Crystal structure of E. COLI K-12 yhdH

Experimental Data Snapshot

  • Resolution: 2.25 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.201 

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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 D Biol Crystallogr 60: 1855

  • DOI: https://doi.org/10.1107/S0907444904020220
  • Primary Citation of Related Structures:  
    1O89, 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 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 Universités Aix-Marseille I and II, 31 Chemin J. Aiguier, F-13402 Marseille 20, France.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
YHDH345Escherichia coli K-12Mutation(s): 0 
Find proteins for P26646 (Escherichia coli (strain K12))
Explore P26646 
Go to UniProtKB:  P26646
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP26646
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.25 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.201 
  • Space Group: P 43 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.671α = 90
b = 55.671β = 90
c = 201.48γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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