1O89

Crystal structure of E. COLI K-12 yhdH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of the Escherichia Coli Yhdh, a Putative Quinone Oxidoreductase

Sulzenbacher, G.Roig-Zamboni, V.Pagot, F.Grisel, S.Salamoni, A.Valencia, C.Campanacci, V.Vincentelli, R.Tegoni, M.Eklund, H.Cambillau, C.

(2004) Acta Crystallogr.,Sect.D 60: 1855

  • DOI: 10.1107/S0907444904020220
  • Primary Citation of Related Structures:  1O8C

  • PubMed Abstract: 
  • As part of a structural genomics project on bacterial gene products of unknown function, the crystal structures of YhdH, a putative quinone oxidoreductase, and its complex with NADP have been determined at 2.25 and 2.6 A resolution, respectively. The ...

    As part of a structural genomics project on bacterial gene products of unknown function, the crystal structures of YhdH, a putative quinone oxidoreductase, and its complex with NADP have been determined at 2.25 and 2.6 A resolution, respectively. The overall fold of YhdH is very similar to that of alcohol dehydrogenases and quinone reductases despite its low sequence identity. The absence of any Zn ion indicates that YdhH is a putative quinone oxidoreductase. YhdH forms a homodimer, with each subunit composed of two domains: a catalytic domain and a coenzyme-binding domain. NADP is bound in a deep cleft formed between the two domains. Large conformational changes occur upon NADP binding, with the two domains closing up to each other and narrowing the NADP-binding cleft. Comparisons of the YdhH active site with those of the quinone oxidoreductases from Escherichia coli and Thermus thermophilus made it possible to identify essential conserved residues as being Asn41, Asp43, Asp64 and Arg318. The active-site size is very narrow and unless an induced fit occurs is accessible only to reagents the size of benzoquinone.


    Organizational Affiliation

    AFMB, UMR 6098, CNRS and Universit├ęs Aix-Marseille I and II, 31 Chemin J. Aiguier, F-13402 Marseille 20, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
YHDH
A
345Escherichia coli (strain K12)Gene Names: acuI (yhdH)
EC: 1.3.1.84
Find proteins for P26646 (Escherichia coli (strain K12))
Go to UniProtKB:  P26646
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.197 
  • Space Group: P 43 2 2
Unit Cell:
Length (Å)Angle (°)
a = 55.671α = 90.00
b = 55.671β = 90.00
c = 201.480γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALAdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-02-26
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance