1XDY

Structural and Biochemical Identification of a Novel Bacterial Oxidoreductase, W-containing cofactor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.226 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural and biochemical identification of a novel bacterial oxidoreductase.

Loschi, L.Brokx, S.J.Hills, T.L.Zhang, G.Bertero, M.G.Lovering, A.L.Weiner, J.H.Strynadka, N.C.

(2004) J.Biol.Chem. 279: 50391-50400

  • DOI: 10.1074/jbc.M408876200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • By using a bioinformatics screen of the Escherichia coli genome for potential molybdenum-containing enzymes, we have identified a novel oxidoreductase conserved in the majority of Gram-negative bacteria. The identified operon encodes for a proposed h ...

    By using a bioinformatics screen of the Escherichia coli genome for potential molybdenum-containing enzymes, we have identified a novel oxidoreductase conserved in the majority of Gram-negative bacteria. The identified operon encodes for a proposed heterodimer, YedYZ in Escherichia coli, consisting of a soluble catalytic subunit termed YedY, which is likely anchored to the membrane by a heme-containing trans-membrane subunit termed YedZ. YedY is uniquely characterized by the presence of one molybdenum molybdopterin not conjugated by an additional nucleotide, and it represents the only molybdoenzyme isolated from E. coli characterized by the presence of this cofactor form. We have further characterized the catalytic subunit YedY in both the molybdenum- and tungsten-substituted forms by using crystallographic analysis. YedY is very distinct in overall architecture from all known bacterial reductases but does show some similarity with the catalytic domain of the eukaryotic chicken liver sulfite oxidase. However, the strictly conserved residues involved in the metal coordination sphere and in the substrate binding pocket of YedY are strikingly different from that of chicken liver sulfite oxidase, suggesting a catalytic activity more in keeping with a reductase than that of a sulfite oxidase. Preliminary kinetic analysis of YedY with a variety of substrates supports our proposal that YedY and its many orthologues may represent a new type of membrane-associated bacterial reductase.


    Organizational Affiliation

    Department of Biochemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Bacterial Sulfite Oxidase
A, B, C, D, E, F, G, H, I, J
298Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: msrP (yedY)
EC: 1.8.5.-
Find proteins for P76342 (Escherichia coli (strain K12))
Go to UniProtKB:  P76342
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MTE
Query on MTE

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J
PHOSPHONIC ACIDMONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,7,8A,9,10,10A-HEXAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL)ESTER
C10 H14 N5 O6 P S2
HPEUEJRPDGMIMY-IFQPEPLCSA-N
 Ligand Interaction
W
Query on W

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J
TUNGSTEN ION
W
FZFRVZDLZISPFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.226 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 84.842α = 90.00
b = 177.513β = 109.73
c = 104.214γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
CCP4data scaling
MOSFLMdata reduction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-10-12
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance