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
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
THIOSULFATE REDUCTASEA, E765Thermus 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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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
NRFC PROTEINB, F195Thermus thermophilus HB27Mutation(s): 0 
Gene Names: nrfC, TT_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
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
HYPOTHETICAL MEMBRANE SPANNING PROTEINC, G253Thermus 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

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View more in-depth experimental data

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