Structure and mechanism of the tRNA-dependent lantibiotic dehydratase NisB.

Publisher: Nature Publishing Group Country of Publication: England NLM ID: 0410462 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1476-4687 (Electronic) Linking ISSN: 00280836 NLM ISO Abbreviation: Nature Subsets: MEDLINE

Publication: Basingstoke : Nature Publishing Group
Original Publication: London, Macmillan Journals ltd.

Bacterial Proteins/*chemistry ; Bacterial Proteins/*metabolism ; Bacteriocins/*metabolism ; Hydro-Lyases/*chemistry ; Hydro-Lyases/*metabolism ; Lactococcus lactis/*enzymology ; Membrane Proteins/*chemistry ; Membrane Proteins/*metabolism ; RNA, Transfer, Glu/*metabolism; Bacterial Proteins/classification ; Bacteriocins/biosynthesis ; Crystallography, X-Ray ; Escherichia coli/genetics ; Glutamic Acid/metabolism ; Hydro-Lyases/classification ; Lactococcus lactis/genetics ; Membrane Proteins/classification ; Models, Molecular ; Nisin/biosynthesis ; Nisin/metabolism ; Phylogeny ; Protein Structure, Tertiary ; RNA, Transfer, Glu/genetics ; Serine/metabolism ; Threonine/metabolism

Lantibiotics are a class of peptide antibiotics that contain one or more thioether bonds. The lantibiotic nisin is an antimicrobial peptide that is widely used as a food preservative to combat food-borne pathogens. Nisin contains dehydroalanine and dehydrobutyrine residues that are formed by the dehydration of Ser/Thr by the lantibiotic dehydratase NisB (ref. 2). Recent biochemical studies revealed that NisB glutamylates Ser/Thr side chains as part of the dehydration process. However, the molecular mechanism by which NisB uses glutamate to catalyse dehydration remains unresolved. Here we show that this process involves glutamyl-tRNA(Glu) to activate Ser/Thr residues. In addition, the 2.9-Å crystal structure of NisB in complex with its substrate peptide NisA reveals the presence of two separate domains that catalyse the Ser/Thr glutamylation and glutamate elimination steps. The co-crystal structure also provides insights into substrate recognition by lantibiotic dehydratases. Our findings demonstrate an unexpected role for aminoacyl-tRNA in the formation of dehydroamino acids in lantibiotics, and serve as a basis for the functional characterization of the many lantibiotic-like dehydratases involved in the biosynthesis of other classes of natural products.

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S10 RR027109 United States RR NCRR NIH HHS; R01 GM 058822 United States GM NIGMS NIH HHS; S10 RR027109 A United States RR NCRR NIH HHS; 5T32-GM070421 United States GM NIGMS NIH HHS; R01 GM058822 United States GM NIGMS NIH HHS; R01 GM079038 United States GM NIGMS NIH HHS; F32 GM112284 United States GM NIGMS NIH HHS; T32 GM070421 United States GM NIGMS NIH HHS

0 (Bacterial Proteins)
0 (Bacteriocins)
0 (Membrane Proteins)
0 (NisB protein, Lactococcus lactis)
0 (RNA, Transfer, Glu)
1414-45-5 (Nisin)
2ZD004190S (Threonine)
3KX376GY7L (Glutamic Acid)
452VLY9402 (Serine)
EC 4.2.1.- (Hydro-Lyases)

Date Created: 20141104 Date Completed: 20150212 Latest Revision: 20211021

20240104

PMC4430201

10.1038/nature13888

25363770