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

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...

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Autores principales:	Stefan Ilic, Sabine R. Akabayov, Roy Froimovici, Ron Meiry, Dan Vilenchik, Alfredo Hernandez, Haribabu Arthanari, Barak Akabayov
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/ddb5b468f6e24d28a55bdb8dbaddae94
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spelling	oai:doaj.org-article:ddb5b468f6e24d28a55bdb8dbaddae942021-12-02T11:52:42ZModulation of RNA primer formation by Mn(II)-substituted T7 DNA primase10.1038/s41598-017-05534-32045-2322https://doaj.org/article/ddb5b468f6e24d28a55bdb8dbaddae942017-07-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-05534-3https://doaj.org/toc/2045-2322Abstract 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.Stefan IlicSabine R. AkabayovRoy FroimoviciRon MeiryDan VilenchikAlfredo HernandezHaribabu ArthanariBarak AkabayovNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-11 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Stefan Ilic Sabine R. Akabayov Roy Froimovici Ron Meiry Dan Vilenchik Alfredo Hernandez Haribabu Arthanari Barak Akabayov Modulation of RNA primer formation by Mn(II)-substituted T7 DNA primase
description	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.
format	article
author	Stefan Ilic Sabine R. Akabayov Roy Froimovici Ron Meiry Dan Vilenchik Alfredo Hernandez Haribabu Arthanari Barak Akabayov
author_facet	Stefan Ilic Sabine R. Akabayov Roy Froimovici Ron Meiry Dan Vilenchik Alfredo Hernandez Haribabu Arthanari Barak Akabayov
author_sort	Stefan Ilic
title	Modulation of RNA primer formation by Mn(II)-substituted T7 DNA primase
title_short	Modulation of RNA primer formation by Mn(II)-substituted T7 DNA primase
title_full	Modulation of RNA primer formation by Mn(II)-substituted T7 DNA primase
title_fullStr	Modulation of RNA primer formation by Mn(II)-substituted T7 DNA primase
title_full_unstemmed	Modulation of RNA primer formation by Mn(II)-substituted T7 DNA primase
title_sort	modulation of rna primer formation by mn(ii)-substituted t7 dna primase
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/ddb5b468f6e24d28a55bdb8dbaddae94
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Modulation of RNA primer formation by Mn(II)-substituted T7 DNA primase

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