2VPW

Polysulfide reductase with bound menaquinone


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.271 
  • R-Value Observed: 0.271 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Molecular Mechanism of Energy Conservation in Polysulfide Respiration.

Jormakka, M.Yokoyama, K.Yano, T.Tamakoshi, M.Akimoto, S.Shimamura, T.Curmi, P.Iwata, S.

(2008) Nat Struct Mol Biol 15: 730

  • DOI: 10.1038/nsmb.1434
  • Primary Citation of Related Structures:  
    2VPW, 2VPX, 2VPY, 2VPZ

  • PubMed 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 ...

    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.


    Organizational Affiliation

    Department of Biophysics, University of New South Wales, Barker Street, Sydney, New South Wales 2052, Australia. m.jormakka@centenary.org.au



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
THIOSULFATE REDUCTASEAE765Thermus thermophilus HB27Mutation(s): 0 
Gene Names: TT_C0155
EC: 1
Find proteins for Q72LA4 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Explore Q72LA4 
Go to UniProtKB:  Q72LA4
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
NRFC PROTEINBF195Thermus thermophilus HB27Mutation(s): 0 
Gene Names: nrfCTT_C0154
Find proteins for Q72LA5 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Explore Q72LA5 
Go to UniProtKB:  Q72LA5
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
HYPOTHETICAL MEMBRANE SPANNING PROTEINCG253Thermus thermophilus HB27Mutation(s): 0 
Gene Names: TT_C0153
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Mo/Wbis-MGD Oxidoreductases
Protein: 
Polysulfide Reductase PsrABC (native)
Find proteins for Q72LA6 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Explore Q72LA6 
Go to UniProtKB:  Q72LA6
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MGD
Query on MGD

Download CCD File 
A, E
2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE
C20 H26 N10 O13 P2 S2
VQAGYJCYOLHZDH-ILXWUORBSA-N
 Ligand Interaction
MQ7
Query on MQ7

Download CCD File 
C, G
MENAQUINONE-7
C46 H64 O2
RAKQPZMEYJZGPI-LJWNYQGCSA-N
 Ligand Interaction
SF4
Query on SF4

Download CCD File 
A, B, E, F
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
MO
Query on MO

Download CCD File 
A, E
MOLYBDENUM ATOM
Mo
ZOKXTWBITQBERF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.271 
  • R-Value Observed: 0.271 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.377α = 90
b = 163.58β = 90
c = 238.891γ = 90
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
MLPHAREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-06-10
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-01-30
    Changes: Data collection, Experimental preparation, Other
  • Version 1.4: 2019-02-06
    Changes: Data collection, Experimental preparation