Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 37.29 kDa 
• Atom Count: 2458 
• Residue Count: 320 
• Unique protein chains: 1

1O89

Crystal structure of E. COLI K-12 yhdH

• DOI: 10.2210/pdb1O89/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2002-11-26 Released: 2004-02-26 
• Deposition Author(s): Sulzenbacher, G., Roig-Zamboni, V., Pagot, F., Grisel, S., Salamoni, A., Valencia, C., Bignon, C., Vincentelli, R., Tegoni, M., Cambillau, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.237 
• R-Value Work: 0.197 
• R-Value Observed: 0.201 

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 D Biol Crystallogr 60: 1855

• PubMed: 15388933 
• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
YHDH	A	345	Escherichia coli K-12	Mutation(s): 0  Gene Names: acuI, yhdH, b3253, JW3222 EC: 1.3.1.84
Find proteins for P26646 (Escherichia coli (strain K12)) Explore P26646  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 
• R-Value Observed: 0.201 
• Space Group: P 4₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.671	α = 90
b = 55.671	β = 90
c = 201.48	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-11-26 
• Released Date: 2004-02-26 
Deposition Author(s): Sulzenbacher, G., Roig-Zamboni, V., Pagot, F., Grisel, S., Salamoni, A., Valencia, C., Bignon, C., Vincentelli, R., Tegoni, M., Cambillau, C.

Revision History 

• 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