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PDBsum entry 2nox

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protein ligands Protein-protein interface(s) links
Oxidoreductase PDB id
2nox
Jmol
Contents
Protein chains
(+ 10 more) 261 a.a. *
Ligands
HEM ×16
Waters ×1543
* Residue conservation analysis
PDB id:
2nox
Name: Oxidoreductase
Title: Crystal structure of tryptophan 2,3-dioxygenase from ralston metallidurans
Structure: Tryptophan 2,3-dioxygenase. Chain: a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p. Ec: 1.13.11.11
Source: Cupriavidus metallidurans. Organism_taxid: 119219
Resolution:
2.40Å     R-factor:   0.210     R-free:   0.270
Authors: Y.Zhang,S.A.Kang,T.Mukherjee,S.Bale,B.R.Crane,T.P.Begley,S.E
Key ref: Y.Zhang et al. (2007). Crystal structure and mechanism of tryptophan 2,3-dioxygenase, a heme enzyme involved in tryptophan catabolism and in quinolinate biosynthesis. Biochemistry, 46, 145-155. PubMed id: 17198384 DOI: 10.1021/bi0620095
Date:
26-Oct-06     Release date:   19-Dec-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q1LK00  (T23O_RALME) -  Tryptophan 2,3-dioxygenase
Seq:
Struc:
299 a.a.
261 a.a.
Key:    PfamA domain  Secondary structure

 Enzyme reactions 
   Enzyme class: E.C.1.13.11.11  - Tryptophan 2,3-dioxygenase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Tryptophan Catabolism
      Reaction: L-tryptophan + O2 = N-formyl-L-kynurenine
L-tryptophan
+ O(2)
= N-formyl-L-kynurenine
      Cofactor: Heme
Heme
Bound ligand (Het Group name = HEM) matches with 95.45% similarity
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     oxidation-reduction process   6 terms 
  Biochemical function     oxidoreductase activity     5 terms  

 

 
    reference    
 
 
DOI no: 10.1021/bi0620095 Biochemistry 46:145-155 (2007)
PubMed id: 17198384  
 
 
Crystal structure and mechanism of tryptophan 2,3-dioxygenase, a heme enzyme involved in tryptophan catabolism and in quinolinate biosynthesis.
Y.Zhang, S.A.Kang, T.Mukherjee, S.Bale, B.R.Crane, T.P.Begley, S.E.Ealick.
 
  ABSTRACT  
 
The structure of tryptophan 2,3-dioxygenase (TDO) from Ralstonia metallidurans was determined at 2.4 A. TDO catalyzes the irreversible oxidation of l-tryptophan to N-formyl kynurenine, which is the initial step in tryptophan catabolism. TDO is a heme-containing enzyme and is highly specific for its substrate l-tryptophan. The structure is a tetramer with a heme cofactor bound at each active site. The monomeric fold, as well as the heme binding site, is similar to that of the large domain of indoleamine 2,3-dioxygenase, an enzyme that catalyzes the same reaction except with a broader substrate tolerance. Modeling of the putative (S)-tryptophan hydroperoxide intermediate into the active site, as well as substrate analogue and mutagenesis studies, are consistent with a Criegee mechanism for the reaction.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20361220 L.Capece, A.Lewis-Ballester, D.Batabyal, N.Di Russo, S.R.Yeh, D.A.Estrin, and M.A.Marti (2010).
The first step of the dioxygenation reaction carried out by tryptophan dioxygenase and indoleamine 2,3-dioxygenase as revealed by quantum mechanical/molecular mechanical studies.
  J Biol Inorg Chem, 15, 811-823.  
20715188 L.Capece, M.Arrar, A.E.Roitberg, S.R.Yeh, M.A.Marti, and D.A.Estrin (2010).
Substrate stereo-specificity in tryptophan dioxygenase and indoleamine 2,3-dioxygenase.
  Proteins, 78, 2961-2972.  
20353179 R.M.Davydov, N.Chauhan, S.J.Thackray, J.L.Anderson, N.D.Papadopoulou, C.G.Mowat, S.K.Chapman, E.L.Raven, and B.M.Hoffman (2010).
Probing the ternary complexes of indoleamine and tryptophan 2,3-dioxygenases by cryoreduction EPR and ENDOR spectroscopy.
  J Am Chem Soc, 132, 5494-5500.  
20636821 U.Grohmann, and V.Bronte (2010).
Control of immune response by amino acid metabolism.
  Immunol Rev, 236, 243-264.  
19805032 A.Lewis-Ballester, D.Batabyal, T.Egawa, C.Lu, Y.Lin, M.A.Marti, L.Capece, D.A.Estrin, and S.R.Yeh (2009).
Evidence for a ferryl intermediate in a heme-based dioxygenase.
  Proc Natl Acad Sci U S A, 106, 17371-17376.  
18612775 A.Macchiarulo, E.Camaioni, R.Nuti, and R.Pellicciari (2009).
Highlights at the gate of tryptophan catabolism: a review on the mechanisms of activation and regulation of indoleamine 2,3-dioxygenase (IDO), a novel target in cancer disease.
  Amino Acids, 37, 219-229.  
19461669 S.Löb, A.Königsrainer, H.G.Rammensee, G.Opelz, and P.Terness (2009).
Inhibitors of indoleamine-2,3-dioxygenase for cancer therapy: can we see the wood for the trees?
  Nat Rev Cancer, 9, 445-452.  
18493661 A.Sheoran, A.King, A.Velasco, J.M.Pero, and S.Garneau-Tsodikova (2008).
Characterization of TioF, a tryptophan 2,3-dioxygenase involved in 3-hydroxyquinaldic acid formation during thiocoraline biosynthesis.
  Mol Biosyst, 4, 622-628.  
18515349 M.von Grotthuss, D.Plewczynski, G.Vriend, and L.Rychlewski (2008).
3D-Fun: predicting enzyme function from structure.
  Nucleic Acids Res, 36, W303-W307.  
19021508 S.J.Thackray, C.G.Mowat, and S.K.Chapman (2008).
Exploring the mechanism of tryptophan 2,3-dioxygenase.
  Biochem Soc Trans, 36, 1120-1123.  
18026683 H.J.Yuasa, M.Takubo, A.Takahashi, T.Hasegawa, H.Noma, and T.Suzuki (2007).
Evolution of vertebrate indoleamine 2,3-dioxygenases.
  J Mol Evol, 65, 705-714.  
17535808 S.R.Thomas, A.C.Terentis, H.Cai, O.Takikawa, A.Levina, P.A.Lay, M.Freewan, and R.Stocker (2007).
Post-translational regulation of human indoleamine 2,3-dioxygenase activity by nitric oxide.
  J Biol Chem, 282, 23778-23787.  
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.