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PDBsum entry 1t3q

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protein ligands Protein-protein interface(s) links
Oxidoreductase PDB id
1t3q
Jmol
Contents
Protein chains
162 a.a. *
786 a.a. *
285 a.a. *
Ligands
FES ×4
GOL ×9
SO4 ×8
MCN-SMO ×2
FAD ×2
Waters ×2533
* Residue conservation analysis
PDB id:
1t3q
Name: Oxidoreductase
Title: Crystal structure of quinoline 2-oxidoreductase from pseudom putida 86
Structure: Quinoline 2-oxidoreductase small subunit. Chain: a, d. Quinoline 2-oxidoreductase large subunit. Chain: b, e. Quinoline 2-oxidoreductase medium subunit. Chain: c, f. Ec: 1.3.99.17
Source: Pseudomonas putida. Organism_taxid: 303. Strain: 86. Strain: 86
Biol. unit: Hexamer (from PQS)
Resolution:
1.80Å     R-factor:   0.186     R-free:   0.207
Authors: I.Bonin,B.M.Martins,V.Purvanov,S.Fetzner,R.Huber,H.Dobbek
Key ref:
I.Bonin et al. (2004). Active site geometry and substrate recognition of the molybdenum hydroxylase quinoline 2-oxidoreductase. Structure, 12, 1425-1435. PubMed id: 15296736 DOI: 10.1016/j.str.2004.05.014
Date:
27-Apr-04     Release date:   14-Sep-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P72223  (P72223_PSEPU) -  Quinoline 2-oxidoreductase
Seq:
Struc:
168 a.a.
162 a.a.
Protein chains
Pfam   ArchSchema ?
P72224  (P72224_PSEPU) -  Quinoline 2-oxidoreductase
Seq:
Struc:
 
Seq:
Struc:
788 a.a.
786 a.a.*
Protein chains
Pfam   ArchSchema ?
P72222  (P72222_PSEPU) -  Quinoline 2-oxidoreductase
Seq:
Struc:
288 a.a.
285 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     oxidation-reduction process   1 term 
  Biochemical function     electron carrier activity     10 terms  

 

 
DOI no: 10.1016/j.str.2004.05.014 Structure 12:1425-1435 (2004)
PubMed id: 15296736  
 
 
Active site geometry and substrate recognition of the molybdenum hydroxylase quinoline 2-oxidoreductase.
I.Bonin, B.M.Martins, V.Purvanov, S.Fetzner, R.Huber, H.Dobbek.
 
  ABSTRACT  
 
The soil bacterium Pseudomonas putida 86 uses quinoline as a sole source of carbon and energy. Quinoline 2-oxidoreductase (Qor) catalyzes the first metabolic step converting quinoline to 2-oxo-1,2-dihydroquinoline. Qor is a member of the molybdenum hydroxylases. The molybdenum ion is coordinated by two ene-dithiolate sulfur atoms, two oxo-ligands, and a catalytically crucial sulfido-ligand, whose position in the active site was controversial. The 1.8 A resolution crystal structure of Qor indicates that the sulfido-ligand occupies the equatorial position at the molybdenum ion. The structural comparison of Qor with the allopurinol-inhibited xanthine dehydrogenase from Rhodobacter capsulatus allows direct insight into the mechanism of substrate recognition and the identification of putative catalytic residues. The active site protein variants QorE743V and QorE743D were analyzed to assess the catalytic role of E743.
 
  Selected figure(s)  
 
Figure 4.
Figure 4. Stereoview of the Moco and Active Site ResiduesColor code as in Figure 1.(A) The distances from the molybdenum ion to the two oxo- and the sulfido-ligands are the average between the values observed in the two monomers. The omit 2F[o] - F[c] electron density map is contoured at 1, 2, and 3s (colored gray, green, and red, respectively).(B) The Moco neighboring residues (the cytosine dinucleotide part of the Moco was removed for clarity) are colored in orange and labeled.
 
  The above figure is reprinted by permission from Cell Press: Structure (2004, 12, 1425-1435) copyright 2004.  
  Figure was selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21120472 J.Jin, A.J.Straathof, M.W.Pinkse, and U.Hanefeld (2011).
Purification, characterization, and cloning of a bifunctional molybdoenzyme with hydratase and alcohol dehydrogenase activity.
  Appl Microbiol Biotechnol, 89, 1831-1840.  
21243161 J.Jin, and U.Hanefeld (2011).
The selective addition of water to C=C bonds; enzymes are the best chemists.
  Chem Commun (Camb), 47, 2502-2510.  
  21151514 M.Neumann, and S.Leimkühler (2011).
The role of system-specific molecular chaperones in the maturation of molybdoenzymes in bacteria.
  Biochem Res Int, 2011, 850924.  
19258534 M.Carmona, M.T.Zamarro, B.Blázquez, G.Durante-Rodríguez, J.F.Juárez, J.A.Valderrama, M.J.Barragán, J.L.García, and E.Díaz (2009).
Anaerobic catabolism of aromatic compounds: a genetic and genomic view.
  Microbiol Mol Biol Rev, 73, 71.  
19452052 M.J.Romão (2009).
Molybdenum and tungsten enzymes: a crystallographic and mechanistic overview.
  Dalton Trans, (), 4053-4068.  
19206188 S.Groysman, and R.H.Holm (2009).
Biomimetic chemistry of iron, nickel, molybdenum, and tungsten in sulfur-ligated protein sites.
  Biochemistry, 48, 2310-2320.  
17139522 A.Thapper, D.R.Boer, C.D.Brondino, J.J.Moura, and M.J.Romão (2007).
Correlating EPR and X-ray structural analysis of arsenite-inhibited forms of aldehyde oxidoreductase.
  J Biol Inorg Chem, 12, 353-366.
PDB code: 3l4p
17327224 J.M.Pauff, C.F.Hemann, N.Jünemann, S.Leimkühler, and R.Hille (2007).
The role of arginine 310 in catalysis and substrate specificity in xanthine dehydrogenase from Rhodobacter capsulatus.
  J Biol Chem, 282, 12785-12790.  
16480912 C.D.Brondino, M.J.Romão, I.Moura, and J.J.Moura (2006).
Molybdenum and tungsten enzymes: the xanthine oxidase family.
  Curr Opin Chem Biol, 10, 109-114.  
16820521 P.Sachelaru, E.Schiltz, and R.Brandsch (2006).
A functional mobA gene for molybdopterin cytosine dinucleotide cofactor biosynthesis is required for activity and holoenzyme assembly of the heterotrimeric nicotine dehydrogenases of Arthrobacter nicotinovorans.
  Appl Environ Microbiol, 72, 5126-5131.  
16333621 R.Brandsch (2006).
Microbiology and biochemistry of nicotine degradation.
  Appl Microbiol Biotechnol, 69, 493-498.  
16332855 B.Carl, and S.Fetzner (2005).
Transcriptional activation of quinoline degradation operons of Pseudomonas putida 86 by the AraC/XylS-type regulator OxoS and cross-regulation of the PqorM promoter by XylS.
  Appl Environ Microbiol, 71, 8618-8626.  
15893671 B.M.Martins, T.Svetlitchnaia, and H.Dobbek (2005).
2-Oxoquinoline 8-monooxygenase oxygenase component: active site modulation by Rieske-[2Fe-2S] center oxidation/reduction.
  Structure, 13, 817-824.
PDB codes: 1z01 1z02 1z03
  16508115 D.R.Boer, A.Müller, S.Fetzner, D.J.Lowe, and M.J.Romão (2005).
On the purification and preliminary crystallographic analysis of isoquinoline 1-oxidoreductase from Brevundimonas diminuta 7.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 137-140.  
15937278 H.Cheng, and N.V.Grishin (2005).
DOM-fold: a structure with crossing loops found in DmpA, ornithine acetyltransferase, and molybdenum cofactor-binding domain.
  Protein Sci, 14, 1902-1910.  
15902470 V.Purvanov, and S.Fetzner (2005).
Replacement of active-site residues of quinoline 2-oxidoreductase involved in substrate recognition and specificity.
  Curr Microbiol, 50, 217-222.  
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 code is shown on the right.