1XDQ

Structural and Biochemical Identification of a Novel Bacterial Oxidoreductase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.230 

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Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/10.1074/jbc.M408876200
  • Primary Citation of Related Structures:  
    1XDQ, 1XDY

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bacterial Sulfite Oxidase
A, B, C, D, E
298Escherichia coliMutation(s): 0 
UniProt
Find proteins for P76342 (Escherichia coli (strain K12))
Explore P76342 
Go to UniProtKB:  P76342
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP76342
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MTE
Query on MTE

Download Ideal Coordinates CCD File 
I [auth A],
M [auth B],
Q [auth C],
U [auth D],
Y [auth E]
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
MO
Query on MO

Download Ideal Coordinates CCD File 
G [auth A],
K [auth B],
O [auth C],
S [auth D],
W [auth E]
MOLYBDENUM ATOM
Mo
ZOKXTWBITQBERF-UHFFFAOYSA-N
URE
Query on URE

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B],
N [auth C],
R [auth D],
V [auth E]
UREA
C H4 N2 O
XSQUKJJJFZCRTK-UHFFFAOYSA-N
O
Query on O

Download Ideal Coordinates CCD File 
H [auth A],
L [auth B],
P [auth C],
T [auth D],
X [auth E]
OXYGEN ATOM
O
XLYOFNOQVPJJNP-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.230 
  • Space Group: I 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.345α = 90
b = 165.064β = 90
c = 181.447γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-10-12
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations