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PDBsum entry 2gqw

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Oxidoreductase PDB id
2gqw
Jmol
Contents
Protein chain
401 a.a. *
Ligands
FAD
GOL
FMT ×5
Waters ×440
* Residue conservation analysis
PDB id:
2gqw
Name: Oxidoreductase
Title: Crystal structure of ferredoxin reductase, bpha4 (oxidized f
Structure: Ferredoxin reductase. Chain: a. Synonym: ferredoxin reductase bpha4. Engineered: yes
Source: Pseudomonas sp. Kks102. Organism_taxid: 307. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
1.40Å     R-factor:   0.179     R-free:   0.196
Authors: T.Senda,M.Senda
Key ref:
M.Senda et al. (2007). Molecular Mechanism of the Redox-dependent Interaction between NADH-dependent Ferredoxin Reductase and Rieske-type [2Fe-2S] Ferredoxin. J Mol Biol, 373, 382-400. PubMed id: 17850818 DOI: 10.1016/j.jmb.2007.08.002
Date:
22-Apr-06     Release date:   22-May-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q52437  (Q52437_PSES1) -  Ferredoxin reductase
Seq:
Struc:
408 a.a.
401 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     oxidation-reduction process   2 terms 
  Biochemical function     nucleotide binding     3 terms  

 

 
DOI no: 10.1016/j.jmb.2007.08.002 J Mol Biol 373:382-400 (2007)
PubMed id: 17850818  
 
 
Molecular Mechanism of the Redox-dependent Interaction between NADH-dependent Ferredoxin Reductase and Rieske-type [2Fe-2S] Ferredoxin.
M.Senda, S.Kishigami, S.Kimura, M.Fukuda, T.Ishida, T.Senda.
 
  ABSTRACT  
 
The electron transfer system of the biphenyl dioxygenase BphA, which is derived from Acidovorax sp. (formally Pseudomonas sp.) strain KKS102, is composed of an FAD-containing NADH-ferredoxin reductase (BphA4) and a Rieske-type [2Fe-2S] ferredoxin (BphA3). Biochemical studies have suggested that the whole electron transfer process from NADH to BphA3 comprises three consecutive elementary electron-transfer reactions, in which BphA3 and BphA4 interact transiently in a redox-dependent manner. Initially, BphA4 receives two electrons from NADH. The reduced BphA4 then delivers one electron each to the [2Fe-2S] cluster of the two BphA3 molecules through redox-dependent transient interactions. The reduced BphA3 transports the electron to BphA1A2, a terminal oxygenase, to support the activation of dioxygen for biphenyl dihydroxylation. In order to elucidate the molecular mechanisms of the sequential reaction and the redox-dependent interaction between BphA3 and BphA4, we determined the crystal structures of the productive BphA3-BphA4 complex, and of free BphA3 and BphA4 in all the redox states occurring in the catalytic cycle. The crystal structures of these reaction intermediates demonstrated that each elementary electron transfer induces a series of redox-dependent conformational changes in BphA3 and BphA4, which regulate the interaction between them. In addition, the conformational changes induced by the preceding electron transfer seem to induce the next electron transfer. The interplay of electron transfer and induced conformational changes seems to be critical to the sequential electron-transfer reaction from NADH to BphA3.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. Redox-dependent conformational changes of BphA4 (I). (a) Single-crystal UV-vis spectra of BphA4(ox, -), BphA4(rd, NAD^+), BphA4(sq, NAD^+) and BphA4(ox, NAD^+). The symbol re-ox represents the re-oxidized form of BphA4 (BphA4(ox, NAD^+)) (b) Conformation of the isoalloxazine ring of FAD in four redox states viewed from the N5 and N10 sides. F[o]–F[c] simulated-annealing (SA) omit maps of (b) and (c) are contoured at 3σ. (c) Conformation of the ribityl chain of FAD. The ribityl chain flips when FAD is in the hydroquinone and semiquinone states. (d) Rigid-body rotation of the NADH/CT domain observed in each state (schematic representations). The FAD-binding, NADH-binding, and C-terminal domains are shown in green, yellow, and blue, respectively. The isoalloxazine rings of FAD are shown with cyan lines. Black arrows show the direction of the rotation.
Figure 6.
Figure 6. Redox-dependent conformational changes of BphA3. Stereo view of the oxidized (green) and reduced (pink) forms of BphA3. The Rieske [2Fe-2S] cluster is shown as a space-filling model (Fe, orange; S, yellow). Conformational change of Glu47[A3] from oxidized to reduced states is shown by the red arrow.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2007, 373, 382-400) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21310654 T.Ohmori, H.Morita, M.Tanaka, K.Miyauchi, D.Kasai, K.Furukawa, K.Miyashita, N.Ogawa, E.Masai, and M.Fukuda (2011).
Development of a strain for efficient degradation of polychlorinated biphenyls by patchwork assembly of degradation pathways.
  J Biosci Bioeng, 111, 437-442.  
21228494 T.Ohmori, H.Morita, M.Tanaka, M.Tomoi, K.Miyauchi, D.Kasai, K.Furukawa, E.Masai, and M.Fukuda (2011).
Expression in Escherichia coli of biphenyl 2,3-dioxygenase genes from a Gram-positive polychlorinated biphenyl degrader, Rhodococcus jostii RHA1.
  Biosci Biotechnol Biochem, 75, 26-33.  
20559823 M.Morikawa (2010).
Dioxygen activation responsible for oxidation of aliphatic and aromatic hydrocarbon compounds: current state and variants.
  Appl Microbiol Biotechnol, 87, 1595-1603.  
19447115 I.F.Sevrioukova (2009).
Redox-linked conformational dynamics in apoptosis-inducing factor.
  J Mol Biol, 390, 924-938.
PDB codes: 3gd3 3gd4
19243237 T.Senda, M.Senda, S.Kimura, and T.Ishida (2009).
Redox control of protein conformation in flavoproteins.
  Antioxid Redox Signal, 11, 1741-1766.  
18558332 K.Furukawa, and H.Fujihara (2008).
Microbial degradation of polychlorinated biphenyls: biochemical and molecular features.
  J Biosci Bioeng, 105, 433-449.  
18249197 T.D.Bugg, and S.Ramaswamy (2008).
Non-heme iron-dependent dioxygenases: unravelling catalytic mechanisms for complex enzymatic oxidations.
  Curr Opin Chem Biol, 12, 134-140.  
  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.  
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.