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PDBsum entry 1vck
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Oxidoreductase PDB id
1vck

 

 

 

 

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Contents
Protein chain
104 a.a. *
Ligands
FES
H2S
Metals
_FE
Waters ×139
* Residue conservation analysis
PDB id:
1vck
Name: Oxidoreductase
Title: Crystal structure of ferredoxin component of carbazole 1,9a- dioxygenase of pseudomonas resinovorans strain ca10
Structure: Ferredoxin component of carbazole. Chain: a. Synonym: rieske-type ferredoxin of carbazole 1,9a-dioxygenase. Engineered: yes
Source: Pseudomonas resinovorans. Organism_taxid: 53412. Strain: ca10. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Trimer (from PQS)
Resolution:
1.90Å     R-factor:   0.202     R-free:   0.236
Authors: J.-W.Nam,H.Noguchi,Z.Fujiomoto,H.Mizuno,S.Fushinobu,N.Kobashi, K.Iwata,T.Yoshida,H.Habe,H.Yamane,T.Omori,H.Nojiri
Key ref:
J.W.Nam et al. (2005). Crystal structure of the ferredoxin component of carbazole 1,9a-dioxygenase of Pseudomonas resinovorans strain CA10, a novel Rieske non-heme iron oxygenase system. Proteins, 58, 779-789. PubMed id: 15645447 DOI: 10.1002/prot.20374
Date:
09-Mar-04     Release date:   01-Mar-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q8GI16  (CARAC_PSERE) -  Ferredoxin CarAc from Pseudomonas resinovorans
Seq:
Struc: 		107 a.a.
104 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

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

 

 
DOI no: 10.1002/prot.20374 Proteins 58:779-789 (2005)
PubMed id: 15645447  
 
 
Crystal structure of the ferredoxin component of carbazole 1,9a-dioxygenase of Pseudomonas resinovorans strain CA10, a novel Rieske non-heme iron oxygenase system.
J.W.Nam, H.Noguchi, Z.Fujimoto, H.Mizuno, Y.Ashikawa, M.Abo, S.Fushinobu, N.Kobashi, T.Wakagi, K.Iwata, T.Yoshida, H.Habe, H.Yamane, T.Omori, H.Nojiri.
 
  ABSTRACT  
 
The carbazole 1,9a-dioxygenase (CARDO) system of Pseudomonas resinovorans strain CA10 catalyzes the dioxygenation of carbazole; the 9aC carbon bonds to a nitrogen atom and its adjacent 1C carbon as the initial reaction in the mineralization pathway. The CARDO system is composed of ferredoxin reductase (CarAd), ferredoxin (CarAc), and terminal oxygenase (CarAa). CarAc acts as a mediator in the electron transfer from CarAd to CarAa. To understand the structural basis of the protein-protein interactions during electron transport in the CARDO system, the crystal structure of CarAc was determined at 1.9 A resolution by molecular replacement using the structure of BphF, the biphenyl 2,3-dioxygenase ferredoxin from Burkholderia cepacia strain LB400 as a search model. CarAc is composed of three beta-sheets, and the structure can be divided into two domains, a cluster-binding domain and a basal domain. The Rieske [2Fe-2S] cluster is located at the tip of the cluster-binding domain, where it is exposed to solvent. While the overall folding of CarAc and BphF is strongly conserved, the properties of their surfaces are very different from each other. The structure of the cluster-binding domain of CarAc is more compact and protruding than that of BphF, and the distribution of electric charge on its molecular surface is very different. Such differences are thought to explain why these ferredoxins can act as electron mediators in respective electron transport chains composed of different-featured components.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Angular dioxygenation of carbazole catalyzed by CARDO composed of CarAa (terminal oxygenase), CarAc (ferredoxin) and CarAd (ferredoxin reductase). The product shown in brackets is unstable and has not been detected directly. 		Figure 3.
Figure 3. (a) The CarAc whole structure in ribbon format and (b) its Rieske center structure in ball-and-stick format. Both panels (a) and (b) are stereoscopic drawings. In panel (a), the Fe and S atoms are shown as orange and yellow spheres respectively. The Rieske center is connected to the protein via cysteine residues 46 and 65, and histidine residues 48 and 68, whose side chains are shown by ball-and-stick models. In panel (b), the hydrogen bonds (C46 N - A51 O, C65 N - G70 O) and hydrogen bond-like interactions (C46 S - H48 N, C65S - F67 N) formed around the Rieske [2Fe-2S] center are indicated by the green and orange broken lines, respectively.
 
