1K03

Crystal Structure of Old Yellow Enzyme Mutant Gln114Asn Complexed with Para-hydroxy Benzaldehyde


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Work: 0.130 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The role of glutamine 114 in old yellow enzyme

Brown, B.J.Hyun, J.Duvvuri, S.D.Karplus, P.A.Massey, V.

(2002) J.Biol.Chem. 277: 2138-2145

  • DOI: 10.1074/jbc.M108453200
  • Primary Citation of Related Structures:  1K02

  • PubMed Abstract: 
  • Glutamine 114 of OYE1 is a well conserved residue in the active site of the Old Yellow Enzyme family. It forms hydrogen bonds to the O2 and N3 of the flavoprotein prosthetic group, FMN. Glutamine 114 was mutated to asparagine, introducing an R-group ...

    Glutamine 114 of OYE1 is a well conserved residue in the active site of the Old Yellow Enzyme family. It forms hydrogen bonds to the O2 and N3 of the flavoprotein prosthetic group, FMN. Glutamine 114 was mutated to asparagine, introducing an R-group that is one methylene group shorter. The resultant enzyme was characterized to determine the effect of the mutation on the mechanistic behavior of the enzyme, and the crystal structure was solved to determine the effect of the mutation on the structure of the protein. The Q114N mutation results in little change in the protein structure, moving the amide group of residue 114 out of H-bonding distance, allowing repositioning of the FMN prosthetic group to form new interactions that replace the lost H-bonds. The mutation decreases the ability to bind ligands, as all dissociation constants for substituted phenols are larger than for the wild type enzyme. The rate constant for the reductive half-reaction with beta-NADPH is slightly greater, whereas that for the oxidative half-reaction with 2-cyclohexenone is smaller than for the wild type enzyme. Oxidation with molecular oxygen is biphasic and involves formation and reaction with O(2), a phenomenon that is more pronounced with this mutation than with wild type enzyme. When superoxide dismutase is added to the reaction, we observe a single-phase reaction typical of the wild type enzyme. Turnover reactions using beta-NADPH with 2-cyclohexenone and molecular oxygen were studied to further characterize the mutant enzyme.


    Organizational Affiliation

    Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109-0606, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NADPH DEHYDROGENASE 1
A
399Saccharomyces pastorianusGene Names: OYE1
EC: 1.6.99.1
Find proteins for Q02899 (Saccharomyces pastorianus)
Go to UniProtKB:  Q02899
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HBA
Query on HBA

Download SDF File 
Download CCD File 
A
P-HYDROXYBENZALDEHYDE
C7 H6 O2
RGHHSNMVTDWUBI-UHFFFAOYSA-N
 Ligand Interaction
FMN
Query on FMN

Download SDF File 
Download CCD File 
A
FLAVIN MONONUCLEOTIDE
RIBOFLAVIN MONOPHOSPHATE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
HBAKd: 1000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Work: 0.130 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 143.000α = 90.00
b = 143.000β = 90.00
c = 43.000γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-09-26
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance