3Q9T

Crystal structure analysis of formate oxidase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Formate oxidase, an enzyme of the glucose-methanol-choline oxidoreductase family, has a His-Arg pair and 8-formyl-FAD at the catalytic site

Doubayashi, D.Ootake, T.Maeda, Y.Oki, M.Tokunaga, Y.Sakurai, A.Nagaosa, Y.Mikami, B.Uchida, H.

(2011) Biosci.Biotechnol.Biochem. 75: 1662-1667

  • DOI: 10.1271/bbb.110153

  • PubMed Abstract: 
  • Formate oxidase of Aspergillus oryzae RIB40 contains an 8-replaced FAD with molecular mass of 799 as cofactor. The ¹H-NMR spectrum of the cofactor fraction obtained from the enzyme indicated that the 8-replaced FAD in the fraction was 8-formyl-FAD, p ...

    Formate oxidase of Aspergillus oryzae RIB40 contains an 8-replaced FAD with molecular mass of 799 as cofactor. The ¹H-NMR spectrum of the cofactor fraction obtained from the enzyme indicated that the 8-replaced FAD in the fraction was 8-formyl-FAD, present in open form and hemiacetal form. The oxidation-reduction potentials of the open and hemiacetal forms were estimated by cyclic voltammetry to be -47 and -177 mV vs. Normal Hydrogen Electrode respectively. The structure of the enzyme was constructed using diffraction data to 2.24 Å resolution collected from a crystal of the enzyme. His₅₁₁ and Arg₅₅₄ were situated close to the pyrimidine part of the isoalloxazine ring of 8-formyl-FAD in open form. The enzyme had 8-formyl-FAD, the oxidation potential of which was approximately 160 mV more positive than that of FAD, and the His-Arg pair at the catalytic site, unlike the other enzymes belonging to the glucose-methanol-choline oxidoreductase family.


    Related Citations: 
    • Crystallization and preliminary X-ray analysis of formate oxidase, an enzyme of the glucose-methanol-choline oxidoreductase family
      Maeda, Y.,Doubayashi, D.,Ootake, T.,Oki, M.,Mikami, B.,Uchida, H.
      (2010) Acta Crystallogr.,Sect.F 66: 1064


    Organizational Affiliation

    Department of Applied Chemistry and Biotechnology, Graduate School of Engineering, University of Fukui.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Choline dehydrogenase and related flavoproteins
A, B, C
577Aspergillus oryzae (strain ATCC 42149 / RIB 40)Mutation(s): 0 
Find proteins for Q2UD26 (Aspergillus oryzae (strain ATCC 42149 / RIB 40))
Go to UniProtKB:  Q2UD26
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
MRD
Query on MRD

Download SDF File 
Download CCD File 
A
(4R)-2-METHYLPENTANE-2,4-DIOL
C6 H14 O2
SVTBMSDMJJWYQN-RXMQYKEDSA-N
 Ligand Interaction
FAY
Query on FAY

Download SDF File 
Download CCD File 
A, B, C
[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4S)-5-(8-formyl-7-methyl-2,4-dioxo-3,4-dihydrobenzo[g]pteridin-10(2H)-yl)-2,3,4-trihydroxypentyl dihydrogen diphosphate
8-FORMYL-FLAVIN-ADENINE DINUCLEOTIDE
C27 H31 N9 O16 P2
WPPWMPSQWPJDHE-UYBVJOGSSA-N
 Ligand Interaction
PEG
Query on PEG

Download SDF File 
Download CCD File 
B
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
MPD
Query on MPD

Download SDF File 
Download CCD File 
C
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.184 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 156.679α = 90.00
b = 156.019β = 90.00
c = 184.696γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
HKL-2000data scaling
HKL-2000data collection
HKL-2000data reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-09-21
    Type: Initial release
  • Version 1.1: 2013-06-26
    Type: Database references
  • Version 1.2: 2017-11-08
    Type: Advisory, Refinement description