1IYZ

Crystal Structures of the Quinone Oxidoreductase from Thermus thermophilus HB8 and Its Complex with NADPH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.224 

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This is version 1.2 of the entry. See complete history


Literature

Crystal Structures of the Quinone Oxidoreductase from Thermus thermophilus HB8 and Its Complex with NADPH: Implication for NADPH and Substrate Recognition

Shimomura, Y.Kakuta, Y.Fukuyama, K.

(2003) J Bacteriol 185: 4211-4218

  • DOI: 10.1128/jb.185.14.4211-4218.2003
  • Primary Citation of Related Structures:  
    1IYZ, 1IZ0

  • PubMed Abstract: 
  • The crystal structures of the zeta-crystalline-like soluble quinone oxidoreductase from Thermus thermophilus HB8 (QOR(Tt)) and of its complex with NADPH have been determined at 2.3- and 2.8-A resolutions, respectively. QOR(Tt) is composed of two domains, and its overall fold is similar to the folds of Escherichia coli quinone oxidoreductase (QOR(Ec)) and horse liver alcohol dehydrogenase ...

    The crystal structures of the zeta-crystalline-like soluble quinone oxidoreductase from Thermus thermophilus HB8 (QOR(Tt)) and of its complex with NADPH have been determined at 2.3- and 2.8-A resolutions, respectively. QOR(Tt) is composed of two domains, and its overall fold is similar to the folds of Escherichia coli quinone oxidoreductase (QOR(Ec)) and horse liver alcohol dehydrogenase. QOR(Tt) forms a homodimer in the crystal by interaction of the betaF-strands in domain II, forming a large beta-sheet that crosses the dimer interface. High thermostability of QOR(Tt) was evidenced by circular dichroic measurement. NADPH is located between the two domains in the QOR(Tt)-NADPH complex. The disordered segment involved in the coenzyme binding of apo-QOR(Tt) becomes ordered upon NADPH binding. The segment covers an NADPH-binding cleft and may serve as a lid. The 2'-phosphate group of the adenine of NADPH is surrounded by polar and positively charged residues in QOR(Tt), suggesting that QOR(Tt) binds NADPH more readily than NADH. The putative substrate-binding site of QOR(Tt), unlike that of QOR(Ec), is largely blocked by nearby residues, permitting access only to small substrates. This may explain why QOR(Tt) has weak p-benzoquinone reduction activity and is inactive with such large substrates of QOR(Ec) as 5-hydroxy-1,4-naphthoquinone and phenanthraquinone.


    Related Citations: 
    • Overproduction, crystallization and preliminary X-ray diffraction analysis of a quinone oxidoreductase from Thermus thermophilus HB8
      Shimomura, Y., Sumiguchi-Agari, K., Masui, R., Kuramitsu, S., Fukuyama, K.
      (2002) Acta Crystallogr D Biol Crystallogr 58: 1365

    Organizational Affiliation

    Department of Biology, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
QUINONE OXIDOREDUCTASEA302Thermus thermophilusMutation(s): 0 
Gene Names: TthHC11_07190
EC: 1.6.5.5
UniProt
Find proteins for Q8L3C8 (Thermus thermophilus)
Explore Q8L3C8 
Go to UniProtKB:  Q8L3C8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8L3C8
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 Ideal Coordinates CCD File 
B [auth A]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: 2.80 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.224 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.633α = 90
b = 77.633β = 90
c = 235.614γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-07-15
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance