9EKM | pdb_00009ekm

Thomasclavelia ramosa Immunoglobulin A Protease Middle (Protease) Domain with C-terminal Domain #1 (Metal Chelated)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 
    0.181 (Depositor), 0.181 (DCC) 
  • R-Value Work: 
    0.139 (Depositor), 0.139 (DCC) 
  • R-Value Observed: 
    0.141 (Depositor) 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history

Literature

Structure of the Thomasclavelia ramosa immunoglobulin A protease reveals a modular and minimizable architecture distinct from other immunoglobulin A proteases.

Tran, N.Frenette, A.Holyoak, T.

(2025) Proc Natl Acad Sci U S A 122: e2503549122-e2503549122

  • DOI: https://doi.org/10.1073/pnas.2503549122
  • Primary Citation Related Structures: 
    9EKK, 9EKM, 9EKN

  • PubMed Abstract: 

    Immunoglobulin A proteases (IgAPs) are a diverse group of enzymes secreted from bacteria that inhabit human mucosal tissues. These enzymes have convergently evolved to cleave human immunoglobulin A as a means of modulating and evading host immunity. Only two of three known IgAP families have been biochemically characterized beyond their initial discovery. Here, we show using solution-scattering, steady-state kinetic, and crystallographic approaches that the protease from Thomasclavelia ramosa , representing the uncharacterized third family, has a truly modular and minimizable protein architecture. This analysis also revealed a unique metal-associated domain that likely functions as a molecular spacer and generated a working hypothesis detailing the structural mechanism behind the enzyme's high substrate specificity. Our work provides an in-depth biochemical account of this IgAP family, paving the way for advancing clinically relevant IgAP-related research and our understanding of IgAPs as a whole.


  • Organizational Affiliation
    • Department of Biology, Faculty of Science, University of Waterloo, Waterloo, ON N2L 3G1, Canada.

Macromolecule Content 

  • Total Structure Weight: 125.61 kDa 
  • Atom Count: 10,467 
  • Modeled Residue Count: 1,094 
  • Deposited Residue Count: 1,096 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
IgA protease
A, B
548Thomasclavelia ramosaMutation(s): 0 
Gene Names: iga
UniProt
Find proteins for Q9AES2 (Thomasclavelia ramosa)
Explore Q9AES2 
Go to UniProtKB:  Q9AES2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9AES2
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free:  0.181 (Depositor), 0.181 (DCC) 
  • R-Value Work:  0.139 (Depositor), 0.139 (DCC) 
  • R-Value Observed: 0.141 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.74α = 90
b = 91.551β = 90.96
c = 86.848γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other private--

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-03
    Type: Initial release
  • Version 1.1: 2025-09-10
    Changes: Database references