9QDI | pdb_00009qdi

Crystal structure of BF3526 peptidase from Bacteroides fragilis in complex with a peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 
    0.213 (Depositor), 0.212 (DCC) 
  • R-Value Work: 
    0.171 (Depositor), 0.171 (DCC) 
  • R-Value Observed: 
    0.173 (Depositor) 

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

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
Lipoprotein
A, B, C, D, E
A, B, C, D, E, F, G, H
409Bacteroides fragilis NCTC 9343Mutation(s): 0 
Gene Names: BF9343_3433
UniProt
Find proteins for Q5L9L3 (Bacteroides fragilis (strain ATCC 25285 / DSM 2151 / CCUG 4856 / JCM 11019 / LMG 10263 / NCTC 9343 / Onslow / VPI 2553 / EN-2))
Explore Q5L9L3 
Go to UniProtKB:  Q5L9L3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5L9L3
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Synthetic peptide SER-THR-PRO-PRO
I, J, K, L
4synthetic constructMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEZ
Query on HEZ

Download Ideal Coordinates CCD File 
WA [auth G]HEXANE-1,6-DIOL
C6 H14 O2
XXMIOPMDWAUFGU-UHFFFAOYSA-N
PEG
Query on PEG

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IA [auth D]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
BU1
Query on BU1

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PA [auth E]1,4-BUTANEDIOL
C4 H10 O2
WERYXYBDKMZEQL-UHFFFAOYSA-N
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
DA [auth D]
EA [auth D]
EB [auth H]
FB [auth H]
KA [auth E]
DA [auth D],
EA [auth D],
EB [auth H],
FB [auth H],
KA [auth E],
LA [auth E],
N [auth A],
O [auth A],
RA [auth F],
SA [auth F],
T [auth B],
U [auth B],
X [auth C],
Y [auth C],
YA [auth G],
ZA [auth G]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO
Query on EDO

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AA [auth C]
AB [auth G]
BB [auth G]
FA [auth D]
GA [auth D]
AA [auth C],
AB [auth G],
BB [auth G],
FA [auth D],
GA [auth D],
GB [auth H],
HA [auth D],
MA [auth E],
NA [auth E],
P [auth A],
R [auth A],
TA [auth F],
V [auth B],
VA [auth F],
Z [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
POL
Query on POL

Download Ideal Coordinates CCD File 
BA [auth C],
CB [auth G],
OA [auth E],
Q [auth A],
UA [auth F]
N-PROPANOL
C3 H8 O
BDERNNFJNOPAEC-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
CA [auth D]
DB [auth H]
JA [auth E]
M [auth A]
QA [auth F]
CA [auth D],
DB [auth H],
JA [auth E],
M [auth A],
QA [auth F],
S [auth B],
W [auth C],
XA [auth G]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free:  0.213 (Depositor), 0.212 (DCC) 
  • R-Value Work:  0.171 (Depositor), 0.171 (DCC) 
  • R-Value Observed: 0.173 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.294α = 74.16
b = 99.435β = 88.13
c = 103.386γ = 82.44
Software Package:
Software NamePurpose
PHENIXrefinement
FAST_DPdata reduction
Aimlessdata 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