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PDBsum entry 2v3a

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protein ligands metals links
Oxidoreductase PDB id
2v3a
Jmol
Contents
Protein chain
381 a.a. *
Ligands
PEG ×6
FAD
Metals
_CL ×2
Waters ×231
* Residue conservation analysis
PDB id:
2v3a
Name: Oxidoreductase
Title: Crystal structure of rubredoxin reductase from pseudomonas aeruginosa.
Structure: Rubredoxin reductase. Chain: a. Engineered: yes
Source: Pseudomonas aeruginosa. Organism_taxid: 208964. Strain: pao1. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
2.40Å     R-factor:   0.168     R-free:   0.202
Authors: G.Hagelueken,L.Wiehlmann,T.M.Adams,H.Kolmar,D.W.Heinz,B.Tuem W.-D.Schubert
Key ref:
G.Hagelueken et al. (2007). Crystal structure of the electron transfer complex rubredoxin rubredoxin reductase of Pseudomonas aeruginosa. Proc Natl Acad Sci U S A, 104, 12276-12281. PubMed id: 17636129 DOI: 10.1073/pnas.0702919104
Date:
14-Jun-07     Release date:   14-Aug-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q9HTK9  (RURE_PSEAE) -  Rubredoxin-NAD(+) reductase
Seq:
Struc:
384 a.a.
381 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.1.18.1.1  - Rubredoxin--NAD(+) reductase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 2 reduced rubredoxin + NAD+ + H+ = 2 oxidized rubredoxin + NADH
2 × reduced rubredoxin
+ NAD(+)
+ H(+)
= 2 × oxidized rubredoxin
+ NADH
      Cofactor: FAD; Fe cation
FAD
Bound ligand (Het Group name = FAD) corresponds exactly
Fe cation
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     oxidation-reduction process   2 terms 
  Biochemical function     oxidoreductase activity     5 terms  

 

 
    reference    
 
 
DOI no: 10.1073/pnas.0702919104 Proc Natl Acad Sci U S A 104:12276-12281 (2007)
PubMed id: 17636129  
 
 
Crystal structure of the electron transfer complex rubredoxin rubredoxin reductase of Pseudomonas aeruginosa.
G.Hagelueken, L.Wiehlmann, T.M.Adams, H.Kolmar, D.W.Heinz, B.Tümmler, W.D.Schubert.
 
  ABSTRACT  
 
Crude oil spills represent a major ecological threat because of the chemical inertness of the constituent n-alkanes. The Gram-negative bacterium Pseudomonas aeruginosa is one of the few bacterial species able to metabolize such compounds. Three chromosomal genes, rubB, rubA1, and rubA2 coding for an NAD(P)H:rubredoxin reductase (RdxR) and two rubredoxins (Rdxs) are indispensable for this ability. They constitute an electron transport (ET) pathway that shuttles reducing equivalents from carbon metabolism to the membrane-bound alkane hydroxylases AlkB1 and AlkB2. The RdxR-Rdx system also is crucial as part of the oxidative stress response in archaea or anaerobic bacteria. The redox couple has been analyzed in detail as a model system for ET processes. We have solved the structure of RdxR of P. aeruginosa both alone and in complex with Rdx, without the need for cross-linking, and both structures were refined at 2.40- and 2.45-A resolution, respectively. RdxR consists of two cofactor-binding domains and a C-terminal domain essential for the specific recognition of Rdx. Only a small number of direct interactions govern mutual recognition of RdxR and Rdx, corroborating the transient nature of the complex. The shortest distance between the redox centers is observed to be 6.2 A.
 
  Selected figure(s)  
 
Figure 2.
Fig. 2. Structure of the Rdx–RdxR complex. (A) Cartoon representation. RdxR colors are as in Fig. 1A, and Rdx is in dark red. FAD, modeled NADH (translucent), and cysteine residues of the iron-binding site are shown in ball-and-stick mode, and Fe^3+ is shown as a green sphere. Anomalous-difference electron density (red) contoured at 6.0 documents the presence of the Fe^3+. Amino acid exchanges between RubA1 and RubA2 are indicated as spheres in Rdx (conservative, orange; nonconservative, blue). (B) Interactions surrounding the redox-active site of the complex. Interacting residues are shown as ball-and-stick models (C of RdxR, yellow, and of Rdx, red-brown). FAD is shown in ball-and-stick mode. (C) Binding curves for the interaction of RdxR to Fe^3+ (red)- and Ni^2+ (green)-substituted Rdx.
Figure 3.
Fig. 3. Phylogenetic topology of structurally characterized enzymes functionally and/or structurally related to RdxR. (A) FNR, plant-type ferredoxin reductase; AdxR, adrenodoxin reductase; AIF, apoptosis inducing factor; LpdR, lipoamide reductase; TptR, trypanothione reductase. Sequence identity to RdxR is indicated by percentage. (B) Superposition of uncomplexed (gray) and complexed RdxR (colored as in Fig. 1A). Cofactors are shown as ball-and-stick models. For clarity, the position of Rdx is indicated by a brown sphere. (C) Comparison of the Rdx (red) and Trx (black) binding sites of RdxR and TrxR. For clarity, only the molecular surface of RdxR is shown. G^0 optimized ET rates (42) between FAD and each point of the RdxR surface are indicated by a color gradient (red, high ET rate; green, medium; blue, low). (Inset) Close-up view of the cofactors involved.
 
  Figures were selected by the author.  
 
 
    Author's comment    
 
  Crude oil spills represent a major ecological threat due to the chemical inertness of the constituent n-alkanes. The Gram-negative bacterium Pseudomonas aeruginosa is one of the few bacterial species able to metabolize such compounds. Three chromosomal genes, rubB, rubA1 and rubA2 coding for an NAD(P)H:rubredoxin oxidoreductase (RdxR) and two rubredoxins (Rdxs) are indispensable for this ability. They constitute an electron transport (ET) pathway that shuttles reducing equivalents from carbon metabolism to the membrane-bound alkane hydroxylases AlkB1 and AlkB2. The RdxR/Rdx system is also crucial as part of the oxidative stress response in archaea or anaerobic bacteria. The redox couple has been analyzed in detail as a model system for ET processes. The crystal structure of RdxR, refined at 2.40 resolution, reveals two domains, a cofactor-binding domains and a C-terminal domain essential for the specific recognition of Rdx. The crystal structure of the RdxR/Rdx complex refined at 2.45Å indicates that mutual recognition is governed by a small number of direct interactions, corroborating the transient nature of the complex. The shortest distance between the redox centers is observed to be 6.2Å.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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
19662168 S.Garvis, A.Munder, G.Ball, S.de Bentzmann, L.Wiehlmann, J.J.Ewbank, B.Tümmler, and A.Filloux (2009).
Caenorhabditis elegans semi-automated liquid screen reveals a specialized role for the chemotaxis gene cheB2 in Pseudomonas aeruginosa virulence.
  PLoS Pathog, 5, e1000540.  
18713742 E.Bitto, C.A.Bingman, L.Bittova, D.A.Kondrashov, R.M.Bannen, B.G.Fox, J.L.Markley, and G.N.Phillips (2008).
Structure of human J-type co-chaperone HscB reveals a tetracysteine metal-binding domain.
  J Biol Chem, 283, 30184-30192.
PDB code: 3bvo
18716757 I.Lüke, G.Butland, K.Moore, G.Buchanan, V.Lyall, S.A.Fairhurst, J.F.Greenblatt, A.Emili, T.Palmer, and F.Sargent (2008).
Biosynthesis of the respiratory formate dehydrogenases from Escherichia coli: characterization of the FdhE protein.
  Arch Microbiol, 190, 685-696.  
18260112 M.Medina, R.Abagyan, C.Gómez-Moreno, and J.Fernandez-Recio (2008).
Docking analysis of transient complexes: interaction of ferredoxin-NADP+ reductase with ferredoxin and flavodoxin.
  Proteins, 72, 848-862.  
18786405 M.V.Petoukhov, J.B.Vicente, P.B.Crowley, M.A.Carrondo, M.Teixeira, and D.I.Svergun (2008).
Quaternary structure of flavorubredoxin as revealed by synchrotron radiation small-angle X-ray scattering.
  Structure, 16, 1428-1436.  
18389511 P.B.Crowley, P.Ganji, and H.Ibrahim (2008).
Protein surface recognition: structural characterisation of cytochrome c-porphyrin complexes.
  Chembiochem, 9, 1029-1033.  
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.