5HR4

Structure of Type IIL restriction-modification enzyme MmeI in complex with DNA has implications for engineering of new specificities

Summary for 5HR4

• Entry DOI: 10.2210/pdb5hr4/pdb
• Descriptor: MmeI, DNA (5'-D(P*TP*AP*TP*CP*CP*GP*AP*CP*AP*TP*AP*AP*C)-3'), DNA (5'-D(P*GP*TP*TP*AP*TP*GP*TP*CP*GP*GP*AP*TP*A)-3'), ... (6 entities in total)
• Functional Keywords: dna-protein complex, restriction-modification enzyme, hydrolase-dna complex, hydrolase/dna
• Biological source: Methylophilus methylotrophus; More
• Total number of polymer chains: 6
• Total formula weight: 227254.67

Authors

Callahan, S.J.,Luyten, Y.A.,Gupta, Y.K.,Wilson, G.G.,Roberts, R.J.,Morgan, R.D.,Aggarwal, A.K. (deposition date: 2016-01-22, release date: 2016-04-27, Last modification date: 2024-03-06)

Primary citation

Callahan, S.J.,Luyten, Y.A.,Gupta, Y.K.,Wilson, G.G.,Roberts, R.J.,Morgan, R.D.,Aggarwal, A.K.
Structure of Type IIL Restriction-Modification Enzyme MmeI in Complex with DNA Has Implications for Engineering New Specificities.
Plos Biol., 14:e1002442-e1002442, 2016

PubMed Abstract: 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.

PubMed: 27082731
DOI: 10.1371/journal.pbio.1002442

Experimental method

X-RAY DIFFRACTION (2.5964 Å)