8GR6 | pdb_00008gr6

Crystal Structure of pilus-specific Sortase C from Streptococcus sanguinis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free: 
    0.199 (Depositor), 0.209 (DCC) 
  • R-Value Work: 
    0.178 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 
    0.179 (Depositor) 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history

Literature

Crystal structure of the pilus-specific sortase from early colonizing oral Streptococcus sanguinis captures an active open-lid conformation.

Yadav, S.Parijat, P.Krishnan, V.

(2023) Int J Biol Macromol 243: 125183-125183

  • DOI: https://doi.org/10.1016/j.ijbiomac.2023.125183
  • Primary Citation Related Structures: 
    8GR6, 8GUU

  • PubMed Abstract: 

    Dental plaque is a complex microbial biofilm community of many species and a major cause of oral infections and infectious endocarditis. Plaque development begins when primary colonizers attach to oral tissues and undergo coaggregation. Primary colonizers facilitate cellular attachment and inter-bacterial interactions through sortase-dependent pili (or fimbriae) extending out from their cell surface. Consequently, the sortase enzyme is viewed as a potential drug target for controlling biofilm formation and avoiding infection. Streptococcus sanguinis is a primary colonizing bacterium whose pili consist of three different pilin subunits that are assembled together by the pilus-specific (C-type) SsaSrtC sortase. Here, we report on the crystal structure determination of the recombinant wild-type and active-site mutant forms of SsaSrtC. Interestingly, the SsaSrtC structure exhibits an open-lid conformation, although a conserved DPX motif is lacking in the lid. Based on molecular docking and structural analysis, we identified the substrate-binding residues essential for pilin recognition and pilus assembly. We also demonstrated that while recombinant SsaSrtC is enzymatically active toward the five-residue LPNTG sorting motif peptide of the pilins, this activity is significantly reduced by the presence of zinc. We further showed that rutin and α-crocin are potential candidate inhibitors of the SsaSrtC sortase via structure-based virtual screening and inhibition assays. The structural knowledge gained from our study will provide the means to develop new approaches that target pilus-mediated attachment, thereby preventing oral biofilm growth and infection.


  • Organizational Affiliation
    • Laboratory of Structural Biology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad 121001, India.

Macromolecule Content 

  • Total Structure Weight: 24.18 kDa 
  • Atom Count: 1,665 
  • Modeled Residue Count: 198 
  • Deposited Residue Count: 218 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Sortase-like protein, putative218Streptococcus sanguinis SK36Mutation(s): 0 
Gene Names: srtCSSA_1631
UniProt
Find proteins for A3CPB4 (Streptococcus sanguinis (strain SK36))
Explore A3CPB4 
Go to UniProtKB:  A3CPB4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA3CPB4
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free:  0.199 (Depositor), 0.209 (DCC) 
  • R-Value Work:  0.178 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 0.179 (Depositor) 
Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 140.019α = 90
b = 140.019β = 90
c = 103.625γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Science and Engineering Research Board (SERB)IndiaCRG/2019/000432

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-21
    Type: Initial release
  • Version 1.1: 2023-06-28
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description