9BLO | pdb_00009blo

T450C mutant of repeat domain 2 from Clostridium perfringens adhesin CPE0147 without intramolecular ester bond


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 
    0.229 (Depositor), 0.232 (DCC) 
  • R-Value Work: 
    0.193 (Depositor), 0.200 (DCC) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Protease mimicry: Dissecting the ester bond crosslinking mechanics in bacterial adhesin proteins.

Yosaatmadja, Y.Ung, V.Liu, X.Zhao, Y.Wardega, J.K.Shetty, A.Schoensee, S.Leung, I.K.H.Keown, J.R.Goldstone, D.C.Baker, E.N.Young, P.G.Mercadante, D.Squire, C.J.

(2025) Protein Sci 34: e70238-e70238

  • DOI: https://doi.org/10.1002/pro.70238
  • Primary Citation of Related Structures:  
    9BLO, 9BLP

  • PubMed Abstract: 

    The ester bond crosslink discovered within bacterial adhesin proteins offers a captivating insight into the convergent evolution of enzyme-like machinery. Crystal structures reveal a putative catalytic triad comprising an acid-base-nucleophile combination and an oxyanion-like site that suggests a serine protease-like mechanism drives the crosslinking process. We now provide confirmation of the mechanism, revealing functional catalytic dyads or triads, and the recapitulation of protease machinery from a Pseudomonas bacterium and a human cytomegalovirus related only by convergent evolution. Molecular dynamics simulations suggest how a conservative threonine-to-serine mutation of the nucleophile induces hydrolysis and eliminates the ester bond crosslink. Collectively, our structural, functional, and computational efforts detail the molecular intricacies of intramolecular ester bond formation and underscore the convergent evolutionary adaptations of bacteria in exploiting enzyme-like machinery to protect essential adhesin proteins from the mechanical, biological, and chemical hostilities of their replicative niche.


  • Organizational Affiliation
    • School of Biological Sciences, The University of Auckland, Auckland, New Zealand.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Surface anchored protein
A, B
156Clostridium perfringens B str. ATCC 3626Mutation(s): 1 
Gene Names: AC1_0147
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free:  0.229 (Depositor), 0.232 (DCC) 
  • R-Value Work:  0.193 (Depositor), 0.200 (DCC) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.983α = 95.135
b = 44.405β = 109.36
c = 50.102γ = 110.122
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Marsden FundNew Zealand--

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-07
    Type: Initial release
  • Version 1.1: 2025-11-19
    Changes: Database references