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PDBsum entry 1wql
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protein ligands metals Protein-protein interface(s) links
Oxidoreductase PDB id
1wql

 

 

 

 

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Contents
Protein chains
436 a.a. *
182 a.a. *
Ligands
FES
OXY
Metals
FE2
Waters ×472
* Residue conservation analysis
PDB id:
1wql
Name: Oxidoreductase
Title: Cumene dioxygenase (cuma1a2) from pseudomonas fluorescens ip01
Structure: Iron-sulfur protein large subunit of cumene dioxygenase. Chain: a. Synonym: cumene dioxygenase large subunit. Engineered: yes. Ethylbenzene dioxygenase small subunit. Chain: b. Synonym: cumene dioxygenase small subunit. Engineered: yes
Source: Pseudomonas fluorescens. Organism_taxid: 294. Gene: cuma1. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Gene: cuma2.
Biol. unit: Hexamer (from PDB file)
Resolution:
2.20Å     R-factor:   0.173     R-free:   0.196
Authors: X.Dong,S.Fushinobu,E.Fukuda,T.Terada,S.Nakamura,K.Shimizu,H.Nojiri, T.Omori,H.Shoun,T.Wakagi
Key ref: X.Dong et al. (2005). Crystal structure of the terminal oxygenase component of cumene dioxygenase from Pseudomonas fluorescens IP01. J Bacteriol, 187, 2483-2490. PubMed id: 15774891
Date:
30-Sep-04     Release date:   29-Mar-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q51743  (Q51743_PSEFL) -  Iron-sulfur protein large subunit of cumene dioxygenase from Pseudomonas fluorescens
Seq:
Struc: 		459 a.a.
436 a.a.
Protein chain
Pfam   ArchSchema ?
Q51744  (Q51744_PSEFL) -  Ethylbenzene dioxygenase small subunit from Pseudomonas fluorescens
Seq:
Struc: 		186 a.a.
182 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains A, B: E.C.1.14.12.-  - ?????
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

 

 
J Bacteriol 187:2483-2490 (2005)
PubMed id: 15774891  
 
 
Crystal structure of the terminal oxygenase component of cumene dioxygenase from Pseudomonas fluorescens IP01.
X.Dong, S.Fushinobu, E.Fukuda, T.Terada, S.Nakamura, K.Shimizu, H.Nojiri, T.Omori, H.Shoun, T.Wakagi.
 
