PDBsum entry 2vpy

Oxidoreductase

PDB id: 2vpy

Contents

Protein chains

735 a.a. *

194 a.a. *

251 a.a. *

Ligands

SF4 ×10

MGD ×4

PCI ×2

Metals

_MO ×2

Waters ×1285

* Residue conservation analysis

PDB id:

2vpy

Name:

Oxidoreductase

Title:

Polysulfide reductase with bound quinone inhibitor, pentachlorophenol (pcp)

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:

2.50Å R-factor: 0.283 R-free: 0.289

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 Biol, 15, 730-737. PubMed id: 18536726 DOI: 10.1038/nsmb.1434

Date:

09-Mar-08 Release date: 10-Jun-08

Protein chains

Q72LA4  (Q72LA4_THET2) -  Thiosulfate reductase from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)

Seq: 765 a.a.

Struc: 735 a.a.

Protein chains

Q72LA5  (Q72LA5_THET2) -  NrfC protein from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)

Seq: 195 a.a.

Struc: 194 a.a.

Protein chains

Q72LA6  (Q72LA6_THET2) -  Hypothetical membrane spanning protein from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)

Seq: 253 a.a.

Struc: 251 a.a.

Enzyme reactions

• Enzyme class 2: Chains A, E: E.C.1.-.-.-
• Enzyme class 3: Chains B, C, F, G: E.C.?

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

DOI no: 10.1038/nsmb.1434

Nat Struct 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 Biol (2008, 15, 730-737) copyright 2008.

Figures were selected by an automated process.