7W6B

Crystal Structure of PitA from pilus islet-2 of Streptococcus oralis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.98 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.253 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

New structural insights into the PI-2 pilus from Streptococcus oralis, an early dental plaque colonizer.

Yadav, R.K.Krishnan, V.

(2022) FEBS J 289: 6342-6366

  • DOI: 10.1111/febs.16527
  • Primary Citation of Related Structures:  
    7F7Y, 7VCN, 7VCR, 7W6B, 7W7I

  • PubMed Abstract: 
  • Streptococcus oralis is a member of the mitis group of oral streptococci and an early colonizer in dental plaque biofilm, a major cause of periodontal disease, dental caries, and other oral infections. S. oralis promotes biofilm growth by coaggregating in a mutualistic partnership with other early colonizers such as Actinomyces oris ...

    Streptococcus oralis is a member of the mitis group of oral streptococci and an early colonizer in dental plaque biofilm, a major cause of periodontal disease, dental caries, and other oral infections. S. oralis promotes biofilm growth by coaggregating in a mutualistic partnership with other early colonizers such as Actinomyces oris. For this cell-to-cell interaction, A. oris is known to use its sortase-dependent pilus (type 2), but whether S. oralis uses its PI-2 (pilus islet 2) pilus is still to be determined. The PI-2 pilus is predicted to have a heterodimeric structure consisting of two different protein subunits with their own location and function: the tip PitA pilin for adhesion and the backbone PitB pilin for length. Thus far, structural information remains incomplete about the role of PI-2 pili in the mutualistic mechanism between S. oralis and A. oris. We now report on the crystal structure analysis of PitA and PitB using X-ray crystallography, small-angle X-ray scattering, and molecular docking studies. Accordingly, we propose a structural model for the PI-2 pilus, wherein repeating PitB subunits are arranged head-to-tail to form the long backbone structure with PitA on the outer tip. By performing both in vitro and in vivo experiments, we examined the role played by PitA in mediating the mutualistic interaction between S. oralis and A. oris, which appears to involve the coaggregation factor CafA. We also reveal that the galactose monosaccharide is a conceivable ligand for PitA and thereby might be used to inhibit coaggregation and control oral biofilm development. DATABASE: Structural coordinates for the PitA fragment, PitA fragment TbXO4 derivative, full-length PitA, and PitB from S. oralis have been deposited at the Protein Data Bank as 7VCR, 7W7I, 7VCN, 7W6B, and 7W7I, respectively. Streptococcus pneumoniae PitB coordinates have been deposited as 7F7Y.


    Organizational Affiliation

    Laboratory of Structural Microbiology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, India.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
von Willebrand factor type A domain proteinA793Streptococcus oralis ATCC 35037Mutation(s): 0 
Gene Names: HMPREF8579_1184
UniProt
Find proteins for D4FSQ3 (Streptococcus oralis ATCC 35037)
Explore D4FSQ3 
Go to UniProtKB:  D4FSQ3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD4FSQ3
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IOD
Query on IOD

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
R [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
B [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.98 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.253 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.271α = 90
b = 422.928β = 90
c = 48.391γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



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: 2022-06-01
    Type: Initial release
  • Version 1.1: 2022-10-26
    Changes: Database references, Derived calculations