9QDI | pdb_00009qdi

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

PDB DOI: https://doi.org/10.2210/pdb9QDI/pdb

Classification: HYDROLASE
Organism(s): Bacteroides fragilis NCTC 9343, synthetic construct
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-03-06 Released: 2025-07-16
Deposition Author(s): Martinez Gascuena, A., Marquez-Monino, M.A., Manzanares-Gomez, A., Aguillo-Urarte, M., Trastoy, B.
Funding Organization(s): Spanish Ministry of Science, Innovation, and Universities

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
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 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 44: 4867-4898

PubMed: 40745064 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s44318-025-00518-w
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 373.7 kDa
Atom Count: 27,337
Modeled Residue Count: 3,234
Deposited Residue Count: 3,288
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipoprotein	A, B, C, D, E A, B, C, D, E, F, G, H	409	Bacteroides fragilis NCTC 9343	Mutation(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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5L9L3
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Synthetic peptide SER-THR-PRO-PRO	I, J, K, L	4	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEZ Query on HEZ Download:Ideal Coordinates CCD File SDF format, chain WA [auth G] MOL2 format, chain WA [auth G] mmCIF format, chain WA [auth G]	WA [auth G]	HEXANE-1,6-DIOL C₆ H₁₄ O₂ XXMIOPMDWAUFGU-UHFFFAOYSA-N		Interactions Focus chain WA [auth G] Interactions & Density Focus chain WA [auth G]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain IA [auth D] MOL2 format, chain IA [auth D] mmCIF format, chain IA [auth D]	IA [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain IA [auth D] Interactions & Density Focus chain IA [auth D]
BU1 Query on BU1 Download:Ideal Coordinates CCD File SDF format, chain PA [auth E] MOL2 format, chain PA [auth E] mmCIF format, chain PA [auth E]	PA [auth E]	1,4-BUTANEDIOL C₄ H₁₀ O₂ WERYXYBDKMZEQL-UHFFFAOYSA-N		Interactions Focus chain PA [auth E] Interactions & Density Focus chain PA [auth E]
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain ZA [auth G] SDF format, chain YA [auth G] SDF format, chain Y [auth C] SDF format, chain X [auth C] SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain SA [auth F] SDF format, chain RA [auth F] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain LA [auth E] SDF format, chain KA [auth E] SDF format, chain FB [auth H] SDF format, chain EB [auth H] SDF format, chain EA [auth D] SDF format, chain DA [auth D] MOL2 format, chain ZA [auth G] MOL2 format, chain YA [auth G] MOL2 format, chain Y [auth C] MOL2 format, chain X [auth C] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain SA [auth F] MOL2 format, chain RA [auth F] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain LA [auth E] MOL2 format, chain KA [auth E] MOL2 format, chain FB [auth H] MOL2 format, chain EB [auth H] MOL2 format, chain EA [auth D] MOL2 format, chain DA [auth D] mmCIF format, chain ZA [auth G] mmCIF format, chain YA [auth G] mmCIF format, chain Y [auth C] mmCIF format, chain X [auth C] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain SA [auth F] mmCIF format, chain RA [auth F] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain LA [auth E] mmCIF format, chain KA [auth E] mmCIF format, chain FB [auth H] mmCIF format, chain EB [auth H] mmCIF format, chain EA [auth D] mmCIF format, chain DA [auth D]	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		Interactions Focus chain DA [auth D] Focus chain EA [auth D] Focus chain EB [auth H] Focus chain FB [auth H] Focus chain KA [auth E] Focus chain LA [auth E] Focus chain N [auth A] Focus chain O [auth A] Focus chain RA [auth F] Focus chain SA [auth F] Focus chain T [auth B] Focus chain U [auth B] Focus chain X [auth C] Focus chain Y [auth C] Focus chain YA [auth G] Focus chain ZA [auth G] Interactions & Density Focus chain DA [auth D] Focus chain EA [auth D] Focus chain EB [auth H] Focus chain FB [auth H] Focus chain KA [auth E] Focus chain LA [auth E] Focus chain N [auth A] Focus chain O [auth A] Focus chain RA [auth F] Focus chain SA [auth F] Focus chain T [auth B] Focus chain U [auth B] Focus chain X [auth C] Focus chain Y [auth C] Focus chain