1O8C

CRYSTAL STRUCTURE OF E. COLI K-12 YHDH WITH BOUND NADPH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of Escherichia Coli Yhdh, a Putative Quinone Oxidoreductase

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

(2004) Acta Crystallogr D Biol Crystallogr 60: 1855

  • DOI: 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 ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
YHDHABCD345Escherichia coli K-12Mutation(s): 0 
Gene Names: acuIyhdHb3253JW3222
EC: 1.3.1.84
Find proteins for P26646 (Escherichia coli (strain K12))
Explore P26646 
Go to UniProtKB:  P26646
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NDP
Query on NDP

Download CCD File 
A, B, C, D
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 189.313α = 90
b = 189.313β = 90
c = 98.654γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-05-21
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance