9QDH | pdb_00009qdh

Crystal structure of IgA protease (323-878) from Thomasclavelia ramosa


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.245 (Depositor), 0.244 (DCC) 
  • R-Value Work: 
    0.194 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 
    0.197 (Depositor) 

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


This is version 1.1 of the entry. See complete history


Literature

Molecular basis of Fab-dependent IgA antibody recognition by gut-bacterial metallopeptidases.

Marquez-Monino, M.A.Martinez Gascuena, A.Azzam, T.Persson, A.Manzanares-Gomez, A.Aguillo-Urarte, M.Brown, T.T.Montero-Sagarminaga, A.Lood, R.Naegeli, A.Connell, S.R.Sastre, D.E.Sundberg, E.J.Trastoy, B.

(2025) EMBO J 

  • DOI: https://doi.org/10.1038/s44318-025-00518-w
  • Primary Citation of Related Structures:  
    9QDH, 9QDI

  • PubMed Abstract: 

    Immunoglobulin A (IgA) is essential for mucosal immunity and has been implicated in autoimmune diseases, such as IgA nephropathy. Certain pathogenic and commensal bacteria produce IgA proteases that selectively cleave IgA, potentially aiding bacterial colonization as well as suggesting therapeutic avenues for IgA nephropathy. Here, we investigate the substrate specificities of two enzymes of the M64 metallopeptidase family, the IgA protease ThomasA from Thomasclavelia ramosa and BF3526 from Bacteroides fragilis. Our structural, biochemical, and mutagenesis analyses demonstrate that ThomasA cleaves IgA through exclusive recognition of the Fab region. This mechanism is distinct from that of other antibody-specific peptidases, which typically require engagement of the Fc region. In contrast, X-ray crystal structures of BF3526 in complex with substrate and product peptides, combined with enzymology assays, show that this enzyme targets the N-terminus of pre-digested proteins, but does not act on intact IgA. These findings reveal divergent substrate recognition strategies between M64 family members, while providing new structural insights into their conserved catalytic mechanism.


  • Organizational Affiliation
    • Structural Glycoimmunology Laboratory, Biobizkaia Health Research Institute, Barakaldo, Spain.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
IgA protease560Thomasclavelia 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: 2.00 Å
  • R-Value Free:  0.245 (Depositor), 0.244 (DCC) 
  • R-Value Work:  0.194 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 0.197 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.739α = 90
b = 85.198β = 90
c = 90.666γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
xia2data scaling
PHASERphasing
Cootmodel building
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Spanish Ministry of Science, Innovation, and UniversitiesSpainMICINN grant (PID2021-122177NA-I00)

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-16
    Type: Initial release
  • Version 1.1: 2025-08-13
    Changes: Database references