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Structure of Type IIL Restriction-Modification Enzyme MmeI in Complex with DNA Has Implications for Engineering New Specificities

The creation of restriction enzymes with programmable DNA-binding and -cleavage specificities has long been a goal of modern biology. The recently discovered Type IIL MmeI family of restriction-and-modification (RM) enzymes that possess a shared target recognition domain provides a framework for eng...

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Autores principales: Callahan, Scott J., Luyten, Yvette A., Gupta, Yogesh K., Wilson, Geoffrey G., Roberts, Richard J., Morgan, Richard D., Aggarwal, Aneel K.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4833311/
https://www.ncbi.nlm.nih.gov/pubmed/27082731
http://dx.doi.org/10.1371/journal.pbio.1002442
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author Callahan, Scott J.
Luyten, Yvette A.
Gupta, Yogesh K.
Wilson, Geoffrey G.
Roberts, Richard J.
Morgan, Richard D.
Aggarwal, Aneel K.
author_facet Callahan, Scott J.
Luyten, Yvette A.
Gupta, Yogesh K.
Wilson, Geoffrey G.
Roberts, Richard J.
Morgan, Richard D.
Aggarwal, Aneel K.
author_sort Callahan, Scott J.
collection PubMed
description The creation of restriction enzymes with programmable DNA-binding and -cleavage specificities has long been a goal of modern biology. The recently discovered Type IIL MmeI family of restriction-and-modification (RM) enzymes that possess a shared target recognition domain provides a framework for engineering such new specificities. However, a lack of structural information on Type IIL enzymes has limited the repertoire that can be rationally engineered. We report here a crystal structure of MmeI in complex with its DNA substrate and an S-adenosylmethionine analog (Sinefungin). The structure uncovers for the first time the interactions that underlie MmeI-DNA recognition and methylation (5’-TCCRAC-3’; R = purine) and provides a molecular basis for changing specificity at four of the six base pairs of the recognition sequence (5’-TCCRAC-3’). Surprisingly, the enzyme is resilient to specificity changes at the first position of the recognition sequence (5’-TCCRAC-3’). Collectively, the structure provides a basis for engineering further derivatives of MmeI and delineates which base pairs of the recognition sequence are more amenable to alterations than others.
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spelling pubmed-48333112016-04-22 Structure of Type IIL Restriction-Modification Enzyme MmeI in Complex with DNA Has Implications for Engineering New Specificities Callahan, Scott J. Luyten, Yvette A. Gupta, Yogesh K. Wilson, Geoffrey G. Roberts, Richard J. Morgan, Richard D. Aggarwal, Aneel K. PLoS Biol Research Article The creation of restriction enzymes with programmable DNA-binding and -cleavage specificities has long been a goal of modern biology. The recently discovered Type IIL MmeI family of restriction-and-modification (RM) enzymes that possess a shared target recognition domain provides a framework for engineering such new specificities. However, a lack of structural information on Type IIL enzymes has limited the repertoire that can be rationally engineered. We report here a crystal structure of MmeI in complex with its DNA substrate and an S-adenosylmethionine analog (Sinefungin). The structure uncovers for the first time the interactions that underlie MmeI-DNA recognition and methylation (5’-TCCRAC-3’; R = purine) and provides a molecular basis for changing specificity at four of the six base pairs of the recognition sequence (5’-TCCRAC-3’). Surprisingly, the enzyme is resilient to specificity changes at the first position of the recognition sequence (5’-TCCRAC-3’). Collectively, the structure provides a basis for engineering further derivatives of MmeI and delineates which base pairs of the recognition sequence are more amenable to alterations than others. Public Library of Science 2016-04-15 /pmc/articles/PMC4833311/ /pubmed/27082731 http://dx.doi.org/10.1371/journal.pbio.1002442 Text en © 2016 Callahan et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Callahan, Scott J.
Luyten, Yvette A.
Gupta, Yogesh K.
Wilson, Geoffrey G.
Roberts, Richard J.
Morgan, Richard D.
Aggarwal, Aneel K.
Structure of Type IIL Restriction-Modification Enzyme MmeI in Complex with DNA Has Implications for Engineering New Specificities
title Structure of Type IIL Restriction-Modification Enzyme MmeI in Complex with DNA Has Implications for Engineering New Specificities
title_full Structure of Type IIL Restriction-Modification Enzyme MmeI in Complex with DNA Has Implications for Engineering New Specificities
title_fullStr Structure of Type IIL Restriction-Modification Enzyme MmeI in Complex with DNA Has Implications for Engineering New Specificities
title_full_unstemmed Structure of Type IIL Restriction-Modification Enzyme MmeI in Complex with DNA Has Implications for Engineering New Specificities
title_short Structure of Type IIL Restriction-Modification Enzyme MmeI in Complex with DNA Has Implications for Engineering New Specificities
title_sort structure of type iil restriction-modification enzyme mmei in complex with dna has implications for engineering new specificities
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4833311/
https://www.ncbi.nlm.nih.gov/pubmed/27082731
http://dx.doi.org/10.1371/journal.pbio.1002442
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