5X5M

Crystal structure of a hydrolase encoded by lin2189 from Listeria innocua

Summary for 5X5M

• Entry DOI: 10.2210/pdb5x5m/pdb
• Related: 5X5R
• Descriptor: Lin2189 protein, DIMETHYL SULFOXIDE, (+)-Yatakemycin, ... (4 entities in total)
• Functional Keywords: hydrolase, hydrolase-antibiotic complex, hydrolase/antibiotic
• Biological source: Listeria innocua serovar 6a (strain ATCC BAA-680 / CLIP 11262)
• Total number of polymer chains: 2
• Total formula weight: 52241.94

Authors

Zhang, J. (deposition date: 2017-02-16, release date: 2017-12-06, Last modification date: 2023-11-22)

Primary citation

Yuan, H.,Zhang, J.,Cai, Y.,Wu, S.,Yang, K.,Chan, H.C.S.,Huang, W.,Jin, W.B.,Li, Y.,Yin, Y.,Igarashi, Y.,Yuan, S.,Zhou, J.,Tang, G.L.
GyrI-like proteins catalyze cyclopropanoid hydrolysis to confer cellular protection
Nat Commun, 8:1485-1485, 2017

PubMed Abstract: GyrI-like proteins are widely distributed in prokaryotes and eukaryotes, and recognized as small-molecule binding proteins. Here, we identify a subfamily of these proteins as cyclopropanoid cyclopropyl hydrolases (CCHs) that can catalyze the hydrolysis of the potent DNA-alkylating agents yatakemycin (YTM) and CC-1065. Co-crystallography and molecular dynamics simulation analyses reveal that these CCHs share a conserved aromatic cage for the hydrolytic activity. Subsequent cytotoxic assays confirm that CCHs are able to protect cells against YTM. Therefore, our findings suggest that the evolutionarily conserved GyrI-like proteins confer cellular protection against diverse xenobiotics via not only binding, but also catalysis.

PubMed: 29133784
DOI: 10.1038/s41467-017-01508-1

Experimental method

X-RAY DIFFRACTION (1.211 Å)