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PDBsum entry 2vpx

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protein ligands metals Protein-protein interface(s) links
Oxidoreductase PDB id
2vpx
Jmol
Contents
Protein chains
735 a.a. *
194 a.a. *
251 a.a. *
Ligands
SF4 ×10
MGD ×4
UQ1 ×2
Metals
_MO ×2
Waters ×1285
* Residue conservation analysis
PDB id:
2vpx
Name: Oxidoreductase
Title: Polysulfide reductase with bound quinone (uq1)
Structure: Thiosulfate reductase. Chain: a, e. Synonym: polysulfide reductase. Nrfc protein. Chain: b, f. Hypothetical membrane spanning protein. Chain: c, g
Source: Thermus thermophilus. Organism_taxid: 262724. Strain: hb27. Strain: hb27
Resolution:
3.10Å     R-factor:   0.301     R-free:   0.314
Authors: M.Jormakka,K.Yokoyama,T.Yano,M.Tamakoshi,S.Akimoto, T.Shimamura,P.Curmi,S.Iwata
Key ref:
M.Jormakka et al. (2008). Molecular mechanism of energy conservation in polysulfide respiration. Nat Struct Mol Biol, 15, 730-737. PubMed id: 18536726 DOI: 10.1038/nsmb.1434
Date:
09-Mar-08     Release date:   10-Jun-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q72LA4  (Q72LA4_THET2) -  Thiosulfate reductase
Seq:
Struc:
 
Seq:
Struc:
765 a.a.
735 a.a.
Protein chains
Pfam   ArchSchema ?
Q72LA5  (Q72LA5_THET2) -  NrfC protein
Seq:
Struc:
195 a.a.
194 a.a.
Protein chains
Pfam   ArchSchema ?
Q72LA6  (Q72LA6_THET2) -  Hypothetical membrane spanning protein
Seq:
Struc:
253 a.a.
251 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     electron carrier activity     6 terms  

 

 
DOI no: 10.1038/nsmb.1434 Nat Struct Mol Biol 15:730-737 (2008)
PubMed id: 18536726  
 
 
Molecular mechanism of energy conservation in polysulfide respiration.
M.Jormakka, K.Yokoyama, T.Yano, M.Tamakoshi, S.Akimoto, T.Shimamura, P.Curmi, S.Iwata.
 
  ABSTRACT  
 
Bacterial polysulfide reductase (PsrABC) is an integral membrane protein complex responsible for quinone-coupled reduction of polysulfide, a process important in extreme environments such as deep-sea vents and hot springs. We determined the structure of polysulfide reductase from Thermus thermophilus at 2.4-A resolution, revealing how the PsrA subunit recognizes and reduces its unique polyanionic substrate. The integral membrane subunit PsrC was characterized using the natural substrate menaquinone-7 and inhibitors, providing a comprehensive representation of a quinone binding site and revealing the presence of a water-filled cavity connecting the quinone binding site on the periplasmic side to the cytoplasm. These results suggest that polysulfide reductase could be a key energy-conserving enzyme of the T. thermophilus respiratory chain, using polysulfide as the terminal electron acceptor and pumping protons across the membrane via a previously unknown mechanism.
 
  Selected figure(s)  
 
Figure 1.
Ribbon representation of the PsrABC dimer viewed parallel to the membrane, with one monomer shown in light gray for clarity. The PsrA, PsrB and PsrC subunits in the monomer to the left are green, ruby and blue, respectively. The MGD cofactors are orange with molybdenum shown as a black sphere. Five [4Fe-4S] clusters are shown in red (iron atoms) and yellow (sulfur atoms), and PCP is shown in black. All distances, including edge-to-edge distances between redox centres, are in given in angstroms. In the catalytic cycle of Psr, menaquinol is reduced on the periplasmic side of the membrane, releasing two protons and electrons (dotted line). The electrons are transported via the iron-sulfur clusters to the active-site molybdenum, where polysulfide is reduced with the evolution of hydrogen sulfide. All structural figures were made using PyMol (http://pymol.sourceforge.net/).
Figure 2.
(a) 2F[o] – F[c] electron density map (blue) is shown for ArgA332 and w201, and F[o] – F[c] map (red) is shown at the position for the oxo (=O) group (omit map for the oxo) bound to the molydenum atom. Maps are contoured at 2 and 4 , respectively. Hydrogen bonds between ArgA332 and water molecules are shown as dotted lines. (b) Stereoviews of the active site and putative proton-delivery channel in PsrA. The surface and interior of the protein are shown in light and dark gray, respectively. Crystallographic water molecules are shown as red spheres.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Mol Biol (2008, 15, 730-737) copyright 2008.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20667175 K.R.Vinothkumar, and R.Henderson (2010).
Structures of membrane proteins.
  Q Rev Biophys, 43, 65.  
20053990 R.A.Rothery, M.G.Bertero, T.Spreter, N.Bouromand, N.C.Strynadka, and J.H.Weiner (2010).
Protein crystallography reveals a role for the FS0 cluster of Escherichia coli nitrate reductase A (NarGHI) in enzyme maturation.
  J Biol Chem, 285, 8801-8807.
PDB codes: 3ir5 3ir6 3ir7
19892705 S.Grimaldi, R.Arias-Cartin, P.Lanciano, S.Lyubenova, B.Endeward, T.F.Prisner, A.Magalon, and B.Guigliarelli (2010).
Direct evidence for nitrogen ligation to the high stability semiquinone intermediate in Escherichia coli nitrate reductase A.
  J Biol Chem, 285, 179-187.  
19542325 J.L.Burns, and T.J.DiChristina (2009).
Anaerobic respiration of elemental sulfur and thiosulfate by Shewanella oneidensis MR-1 requires psrA, a homolog of the phsA gene of Salmonella enterica serovar typhimurium LT2.
  Appl Environ Microbiol, 75, 5209-5217.  
19710024 J.Ruprecht, V.Yankovskaya, E.Maklashina, S.Iwata, and G.Cecchini (2009).
Structure of Escherichia coli succinate:quinone oxidoreductase with an occupied and empty quinone-binding site.
  J Biol Chem, 284, 29836-29846.
PDB codes: 2wdq 2wdr 2wdv
19420717 T.Hiratsuka, N.Itoh, H.Seto, and T.Dairi (2009).
Enzymatic properties of futalosine hydrolase, an enzyme essential to a newly identified menaquinone biosynthetic pathway.
  Biosci Biotechnol Biochem, 73, 1137-1141.  
19233927 X.Li, Q.Luo, N.Q.Wofford, K.L.Keller, M.J.McInerney, J.D.Wall, and L.R.Krumholz (2009).
A molybdopterin oxidoreductase is involved in H2 oxidation in Desulfovibrio desulfuricans G20.
  J Bacteriol, 191, 2675-2682.  
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.