2VPW | pdb_00002vpw

Polysulfide reductase with bound menaquinone

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 
    0.275 (Depositor) 
  • R-Value Work: 
    0.271 (Depositor), 0.260 (DCC) 
  • R-Value Observed: 
    0.271 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 1.5 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: https://doi.org/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 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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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
THIOSULFATE REDUCTASEA,
D [auth E]		765Thermus thermophilus HB27Mutation(s): 0 
EC: 1
UniProt
Find proteins for Q72LA4 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27))
Explore Q72LA4 
Go to UniProtKB:  Q72LA4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ72LA4
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NRFC PROTEINB,
E [auth F]		195Thermus thermophilus HB27Mutation(s): 0 
UniProt
Find proteins for Q72LA5 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27))
Explore Q72LA5 
Go to UniProtKB:  Q72LA5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ72LA5
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
HYPOTHETICAL MEMBRANE SPANNING PROTEINC,
F [auth G]		253Thermus thermophilus HB27Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q72LA6 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27))
Explore Q72LA6 
Go to UniProtKB:  Q72LA6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ72LA6
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MGD
Query on MGD
Download Ideal Coordinates CCD File 
H [auth A],
I [auth A],
Q [auth E],
R [auth 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
MQ7
Query on MQ7
Download Ideal Coordinates CCD File 
O [auth C],
X [auth G]		MENAQUINONE-7
C46 H64 O2
RAKQPZMEYJZGPI-LJWNYQGCSA-N
SF4
Query on SF4
Download Ideal Coordinates CCD File 
G [auth A]
K [auth B]
L [auth B]
M [auth B]
N [auth B]
G [auth A],
K [auth B],
L [auth B],
M [auth B],
N [auth B],
P [auth E],
T [auth F],
U [auth F],
V [auth F],
W [auth F]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
MO
Query on MO
Download Ideal Coordinates CCD File 
J [auth A],
S [auth E]		MOLYBDENUM ATOM
Mo
ZOKXTWBITQBERF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free:  0.275 (Depositor) 
  • R-Value Work:  0.271 (Depositor), 0.260 (DCC) 
  • R-Value Observed: 0.271 (Depositor) 
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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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.5: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Other