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Oxidoreductase PDB id
1d7y
Jmol
Contents
Protein chain
401 a.a. *
Ligands
FAD
Waters ×120
* Residue conservation analysis
PDB id:
1d7y
Name: Oxidoreductase
Title: Crystal structure of nadh-dependent ferredoxin reductase, bp
Structure: Ferredoxin reductase. Chain: a. Engineered: yes
Source: Pseudomonas sp.. Organism_taxid: 307. Strain: kks102. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
2.10Å     R-factor:   0.183     R-free:   0.228
Authors: T.Senda,T.Yamada,N.Sakurai,M.Kubota,T.Nishizaki,E.Masai,M.Fu Y.Mitsui
Key ref:
T.Senda et al. (2000). Crystal structure of NADH-dependent ferredoxin reductase component in biphenyl dioxygenase. J Mol Biol, 304, 397-410. PubMed id: 11090282 DOI: 10.1006/jmbi.2000.4200
Date:
21-Oct-99     Release date:   20-Dec-00    
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!
  Cellular component     cytoplasm   1 term 
  Biological process     oxidation-reduction process   2 terms 
  Biochemical function     nucleotide binding     3 terms  

 

 
DOI no: 10.1006/jmbi.2000.4200 J Mol Biol 304:397-410 (2000)
PubMed id: 11090282  
 
 
Crystal structure of NADH-dependent ferredoxin reductase component in biphenyl dioxygenase.
T.Senda, T.Yamada, N.Sakurai, M.Kubota, T.Nishizaki, E.Masai, M.Fukuda, Y.Mitsuidagger.
 
  ABSTRACT  
 
Oxidative biodegradation of aromatic compounds by bacteria usually begins with hydroxylation of the aromatic ring by multi-component dioxygenases like benzene dioxygenase, biphenyl dioxygenase, and others. These enzymes are composed of ferredoxin reductase, ferredoxin, and terminal oxygenase. Reducing equivalents that originate from NADH are transferred from ferredoxin reductase to ferredoxin and, in turn, to the terminal oxygenase, thus resulting in the activation of a dioxygen. BphA4 is the ferredoxin reductase component of biphenyl dioxygenase from Pseudomonas sp. strain KKS102. The amino acid sequence of BphA4 exhibits significant homology with the putidaredoxin reductase of the cytochrome P450cam system in Pseudomonas putida, as well as with various other oxygenase-coupled NADH-dependent ferredoxin reductases (ONFRs) of bacteria. To date, no structural information has been provided for the ferredoxin reductase component of the dioxygenase systems. In order to provide a structural basis for discussing the mechanism of electron transport between ferredoxin reductase and ferredoxin, crystal structures of BphA4 and its NADH complex were solved. The three-dimensional structure of BphA4 is different from those of ferredoxin reductases whose structures have already been determined, but adopts essentially the same fold as the enzymes of the glutathione reductase (GR) family. Also the three-dimensional structure of the first two domains of BphA4 adopts a fold similar to that of adrenodoxin reductase (AdR) in the mitochondrial cytochrome P450 system. Comparing the amino acid sequence with what is known of the three-dimensional structure of BphA4 strongly suggests that the other ONFRs have secondary structural features that are similar to that of BphA4. This analysis of the crystal structures of BphA4 suggests that Lys53 and Glu159 seem to be involved in the hydride transfer from NADH to FAD. Since the amino acid residues around the active site, some of which seem to be important to electron transport, are highly conserved among ONFRs, it is likely that the mechanism of electron transport of BphA4 is quite applicable to other ONFRs.
 
  Selected figure(s)  
 
