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PDBsum entry 2bgj

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protein ligands Protein-protein interface(s) links
Oxidoreductase PDB id
2bgj
Jmol
Contents
Protein chains
260 a.a. *
Ligands
FAD ×4
Waters ×351
* Residue conservation analysis
PDB id:
2bgj
Name: Oxidoreductase
Title: X-ray structure of the ferredoxin-NADP(h) reductase from rhodobacter capsulatus at 2.1 angstroms
Structure: Ferredoxin-NADP(h) reductase. Chain: a, b, c, d. Engineered: yes. Mutation: yes
Source: Rhodobacter capsulatus. Organism_taxid: 1061. Strain: 37b4. Variant: dsm938. Expressed in: escherichia coli. Expression_system_taxid: 511693.
Resolution:
2.1Å     R-factor:   0.215     R-free:   0.243
Authors: J.I.Perez-Dorado,J.A.Hermoso,I.Nogues,S.Frago,C.Bittel, S.G.Mayhew,C.Gomez-Moreno,M.Medina,N.Cortez,N.Carrillo
Key ref:
I.Nogués et al. (2005). The ferredoxin-NADP(H) reductase from Rhodobacter capsulatus: molecular structure and catalytic mechanism. Biochemistry, 44, 11730-11740. PubMed id: 16128574 DOI: 10.1021/bi0508183
Date:
23-Dec-04     Release date:   07-Sep-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q9L6V3  (Q9L6V3_RHOCA) -  NADPH:ferredoxin reductase (Fragment)
Seq:
Struc:
272 a.a.
260 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     oxidation-reduction process   1 term 
  Biochemical function     nucleotide binding     2 terms  

 

 
DOI no: 10.1021/bi0508183 Biochemistry 44:11730-11740 (2005)
PubMed id: 16128574  
 
 
The ferredoxin-NADP(H) reductase from Rhodobacter capsulatus: molecular structure and catalytic mechanism.
I.Nogués, I.Pérez-Dorado, S.Frago, C.Bittel, S.G.Mayhew, C.Gómez-Moreno, J.A.Hermoso, M.Medina, N.Cortez, N.Carrillo.
 
  ABSTRACT  
 
The photosynthetic bacterium Rhodobacter capsulatus contains a ferredoxin (flavodoxin)-NADP(H) oxidoreductase (FPR) that catalyzes electron transfer between NADP(H) and ferredoxin or flavodoxin. The structure of the enzyme, determined by X-ray crystallography, contains two domains harboring the FAD and NADP(H) binding sites, as is typical of the FPR structural family. The FAD molecule is in a hairpin conformation in which stacking interactions can be established between the dimethylisoalloxazine and adenine moieties. The midpoint redox potentials of the various transitions undergone by R. capsulatus FPR were similar to those reported for their counterparts involved in oxygenic photosynthesis, but its catalytic activity is orders of magnitude lower (1-2 s(-)(1) versus 200-500 s(-)(1)) as is true for most of its prokaryotic homologues. To identify the mechanistic basis for the slow turnover in the bacterial enzymes, we dissected the R. capsulatus FPR reaction into hydride transfer and electron transfer steps, and determined their rates using stopped-flow methods. Hydride exchange between the enzyme and NADP(H) occurred at 30-150 s(-)(1), indicating that this half-reaction does not limit FPR activity. In contrast, electron transfer to flavodoxin proceeds at 2.7 s(-)(1), in the range of steady-state catalysis. Flavodoxin semiquinone was a better electron acceptor for FPR than oxidized flavodoxin under both single turnover and steady-state conditions. The results indicate that one-electron reduction of oxidized flavodoxin limits the enzyme activity in vitro, and support the notion that flavodoxin oscillates between the semiquinone and fully reduced states when FPR operates in vivo.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
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
19626353 M.S.Till, and G.M.Ullmann (2010).
McVol - a program for calculating protein volumes and identifying cavities by a Monte Carlo algorithm.
  J Mol Model, 16, 419-429.  
19583765 M.Medina (2009).
Structural and mechanistic aspects of flavoproteins: photosynthetic electron transfer from photosystem I to NADP+.
  FEBS J, 276, 3942-3958.  
18605699 A.Wang, J.C.Rodríguez, H.Han, E.Schönbrunn, and M.Rivera (2008).
X-ray crystallographic and solution state nuclear magnetic resonance spectroscopic investigations of NADP+ binding to ferredoxin NADP reductase from Pseudomonas aeruginosa.
  Biochemistry, 47, 8080-8093.
PDB code: 3crz
  18453705 I.Pérez-Dorado, A.Bortolotti, N.Cortez, and J.A.Hermoso (2008).
Crystallization of a flavodoxin involved in nitrogen fixation in Rhodobacter capsulatus.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 375-377.  
18279389 M.A.Musumeci, A.K.Arakaki, D.V.Rial, D.L.Catalano-Dupuy, and E.A.Ceccarelli (2008).
Modulation of the enzymatic efficiency of ferredoxin-NADP(H) reductase by the amino acid volume around the catalytic site.
  FEBS J, 275, 1350-1366.  
17958910 A.S.Nascimento, D.L.Catalano-Dupuy, A.Bernardes, M.d.e. .O.Neto, M.A.Santos, E.A.Ceccarelli, and I.Polikarpov (2007).
Crystal structures of Leptospira interrogans FAD-containing ferredoxin-NADP+ reductase and its complex with NADP+.
  BMC Struct Biol, 7, 69.
PDB codes: 2rc5 2rc6
  16820688 A.S.Nascimento, T.Ferrarezi, D.L.Catalano-Dupuy, E.A.Ceccarelli, and I.Polikarpov (2006).
Crystallization and preliminary X-ray diffraction studies of ferredoxin reductase from Leptospira interrogans.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 662-664.  
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.