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Sci Rep. 2017 Jul 19;7(1):5797. doi: 10.1038/s41598-017-05534-3.

Modulation of RNA primer formation by Mn(II)-substituted T7 DNA primase.

Author information

1
Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, 8410501, Israel.
2
Department of Communication Systems Engineering, Ben-Gurion University of the Negev, Beer-Sheva, 8410501, Israel.
3
Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Ave., Boston, Massachusetts, 02115, USA.
4
Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, 8410501, Israel. akabayov@bgu.ac.il.

Abstract

Lagging strand DNA synthesis by DNA polymerase requires RNA primers produced by DNA primase. The N-terminal primase domain of the gene 4 protein of phage T7 comprises a zinc-binding domain that recognizes a specific DNA sequence and an RNA polymerase domain that catalyzes RNA polymerization. Based on its crystal structure, the RNA polymerase domain contains two Mg(II) ions. Mn(II) substitution leads to elevated RNA primer synthesis by T7 DNA primase. NMR analysis revealed that upon binding Mn(II), T7 DNA primase undergoes conformational changes near the metal cofactor binding site that are not observed when the enzyme binds Mg(II). A machine-learning algorithm called linear discriminant analysis (LDA) was trained by using the large collection of Mn(II) and Mg(II) binding sites available in the protein data bank (PDB). Application of the model to DNA primase revealed a preference in the enzyme's second metal binding site for Mn(II) over Mg(II), suggesting that T7 DNA primase activity modulation when bound to Mn(II) is based on structural changes in the enzyme.

PMID:
28724886
PMCID:
PMC5517523
DOI:
10.1038/s41598-017-05534-3
[Indexed for MEDLINE]
Free PMC Article

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