8A56

Coenzyme A-persulfide reductase (CoAPR) from Enterococcus faecalis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.189 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Metabolic and Structural Insights into Hydrogen Sulfide Mis-Regulation in Enterococcus faecalis.

Walsh, B.J.C.Costa, S.S.Edmonds, K.A.Trinidad, J.C.Issoglio, F.M.Brito, J.A.Giedroc, D.P.

(2022) Antioxidants (Basel) 11

  • DOI: https://doi.org/10.3390/antiox11081607
  • Primary Citation of Related Structures:  
    8A56

  • PubMed Abstract: 

    Hydrogen sulfide (H 2 S) is implicated as a cytoprotective agent that bacteria employ in response to host-induced stressors, such as oxidative stress and antibiotics. The physiological benefits often attributed to H 2 S, however, are likely a result of downstream, more oxidized forms of sulfur, collectively termed reactive sulfur species (RSS) and including the organic persulfide (RSSH). Here, we investigated the metabolic response of the commensal gut microorganism Enterococcus faecalis to exogenous Na 2 S as a proxy for H 2 S/RSS toxicity. We found that exogenous sulfide increases protein abundance for enzymes responsible for the biosynthesis of coenzyme A (CoA). Proteome S -sulfuration (persulfidation), a posttranslational modification implicated in H 2 S signal transduction, is also widespread in this organism and is significantly elevated by exogenous sulfide in CstR, the RSS sensor, coenzyme A persulfide (CoASSH) reductase (CoAPR) and enzymes associated with de novo fatty acid biosynthesis and acetyl-CoA synthesis. Exogenous sulfide significantly impacts the speciation of fatty acids as well as cellular concentrations of acetyl-CoA, suggesting that protein persulfidation may impact flux through these pathways. Indeed, CoASSH is an inhibitor of E. faecalis phosphotransacetylase (Pta), suggesting that an important metabolic consequence of increased levels of H 2 S/RSS may be over-persulfidation of this key metabolite, which, in turn, inhibits CoA and acyl-CoA-utilizing enzymes. Our 2.05 Å crystallographic structure of CoA-bound CoAPR provides new structural insights into CoASSH clearance in E. faecalis .


  • Organizational Affiliation

    Department of Chemistry, Indiana University, Bloomington, IN 47405-7102, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Coenzyme A-persulfide reductase
A, B
571Enterococcus faecalisMutation(s): 0 
UniProt
Find proteins for Q82ZQ9 (Enterococcus faecalis (strain ATCC 700802 / V583))
Explore Q82ZQ9 
Go to UniProtKB:  Q82ZQ9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ82ZQ9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD (Subject of Investigation/LOI)
Query on FAD

Download Ideal Coordinates CCD File 
C [auth A],
K [auth B]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
PAP (Subject of Investigation/LOI)
Query on PAP

Download Ideal Coordinates CCD File 
I [auth A],
J [auth B]
3'-PHOSPHATE-ADENOSINE-5'-DIPHOSPHATE
C10 H16 N5 O13 P3
GBBWIZKLHXYJOA-KQYNXXCUSA-N
IOD
Query on IOD

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
H [auth A]
M [auth B]
N [auth B]
E [auth A],
F [auth A],
H [auth A],
M [auth B],
N [auth B],
P [auth B]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A],
L [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
G [auth A],
O [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.189 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 139.797α = 90
b = 194.809β = 90
c = 91.46γ = 90
Software Package:
Software NamePurpose
autoPROCdata processing
XDSdata reduction
Aimlessdata scaling
STARANISOdata scaling
PHASERphasing
RESOLVEmodel building
PHENIXrefinement
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Fundacao para a Ciencia e a TecnologiaPortugalUIDB/04612/2020
Fundacao para a Ciencia e a TecnologiaPortugalUIDP/04612/2020
Fundacao para a Ciencia e a TecnologiaPortugalLA/P/0087/2020
Fundacao para a Ciencia e a TecnologiaPortugalArticle 23 of Decree-Law No. 57/2017 of August 29
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesGM097225
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesGM118157

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-14
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description