Figure 6.
Figure 6. Conformational change upon binding NADH around the active site (stereo view). The structure of the NADH free form (colored red) is superimposed with that of NADH complex form (colored blue). Val155 and Ile156 are shown in bold lines. This Figure was prepared by the program MOLSCRIPT [Kraulis 1991]. 		Figure 7.
Figure 7. Structural comparison of FAD and NADH in BphA4 and GR. Lys53 and Glu159 of BphA4 as well as Lys50 and Glu181 of GR (1get) are also shown (stereo view). The atoms of BphA4 and GR are superimposed using the equivalent atoms of the isoalloxazine and the nicotinamide rings. The BphA4 and GR are colored red and blue, respectively. This Figure was prepared by the program MOLSCRIPT [Kraulis 1991].
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2000, 304, 397-410) copyright 2000.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20857287 Y.Qu, H.Zhou, A.Li, F.Ma, and J.Zhou (2011).
Nitroreductase activity of ferredoxin reductase BphA4 from Dyella ginsengisoli LA-4 by catalytic and structural properties analysis.
  Appl Microbiol Biotechnol, 89, 655-663.  
20878669 H.Komori, D.Seo, T.Sakurai, and Y.Higuchi (2010).
Crystal structure analysis of Bacillus subtilis ferredoxin-NADP(+) oxidoreductase and the structural basis for its substrate selectivity.
  Protein Sci, 19, 2279-2290.
PDB codes: 3lzw 3lzx
20017214 K.Nishikawa, Y.Shomura, S.Kawasaki, Y.Niimura, and Y.Higuchi (2010).
Crystal structure of NADH:rubredoxin oxidoreductase from Clostridium acetobutylicum: a key component of the dioxygen scavenging system in obligatory anaerobes.
  Proteins, 78, 1066-1070.
PDB code: 3klj
19626710 F.Xu, S.G.Bell, Y.Peng, E.O.Johnson, M.Bartlam, Z.Rao, and L.L.Wong (2009).
Crystal structure of a ferredoxin reductase for the CYP199A2 system from Rhodopseudomonas palustris.
  Proteins, 77, 867-880.
PDB code: 3fg2
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.  
18167347 I.Y.Churbanova, and I.F.Sevrioukova (2008).
Redox-dependent changes in molecular properties of mitochondrial apoptosis-inducing factor.
  J Biol Chem, 283, 5622-5631.  
18558332 K.Furukawa, and H.Fujihara (2008).
Microbial degradation of polychlorinated biphenyls: biochemical and molecular features.
  J Biosci Bioeng, 105, 433-449.  
17636129 G.Hagelueken, L.Wiehlmann, T.M.Adams, H.Kolmar, D.W.Heinz, B.Tümmler, and W.D.Schubert (2007).
Crystal structure of the electron transfer complex rubredoxin rubredoxin reductase of Pseudomonas aeruginosa.
  Proc Natl Acad Sci U S A, 104, 12276-12281.
PDB codes: 2v3a 2v3b
  17401203 M.Senda, S.Kishigami, S.Kimura, and T.Senda (2007).
Crystallization and preliminary X-ray analysis of the reduced Rieske-type [2Fe-2S] ferredoxin derived from Pseudomonas sp. strain KKS102.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 311-314.  
  17554177 M.Senda, S.Kishigami, S.Kimura, and T.Senda (2007).
Crystallization and preliminary X-ray analysis of the electron-transfer complex of Rieske-type [2Fe-2S] ferredoxin and NADH-dependent ferredoxin reductase derived from Acidovorax sp. strain KKS102.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 520-523.  
  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.  
  17565187 Y.Peng, F.Xu, S.G.Bell, L.L.Wong, and Z.Rao (2007).
Crystallization and preliminary X-ray diffraction studies of a ferredoxin reductase from Rhodopseudomonas palustris CGA009.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 422-425.  
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.  
  16754990 M.Senda, S.Kimura, S.Kishigami, and T.Senda (2006).
Crystallization and preliminary X-ray analysis of the Rieske-type [2Fe-2S] ferredoxin component of biphenyl dioxygenase from Pseudomonas sp. strain KKS102.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 590-592.  
16278674 N.Vahsen, C.Candé, P.Dupaigne, F.Giordanetto, R.T.Kroemer, E.Herker, S.Scholz, N.Modjtahedi, F.Madeo, E.Le Cam, and G.Kroemer (2006).
Physical interaction of apoptosis-inducing factor with DNA and RNA.
  Oncogene, 25, 1763-1774.  
15849415 S.Sano, S.Tao, Y.Endo, T.Inaba, M.A.Hossain, C.Miyake, M.Matsuo, H.Aoki, K.Asada, and K.Saito (2005).
Purification and cDNA cloning of chloroplastic monodehydroascorbate reductase from spinach.
  Biosci Biotechnol Biochem, 69, 762-772.  
15716266 V.Y.Kuznetsov, E.Blair, P.J.Farmer, T.L.Poulos, A.Pifferitti, and I.F.Sevrioukova (2005).
The putidaredoxin reductase-putidaredoxin electron transfer complex: theoretical and experimental studies.
  J Biol Chem, 280, 16135-16142.  
15292119 K.Furukawa, H.Suenaga, and M.Goto (2004).
Biphenyl dioxygenases: functional versatilities and directed evolution.
  J Bacteriol, 186, 5189-5196.  
14966111 K.Panda, S.Adak, D.Konas, M.Sharma, and D.J.Stuehr (2004).
A conserved aspartate (Asp-1393) regulates NADPH reduction of neuronal nitric-oxide synthase: implications for catalysis.
  J Biol Chem, 279, 18323-18333.  
15598351 S.Cheek, Y.Qi, S.S.Krishna, L.N.Kinch, and N.V.Grishin (2004).
4SCOPmap: automated assignment of protein structures to evolutionary superfamilies.
  BMC Bioinformatics, 5, 197.  
15272189 S.Sano, Y.N.Kang, H.Shigemizu, N.Morishita, H.J.Yoon, K.Saito, K.Asada, and B.Mikami (2004).
Crystallization and preliminary crystallographic analysis of monodehydroascorbate radical reductase from cucumber.
  Acta Crystallogr D Biol Crystallogr, 60, 1498-1499.  
15340917 Y.Sargisova, F.M.Pierfederici, A.Scirè, E.Bertoli, F.Tanfani, F.Febbraio, R.Briante, Y.Karapetyan, and S.Mardanyan (2004).
Computational, spectroscopic, and resonant mirror biosensor analysis of the interaction of adrenodoxin with native and tryptophan-modified NADPH-adrenodoxin reductase.
  Proteins, 57, 302-310.  
12198487 H.Ye, C.Cande, N.C.Stephanou, S.Jiang, S.Gurbuxani, N.Larochette, E.Daugas, C.Garrido, G.Kroemer, and H.Wu (2002).
DNA binding is required for the apoptogenic action of apoptosis inducing factor.
  Nat Struct Biol, 9, 680-684.
PDB code: 1m6i
12011076 I.F.Sevrioukova, and T.L.Poulos (2002).
Putidaredoxin reductase, a new function for an old protein.
  J Biol Chem, 277, 25831-25839.  
12450807 J.W.Nam, H.Nojiri, H.Noguchi, H.Uchimura, T.Yoshida, H.Habe, H.Yamane, and T.Omori (2002).
Purification and characterization of carbazole 1,9a-dioxygenase, a three-component dioxygenase system of Pseudomonas resinovorans strain CA10.
  Appl Environ Microbiol, 68, 5882-5890.  
11967568 M.J.Maté, M.Ortiz-Lombardía, B.Boitel, A.Haouz, D.Tello, S.A.Susin, J.Penninger, G.Kroemer, and P.M.Alzari (2002).
The crystal structure of the mouse apoptosis-inducing factor AIF.
  Nat Struct Biol, 9, 442-446.
PDB code: 1gv4
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.