7T8N | pdb_00007t8n

Crystal structure of the PNAG binding module PgaA-TPR 220-359


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 
    0.264 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.235 (Depositor), 0.230 (DCC) 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The TPR domain of PgaA is a multifunctional scaffold that binds PNAG and modulates PgaB-dependent polymer processing.

Pfoh, R.Subramanian, A.S.Huang, J.Little, D.J.Forman, A.DiFrancesco, B.R.Balouchestani-Asli, N.Kitova, E.N.Klassen, J.S.Pomes, R.Nitz, M.Howell, P.L.

(2022) PLoS Pathog 18: e1010750-e1010750

  • DOI: https://doi.org/10.1371/journal.ppat.1010750
  • Primary Citation of Related Structures:  
    7T8N

  • PubMed Abstract: 

    The synthesis of exopolysaccharides as biofilm matrix components by pathogens is a crucial factor for chronic infections and antibiotic resistance. Many periplasmic proteins involved in polymer processing and secretion in Gram-negative synthase dependent exopolysaccharide biosynthetic systems have been individually characterized. The operons responsible for the production of PNAG, alginate, cellulose and the Pel polysaccharide each contain a gene that encodes an outer membrane associated tetratricopeptide repeat (TPR) domain containing protein. While the TPR domain has been shown to bind other periplasmic proteins, the functional consequences of these interactions for the polymer remain poorly understood. Herein, we show that the C-terminal TPR region of PgaA interacts with the de-N-acetylase domain of PgaB, and increases its deacetylase activity. Additionally, we found that when the two proteins form a complex, the glycoside hydrolase activity of PgaB is also increased. To better understand structure-function relationships we determined the crystal structure of a stable TPR module, which has a conserved groove formed by three repeat motifs. Tryptophan quenching, mass spectrometry analysis and molecular dynamics simulation studies suggest that the crystallized TPR module can bind PNAG/dPNAG via its electronegative groove on the concave surface, and potentially guide the polymer through the periplasm towards the porin for export. Our results suggest a scaffolding role for the TPR domain that combines PNAG/dPNAG translocation with the modulation of its chemical structure by PgaB.


  • Organizational Affiliation

    Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Poly-beta-1,6-N-acetyl-D-glucosamine export proteinA [auth AAA],
B [auth BBB]
148Escherichia coli K-12Mutation(s): 0 
Gene Names: pgaAycdSb1024JW1010
UniProt
Find proteins for P69434 (Escherichia coli (strain K12))
Explore P69434 
Go to UniProtKB:  P69434
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP69434
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free:  0.264 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.235 (Depositor), 0.230 (DCC) 
Space Group: P 62
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.67α = 90
b = 60.67β = 90
c = 185.52γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
SHELXDEphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)Canada--

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-03
    Type: Initial release
  • Version 1.1: 2022-08-17
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Refinement description