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DNA Binding Specificity of MunI Restriction Endonuclease Is Controlled by pH and Calcium Ions:  Involvement of Active Site Carboxylate Residues

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    DNA Binding Specificity of MunI Restriction Endonuclease Is Controlled by pH and Calcium Ions:  Involvement of Active Site Carboxylate Residues†
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    Institute of Biotechnology, Graiciuno 8, Vilnius 2028, Lithuania
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    Biochemistry

    Cite this: Biochemistry 1997, 36, 37, 11093–11099
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    https://doi.org/10.1021/bi963126a
    Published September 16, 1997
    Copyright © 1997 American Chemical Society
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    Abstract

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    Gel shift analysis reveals [Lagunavicius, A., & Siksnys, V. (1997) Biochemistry 36 (preceding paper in this issue)] that at pH 8.3 in the absence of Mg2+, MunI restriction endonuclease exhibits little DNA binding specificity, as compared with the D83A and E98A mutants of MunI. This suggests that charged carboxylate residue(s) influence the DNA binding specificity of MunI. In our efforts to establish the determinants of MunI binding specificity, we investigated the possible role of the ionic milieu, and we found that lowering pH or elevating Ca2+ levels per se induces specific DNA recognition by WT MunI. In contrast to the binding experiments at pH 8.3, gel shift analysis at pH 6.5 indicated tight sequence-specific binding of WT MunI in the absence of Mg2+, suggesting that protonation of active site carboxylate residue(s) which manifest anomalously high pKa value(s) control binding specificity. Interestingly, Ca2+ ion concentrations, which did not support DNA cleavage by MunI also induced DNA binding specificity in WT MunI at pH 8.3. To explore possible structural changes upon DNA binding, we then used a limited proteolysis technique. Trypsin cleavage of MunI−DNA complexes indicated that in the presence of cognate DNA the MunI restriction endonuclease became resistant to proteolytic cleavage, suggesting that binding of specific DNA induced a structural change. CD measurements confirmed this observation, suggesting minor secondary structural differences between complexes of MunI with cognate and noncognate DNA. These results therefore suggest that binding of MunI to its recognition sequence triggers a conformational transition that correctly juxtaposes active site carboxylate residues, which then chelate Mg2+ ions. In the absence of Mg2+ ions, at pH 8.3, conditions in which carboxylate groups would be expected to be completely ionized, electrostatic repulsion between charged carboxylates and phosphate oxygens is enhanced such as to interfere with specific DNA binding. Elimination of such repulsive constraints by replacement of carboxylate residues, by lowering pH, or by metal ion binding, then promotes MunI binding specificity.

    Copyright © 1997 American Chemical Society

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    †

     This work has been supported in part by Grant Nos. LAL000 and LHK100 from International Science Foundation and Volkswagen Stiftung.

    ‡

     Present address:  MPI of Biochemistry, Am Klopferspitz 18a, Martinsried-Plannegg, D-82152, Germany.

    *

     To whom all correspondence should be addressed. FAX:  +370-2-642624. Tel.:  +370-2-642490.

    ✗

     Abstract published in Advance ACS Abstracts, August 1, 1997.

    Cited By

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    This article is cited by 37 publications.

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    37. . Short Communication. bchm 1998, 535-630. https://doi.org/10.1515/bchm.1998.379.4-5.535
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    Biochemistry

    Cite this: Biochemistry 1997, 36, 37, 11093–11099
    Click to copy citationCitation copied!
    https://doi.org/10.1021/bi963126a
    Published September 16, 1997
    Copyright © 1997 American Chemical Society
    Request reuse permissions

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