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PDBsum entry 1iyz

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Oxidoreductase PDB id
1iyz
Jmol
Contents
Protein chain
299 a.a. *
Ligands
NDP
Waters ×36
* Residue conservation analysis
PDB id:
1iyz
Name: Oxidoreductase
Title: Crystal structures of the quinone oxidoreductase from thermus thermophilus hb8 and its complex with NADPH
Structure: Quinone oxidoreductase. Chain: a. Engineered: yes
Source: Thermus thermophilus. Organism_taxid: 274. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Dimer (from PDB file)
Resolution:
2.80Å     R-factor:   0.219     R-free:   0.256
Authors: Y.Shimomura,Y.Kakuta,K.Fukuyama,Riken Structural Genomics/proteomics Initiative (Rsgi)
Key ref: Y.Shimomura et al. (2003). Crystal structures of the quinone oxidoreductase from Thermus thermophilus HB8 and its complex with NADPH: implication for NADPH and substrate recognition. J Bacteriol, 185, 4211-4218. PubMed id: 12837796
Date:
17-Sep-02     Release date:   15-Jul-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q8L3C8  (Q8L3C8_THETH) -  Probable quinone oxidoreductase
Seq:
Struc:
302 a.a.
299 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.1.6.5.5  - NADPH:quinone reductase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: NADPH + 2 quinone = NADP+ + 2 semiquinone
NADPH
Bound ligand (Het Group name = NDP)
corresponds exactly
+ 2 × quinone
= NADP(+)
+ 2 × semiquinone
      Cofactor: Zn(2+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     oxidation-reduction process   1 term 
  Biochemical function     nucleotide binding     4 terms  

 

 
    reference    
 
 
J Bacteriol 185:4211-4218 (2003)
PubMed id: 12837796  
 
 
Crystal structures of the quinone oxidoreductase from Thermus thermophilus HB8 and its complex with NADPH: implication for NADPH and substrate recognition.
Y.Shimomura, Y.Kakuta, K.Fukuyama.
 
  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.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20835842 S.Porté, A.Moeini, I.Reche, N.Shafqat, U.Oppermann, J.Farrés, and X.Parés (2011).
Kinetic and structural evidence of the alkenal/one reductase specificity of human ΞΆ-crystallin.
  Cell Mol Life Sci, 68, 1065-1077.  
20731893 T.Maier, M.Leibundgut, D.Boehringer, and N.Ban (2010).
Structure and function of eukaryotic fatty acid synthases.
  Q Rev Biophys, 43, 373-422.  
19458256 T.J.Erb, V.Brecht, G.Fuchs, M.Müller, and B.E.Alber (2009).
Carboxylation mechanism and stereochemistry of crotonyl-CoA carboxylase/reductase, a carboxylating enoyl-thioester reductase.
  Proc Natl Acad Sci U S A, 106, 8871-8876.  
18772430 T.Maier, M.Leibundgut, and N.Ban (2008).
The crystal structure of a mammalian fatty acid synthase.
  Science, 321, 1315-1322.
PDB codes: 2vz8 2vz9
17898897 S.Smith, and S.C.Tsai (2007).
The type I fatty acid and polyketide synthases: a tale of two megasynthases.
  Nat Prod Rep, 24, 1041-1072.  
16914438 B.V.Kranthi, N.Balasubramanian, and P.N.Rangarajan (2006).
Isolation of a single-stranded DNA-binding protein from the methylotrophic yeast, Pichia pastoris and its identification as zeta crystallin.
  Nucleic Acids Res, 34, 4060-4068.  
15388933 G.Sulzenbacher, V.Roig-Zamboni, F.Pagot, S.Grisel, A.Salomoni, C.Valencia, V.Campanacci, R.Vincentelli, M.Tegoni, H.Eklund, and C.Cambillau (2004).
Structure of Escherichia coli YhdH, a putative quinone oxidoreductase.
  Acta Crystallogr D Biol Crystallogr, 60, 1855-1862.
PDB codes: 1o89 1o8c
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.