YA [auth G] Focus chain ZA [auth G]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain Z [auth C] SDF format, chain VA [auth F] SDF format, chain V [auth B] SDF format, chain TA [auth F] SDF format, chain R [auth A] SDF format, chain P [auth A] SDF format, chain NA [auth E] SDF format, chain MA [auth E] SDF format, chain HA [auth D] SDF format, chain GB [auth H] SDF format, chain GA [auth D] SDF format, chain FA [auth D] SDF format, chain BB [auth G] SDF format, chain AB [auth G] SDF format, chain AA [auth C] MOL2 format, chain Z [auth C] MOL2 format, chain VA [auth F] MOL2 format, chain V [auth B] MOL2 format, chain TA [auth F] MOL2 format, chain R [auth A] MOL2 format, chain P [auth A] MOL2 format, chain NA [auth E] MOL2 format, chain MA [auth E] MOL2 format, chain HA [auth D] MOL2 format, chain GB [auth H] MOL2 format, chain GA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain BB [auth G] MOL2 format, chain AB [auth G] MOL2 format, chain AA [auth C] mmCIF format, chain Z [auth C] mmCIF format, chain VA [auth F] mmCIF format, chain V [auth B] mmCIF format, chain TA [auth F] mmCIF format, chain R [auth A] mmCIF format, chain P [auth A] mmCIF format, chain NA [auth E] mmCIF format, chain MA [auth E] mmCIF format, chain HA [auth D] mmCIF format, chain GB [auth H] mmCIF format, chain GA [auth D] mmCIF format, chain FA [auth D] mmCIF format, chain BB [auth G] mmCIF format, chain AB [auth G] mmCIF format, chain AA [auth C]	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		Interactions Focus chain AA [auth C] Focus chain AB [auth G] Focus chain BB [auth G] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain GB [auth H] Focus chain HA [auth D] Focus chain MA [auth E] Focus chain NA [auth E] Focus chain P [auth A] Focus chain R [auth A] Focus chain TA [auth F] Focus chain V [auth B] Focus chain VA [auth F] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain AB [auth G] Focus chain BB [auth G] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain GB [auth H] Focus chain HA [auth D] Focus chain MA [auth E] Focus chain NA [auth E] Focus chain P [auth A] Focus chain R [auth A] Focus chain TA [auth F] Focus chain V [auth B] Focus chain VA [auth F] Focus chain Z [auth C]
POL Query on POL Download:Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain OA [auth E] SDF format, chain Q [auth A] SDF format, chain UA [auth F] SDF format, chain CB [auth G] MOL2 format, chain BA [auth C] MOL2 format, chain OA [auth E] MOL2 format, chain Q [auth A] MOL2 format, chain UA [auth F] MOL2 format, chain CB [auth G] mmCIF format, chain BA [auth C] mmCIF format, chain OA [auth E] mmCIF format, chain Q [auth A] mmCIF format, chain UA [auth F] mmCIF format, chain CB [auth G]	BA [auth C], CB [auth G], OA [auth E], Q [auth A], UA [auth F]	N-PROPANOL C₃ H₈ O BDERNNFJNOPAEC-UHFFFAOYSA-N		Interactions Focus chain BA [auth C] Focus chain CB [auth G] Focus chain OA [auth E] Focus chain Q [auth A] Focus chain UA [auth F] Interactions & Density Focus chain BA [auth C] Focus chain CB [auth G] Focus chain OA [auth E] Focus chain Q [auth A] Focus chain UA [auth F]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain XA [auth G] SDF format, chain W [auth C] SDF format, chain S [auth B] SDF format, chain QA [auth F] SDF format, chain M [auth A] SDF format, chain JA [auth E] SDF format, chain DB [auth H] SDF format, chain CA [auth D] MOL2 format, chain XA [auth G] MOL2 format, chain W [auth C] MOL2 format, chain S [auth B] MOL2 format, chain QA [auth F] MOL2 format, chain M [auth A] MOL2 format, chain JA [auth E] MOL2 format, chain DB [auth H] MOL2 format, chain CA [auth D] mmCIF format, chain XA [auth G] mmCIF format, chain W [auth C] mmCIF format, chain S [auth B] mmCIF format, chain QA [auth F] mmCIF format, chain M [auth A] mmCIF format, chain JA [auth E] mmCIF format, chain DB [auth H] mmCIF format, chain CA [auth D]	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		Interactions Focus chain CA [auth D] Focus chain DB [auth H] Focus chain JA [auth E] Focus chain M [auth A] Focus chain QA [auth F] Focus chain S [auth B] Focus chain W [auth C] Focus chain XA [auth G] Interactions & Density Focus chain CA [auth D] Focus chain DB [auth H] Focus chain JA [auth E] Focus chain M [auth A] Focus chain QA [auth F] Focus chain S [auth B] Focus chain W [auth C] Focus chain XA [auth G]