8ES6

Crystal structure of an unusual amidase ClbL from colibactin gene cluster

Summary for 8ES6

• Entry DOI: 10.2210/pdb8es6/pdb
• Descriptor: Colibactin biosynthesis amidase ClbL (2 entities in total)
• Functional Keywords: amidase, colibactin, cancer, biosynthetic protein
• Biological source: Escherichia coli
• Total number of polymer chains: 2
• Total formula weight: 107569.41

Authors

Tripathi, P.,Bruner, S.D. (deposition date: 2022-10-13, release date: 2023-09-20)

Primary citation

Tripathi, P.,Mousa, J.J.,Guntaka, N.S.,Bruner, S.D.
Structural basis of the amidase ClbL central to the biosynthesis of the genotoxin colibactin.
Acta Crystallogr D Struct Biol, 79:830-836, 2023

PubMed Abstract: Colibactin is a genotoxic natural product produced by select commensal bacteria in the human gut microbiota. The compound is a bis-electrophile that is predicted to form interstrand DNA cross-links in target cells, leading to double-strand DNA breaks. The biosynthesis of colibactin is carried out by a mixed NRPS-PKS assembly line with several noncanonical features. An amidase, ClbL, plays a key role in the pathway, catalyzing the final step in the formation of the pseudodimeric scaffold. ClbL couples α-aminoketone and β-ketothioester intermediates attached to separate carrier domains on the NRPS-PKS assembly. Here, the 1.9 Å resolution structure of ClbL is reported, providing a structural basis for this key step in the colibactin biosynthetic pathway. The structure reveals an open hydrophobic active site surrounded by flexible loops, and comparison with homologous amidases supports its unusual function and predicts macromolecular interactions with pathway carrier-protein substrates. Modeling protein-protein interactions supports a predicted molecular basis for enzyme-carrier domain interactions. Overall, the work provides structural insight into this unique enzyme that is central to the biosynthesis of colibactin.

PubMed: 37561403
DOI: 10.1107/S2059798323005703

Experimental method

X-RAY DIFFRACTION (1.9 Å)