  The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2005, 58, 779-789) copyright 2005.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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
18719951 E.N.Brown, R.Friemann, A.Karlsson, J.V.Parales, M.M.Couture, L.D.Eltis, and S.Ramaswamy (2008).
Determining Rieske cluster reduction potentials.
  J Biol Inorg Chem, 13, 1301-1313.
PDB code: 2qpz
18165299 J.B.Goldberg, R.E.Hancock, R.E.Parales, J.Loper, and P.Cornelis (2008).
Pseudomonas 2007.
  J Bacteriol, 190, 2649-2662.  
  18607094 T.Umeda, J.Katsuki, Y.Usami, K.Inoue, H.Noguchi, Z.Fujimoto, Y.Ashikawa, H.Yamane, and H.Nojiri (2008).
Crystallization and preliminary X-ray diffraction studies of a novel ferredoxin involved in the dioxygenation of carbazole by Novosphingobium sp. KA1.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 632-635.  
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
  17909288 K.Inoue, Y.Ashikawa, Y.Usami, H.Noguchi, Z.Fujimoto, H.Yamane, and H.Nojiri (2007).
Crystallization and preliminary crystallographic analysis of the ferredoxin component of carbazole 1,9a-dioxygenase from Nocardioides aromaticivorans IC177.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 855-857.  
  17554172 Y.Ashikawa, H.Uchimura, Z.Fujimoto, K.Inoue, H.Noguchi, H.Yamane, and H.Nojiri (2007).
Crystallization and preliminary X-ray diffraction studies of the ferredoxin reductase component in the Rieske nonhaem iron oxygenase system carbazole 1,9a-dioxygenase.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 499-502.  
16933133 B.G.Keenan, and T.K.Wood (2006).
Orthric Rieske dioxygenases for degrading mixtures of 2,4-dinitrotoluene/naphthalene and 2-amino-4,6-dinitrotoluene/4-amino-2,6-dinitrotoluene.
  Appl Microbiol Biotechnol, 73, 827-838.  
16672473 K.Inoue, H.Habe, H.Yamane, and H.Nojiri (2006).
Characterization of novel carbazole catabolism genes from gram-positive carbazole degrader Nocardioides aromaticivorans IC177.
  Appl Environ Microbiol, 72, 3321-3329.  
  17142899 K.Inoue, Y.Ashikawa, Y.Usami, H.Noguchi, Z.Fujimoto, H.Yamane, and H.Nojiri (2006).
Crystallization and preliminary X-ray diffraction studies of the terminal oxygenase component of carbazole 1,9a-dioxygenase from Nocardioides aromaticivorans IC177.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 1212-1214.  
16627939 L.A.Moe, C.A.Bingman, G.E.Wesenberg, G.N.Phillips, and B.G.Fox (2006).
Structure of T4moC, the Rieske-type ferredoxin component of toluene 4-monooxygenase.
  Acta Crystallogr D Biol Crystallogr, 62, 476-482.
PDB code: 1vm9
  16511100 Y.Ashikawa, Z.Fujimoto, H.Noguchi, H.Habe, T.Omori, H.Yamane, and H.Nojiri (2005).
Crystallization and preliminary X-ray diffraction analysis of the electron-transfer complex between the terminal oxygenase component and ferredoxin in the Rieske non-haem iron oxygenase system carbazole 1,9a-dioxygenase.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 577-580.  
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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