 10.1002/pro.3370
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The dynamics of enzyme catalysis range from the slow time scale (∼ms) for substrate binding and conformational changes to the fast time (∼ps) scale for reorganization of substrates in the chemical step. The contribution of global dynamics to catalysi ...

    The dynamics of enzyme catalysis range from the slow time scale (∼ms) for substrate binding and conformational changes to the fast time (∼ps) scale for reorganization of substrates in the chemical step. The contribution of global dynamics to catalysis by alcohol dehydrogenase was tested by substituting five different, conserved amino acid residues that are distal from the active site and located in the hinge region for the conformational change or in hydrophobic clusters. X-ray crystallography shows that the structures for the G173A, V197I, I220 (V, L, or F), V222I, and F322L enzymes complexed with NAD+ and an analogue of benzyl alcohol are almost identical, except for small perturbations at the sites of substitution. The enzymes have very similar kinetic constants for the oxidation of benzyl alcohol and reduction of benzaldehyde as compared to the wild-type enzyme, and the rates of conformational changes are not altered. Less conservative substitutions of these amino acid residues, such as G173(V, E, K, or R), V197(G, S, or T), I220(G, S, T, or N), and V222(G, S, or T) produced unstable or poorly expressed proteins, indicating that the residues are critical for global stability. The enzyme scaffold accommodates conservative substitutions of distal residues, and there is no evidence that fast, global dynamics significantly affect the rate constants for hydride transfers. In contrast, other studies show that proximal residues significantly participate in catalysis.


    Organizational Affiliation

    Department of Biochemistry, The University of Iowa, Iowa City, IA, 52242-1109.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Alcohol dehydrogenase E chain
A, B
374Equus caballusMutation(s): 1 
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
NAJ
Query on NAJ

Download SDF File 
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
PFB
Query on PFB

Download SDF File 
Download CCD File 
A, B
2,3,4,5,6-PENTAFLUOROBENZYL ALCOHOL
C7 H3 F5 O
PGJYYCIOYBZTPU-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.14 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.136 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 44.470α = 91.92
b = 51.650β = 103.01
c = 92.680γ = 110.17
Software Package:
Software NamePurpose
d*TREKdata scaling
REFMACphasing
REFMACrefinement
d*TREKdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2016-06-17 
  • Released Date: 2016-07-06 
  • Deposition Author(s): Plapp, B.V.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM078446

Revision History 

  • Version 1.0: 2016-07-06
    Type: Initial release
  • Version 1.1: 2017-09-27
    Type: Author supporting evidence, Derived calculations
  • Version 1.2: 2018-01-03
    Type: Database references
  • Version 1.3: 2018-02-28
    Type: Database references