  ABSTRACT  
 
The crystal structure of the terminal component of the cumene dioxygenase multicomponent enzyme system of Pseudomonas fluorescens IP01 (CumDO) was determined at a resolution of 2.2 A by means of molecular replacement by using the crystal structure of the terminal oxygenase component of naphthalene dioxygenase from Pseudomonas sp. strain NCIB 9816-4 (NphDO). The ligation of the two catalytic centers of CumDO (i.e., the nonheme iron and Rieske [2Fe-2S] centers) and the bridging between them in neighboring catalytic subunits by hydrogen bonds through a single amino acid residue, Asp231, are similar to those of NphDO. An unidentified external ligand, possibly dioxygen, was bound at the active site nonheme iron. The entrance to the active site of CumDO is different from the entrance to the active site of NphDO, as the two loops forming the lid exhibit great deviation. On the basis of the complex structure of NphDO, a biphenyl substrate was modeled in the substrate-binding pocket of CumDO. The residues surrounding the modeled biphenyl molecule include residues that have already been shown to be important for its substrate specificity by a number of engineering studies of biphenyl dioxygenases.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20966097 R.M.Summers, T.M.Louie, C.L.Yu, and M.Subramanian (2011).
Characterization of a broad-specificity non-haem iron N-demethylase from Pseudomonas putida CBB5 capable of utilizing several purine alkaloids as sole carbon and nitrogen source.
  Microbiology, 157, 583-592.  
20082074 D.Kim, K.Y.Choi, M.Yoo, J.N.Choi, C.H.Lee, G.J.Zylstra, B.S.Kang, and E.Kim (2010).
Benzylic and aryl hydroxylations of m-xylene by o-xylene dioxygenase from Rhodococcus sp. strain DK17.
  Appl Microbiol Biotechnol, 86, 1841-1847.  
19776767 S.Iwai, B.Chai, W.J.Sul, J.R.Cole, S.A.Hashsham, and J.M.Tiedje (2010).
Gene-targeted-metagenomics reveals extensive diversity of aromatic dioxygenase genes in the environment.
  ISME J, 4, 279-285.  
20652238 T.Sakaki, and E.Munetsuna (2010).
Enzyme systems for biodegradation of polychlorinated dibenzo-p-dioxins.
  Appl Microbiol Biotechnol, 88, 23-30.  
18813921 E.L.Ang, J.P.Obbard, and H.Zhao (2009).
Directed evolution of aniline dioxygenase for enhanced bioremediation of aromatic amines.
  Appl Microbiol Biotechnol, 81, 1063-1070.  
19234303 J.K.Capyk, I.D'Angelo, N.C.Strynadka, and L.D.Eltis (2009).
Characterization of 3-ketosteroid 9{alpha}-hydroxylase, a Rieske oxygenase in the cholesterol degradation pathway of Mycobacterium tuberculosis.
  J Biol Chem, 284, 9937-9946.
PDB code: 2zyl
19464996 M.Tarasev, S.Pullela, and D.P.Ballou (2009).
Distal end of 105-125 loop--a putative reductase binding domain of phthalate dioxygenase.
  Arch Biochem Biophys, 487, 10-18.  
18277980 E.G.Kovaleva, and J.D.Lipscomb (2008).
Versatility of biological non-heme Fe(II) centers in oxygen activation reactions.
  Nat Chem Biol, 4, 186-193.  
18703841 E.J.Levin, N.L.Elsen, K.D.Seder, J.G.McCoy, B.G.Fox, and G.N.Phillips (2008).
X-ray structure of a soluble Rieske-type ferredoxin from Mus musculus.
  Acta Crystallogr D Biol Crystallogr, 64, 933-940.
PDB code: 3d89
19020684 P.C.Bruijnincx, G.van Koten, and R.J.Klein Gebbink (2008).
Mononuclear non-heme iron enzymes with the 2-His-1-carboxylate facial triad: recent developments in enzymology and modeling studies.
  Chem Soc Rev, 37, 2716-2744.  
18189388 T.Ohta, S.Chakrabarty, J.D.Lipscomb, and E.I.Solomon (2008).
Near-IR MCD of the nonheme ferrous active site in naphthalene 1,2-dioxygenase: correlation to crystallography and structural insight into the mechanism of Rieske dioxygenases.
  J Am Chem Soc, 130, 1601-1610.  
17693557 D.A.de Cárcer, M.Martín, U.Karlson, and R.Rivilla (2007).
Changes in bacterial populations and in biphenyl dioxygenase gene diversity in a polychlorinated biphenyl-polluted soil after introduction of willow trees for rhizoremediation.
  Appl Environ Microbiol, 73, 6224-6232.  
17349044 D.J.Ferraro, E.N.Brown, C.L.Yu, R.E.Parales, D.T.Gibson, and S.Ramaswamy (2007).
Structural investigations of the ferredoxin and terminal oxygenase components of the biphenyl 2,3-dioxygenase from Sphingobium yanoikuyae B1.
  BMC Struct Biol, 7, 10.
PDB codes: 2gbw 2gbx 2i7f
17269935 E.L.Ang, J.P.Obbard, and H.Zhao (2007).
Probing the molecular determinants of aniline dioxygenase substrate specificity by saturation mutagenesis.
  FEBS J, 274, 928-939.  
17157819 J.Jakoncic, Y.Jouanneau, C.Meyer, and V.Stojanoff (2007).
The catalytic pocket of the ring-hydroxylating dioxygenase from Sphingomonas CHY-1.
  Biochem Biophys Res Commun, 352, 861-866.
PDB code: 2ckf
17142386 J.Vézina, D.Barriault, and M.Sylvestre (2007).
Family shuffling of soil DNA to change the regiospecificity of Burkholderia xenovorans LB400 biphenyl dioxygenase.
  J Bacteriol, 189, 779-788.  
17318598 M.A.Carrondo, I.Bento, P.M.Matias, and P.F.Lindley (2007).
Crystallographic evidence for dioxygen interactions with iron proteins.
  J Biol Inorg Chem, 12, 429-442.  
17567152 M.B.Neibergall, A.Stubna, Y.Mekmouche, E.Münck, and J.D.Lipscomb (2007).
Hydrogen peroxide dependent cis-dihydroxylation of benzoate by fully oxidized benzoate 1,2-dioxygenase.
  Biochemistry, 46, 8004-8016.  
17764654 M.Tarasev, C.S.Kaddis, S.Yin, J.A.Loo, J.Burgner, and D.P.Ballou (2007).
Similar enzymes, different structures: phthalate dioxygenase is an alpha3alpha3 stacked hexamer, not an alpha3beta3 trimer like "normal" Rieske oxygenases.
  Arch Biochem Biophys, 466, 31-39.  
16391757 D.R.Boyd, and T.D.Bugg (2006).
Arene cis-dihydrodiol formation: from biology to application.
  Org Biomol Chem, 4, 181-192.  
16922496 M.Tarasev, A.Pinto, D.Kim, S.J.Elliott, and D.P.Ballou (2006).
The "bridging" aspartate 178 in phthalate dioxygenase facilitates interactions between the Rieske center and the iron(II)--mononuclear center.
  Biochemistry, 45, 10208-10216.  
16672497 R.Witzig, H.Junca, H.J.Hecht, and D.H.Pieper (2006).
Assessment of toluene/biphenyl dioxygenase gene diversity in benzene-polluted soils: links between benzene biodegradation and genes similar to those encoding isopropylbenzene dioxygenases.
  Appl Environ Microbiol, 72, 3504-3514.  
16237006 L.Gakhar, Z.A.Malik, C.C.Allen, D.A.Lipscomb, M.J.Larkin, and S.Ramaswamy (2005).
Structure and increased thermostability of Rhodococcus sp. naphthalene 1,2-dioxygenase.
  J Bacteriol, 187, 7222-7231.
PDB codes: 2b1x 2b24
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.

 

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