6OWN

Crystal structure of Msm DnaB1 intein splicing domain bound with zinc

Summary for 6OWN

• Entry DOI: 10.2210/pdb6own/pdb
• Descriptor: Replicative DNA helicase, ZINC ION (3 entities in total)
• Functional Keywords: splicing intein, hydrolase
• Biological source: Mycobacterium smegmatis
• Total number of polymer chains: 3
• Total formula weight: 43975.38

Authors

Bacot-Davis, V.R.,Belfort, M.,Lennon, C. (deposition date: 2019-05-10, release date: 2020-05-13, Last modification date: 2023-10-11)

Primary citation

Woods, D.,Vangaveti, S.,Egbanum, I.,Sweeney, A.M.,Li, Z.,Bacot-Davis, V.,LeSassier, D.S.,Stanger, M.,Hardison, G.E.,Li, H.,Belfort, M.,Lennon, C.W.
Conditional DnaB Protein Splicing Is Reversibly Inhibited by Zinc in Mycobacteria.
Mbio, 11:-, 2020

PubMed Abstract: Inteins, as posttranslational regulatory elements, can tune protein function to environmental changes by conditional protein splicing (CPS). Translated as subdomains interrupting host proteins, inteins splice to scarlessly join flanking sequences (exteins). We used DnaB-intein1 (DnaBi1) from a replicative helicase of to build a anamycin ntein plicing eporter (KISR) that links splicing of DnaBi1 to kanamycin resistance. Using expression in heterologous , we observed phenotypic classes of various levels of splicing-dependent resistance (SDR) and related these to the insertion position of DnaBi1 within the kanamycin resistance protein (KanR). The KanR-DnaBi1 construct demonstrating the most stringent SDR was used to probe for CPS of DnaB in the native host environment, We show here that zinc, important during mycobacterial pathogenesis, inhibits DnaB splicing in Using an reporter system, we demonstrated that zinc potently and reversibly inhibited DnaBi1 splicing, as well as splicing of a comparable intein from Finally, in a 1.95 Å crystal structure, we show that zinc inhibits splicing through binding to the very cysteine that initiates the splicing reaction. Together, our results provide compelling support for a model whereby mycobacterial DnaB protein splicing, and thus DNA replication, is responsive to environmental zinc. Inteins are present in a large fraction of prokaryotes and localize within conserved proteins, including the mycobacterial replicative helicase DnaB. In addition to their extensive protein engineering applications, inteins have emerged as environmentally responsive posttranslational regulators of the genes that encode them. While several studies have shown compelling evidence of conditional protein splicing (CPS), examination of splicing in the native host of the intein has proven to be challenging. Here, we demonstrated through a number of measures, including the use of a splicing-dependent sensor capable of monitoring intein activity in the native host, that zinc is a potent and reversible inhibitor of mycobacterial DnaB splicing. This work also expands our knowledge of site selection for intein insertion within nonnative proteins, demonstrating that splicing-dependent host protein activation correlates with proximity to the active site. Additionally, we surmise that splicing regulation by zinc has mycobacteriocidal and CPS application potential.

PubMed: 32665276
DOI: 10.1128/mBio.01403-20

Experimental method

X-RAY DIFFRACTION (1.95 Å)