Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 32.87 kDa 
• Atom Count: 2211 
• Modelled Residue Count: 299 
• Deposited Residue Count: 302 
• Unique protein chains: 1

1IYZ

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

• PDB DOI: 10.2210/pdb1IYZ/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Thermus thermophilus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2002-09-17 Released: 2003-07-15 
• Deposition Author(s): Shimomura, Y., Kakuta, Y., Fukuyama, K., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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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 

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

• PubMed: 12837796 
• 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. 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.

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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

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
QUINONE OXIDOREDUCTASE	A	302	Thermus thermophilus	Mutation(s): 0  Gene Names: TthHC11_07190 EC: 1.6.5.5
UniProt
Find proteins for Q8L3C8 (Thermus thermophilus) Explore Q8L3C8  Go to UniProtKB:  Q8L3C8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDP	B [auth A]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H30 N7 O17 P3 ACFIXJIJDZMPPO-NNYOXOHSSA-N

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 = 77.633	α = 90
b = 77.633	β = 90
c = 235.614	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-09-17 
• Released Date: 2003-07-15 
Deposition Author(s): Shimomura, Y., Kakuta, Y., Fukuyama, K., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• 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