Crystal structure of the Human Pol α B subunit in complex with the C-terminal domain of the catalytic subunit

Yoshiaki Suwa, Jianyou Gu, Andrey G. Baranovskiy, Nigar D. Babayeva, Youri I Pavlov, Tahir H Tahirov

Research output: Contribution to journalArticle

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Abstract

In eukaryotic DNA replication, short RNA-DNA hybrid primers synthesized by primase-DNA polymerase α (Prim-Pol α) are needed to start DNA replication by the replicative DNA polymerases, Pol S and Pol e. The C terminus of the Pol α catalytic subunit (p180C) in complex with the B subunit (p70) regulates the RNA priming and DNA polymerizing activities of Prim-Pol α. It tethers Pol α and primase, facilitating RNA primer handover from primase to Pol α. To understand these regulatory mechanisms and to reveal the details of human Pol α organization, we determined the crystal structure of p70 in complex with p180C. The structured portion of p70 includes a phosphodiesterase (PDE) domain and an oligonucleotide/oligosaccharide binding (OB) domain. The N-terminal domain and the linker connecting it to the PDE domain are disordered in the reported crystal structure. The p180C adopts an elongated asymmetric saddle shape, with a three-helix bundle in the middle and zinc-binding modules (Zn1 and Zn2) on each side. The extensive p180C-p70 interactions involve 20 hydrogen bonds and a number of hydrophobic interactions resulting in an extended buried surface of 4080 å2. Importantly, in the structure of the p180C-p70 complex with full-length p70, the residues from the N-terminal to the OB domain contribute to interactions with p180C. The comparative structural analysis revealed both the conserved features and the differences between the human and yeast Pol α complexes.

Original languageEnglish (US)
Pages (from-to)14328-14337
Number of pages10
JournalJournal of Biological Chemistry
Volume290
Issue number23
DOIs
StatePublished - Jun 5 2015

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DNA Primase
Catalytic Domain
DNA-Directed DNA Polymerase
Crystal structure
DNA
Phosphoric Diester Hydrolases
DNA Replication
Oligosaccharides
RNA
DNA Primers
Hydrophobic and Hydrophilic Interactions
Structural analysis
Oligonucleotides
Yeast
Zinc
Hydrogen
Hydrogen bonds
Yeasts

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Cell Biology

Cite this

Crystal structure of the Human Pol α B subunit in complex with the C-terminal domain of the catalytic subunit. / Suwa, Yoshiaki; Gu, Jianyou; Baranovskiy, Andrey G.; Babayeva, Nigar D.; Pavlov, Youri I; Tahirov, Tahir H.

In: Journal of Biological Chemistry, Vol. 290, No. 23, 05.06.2015, p. 14328-14337.

Research output: Contribution to journalArticle

Suwa, Yoshiaki ; Gu, Jianyou ; Baranovskiy, Andrey G. ; Babayeva, Nigar D. ; Pavlov, Youri I ; Tahirov, Tahir H. / Crystal structure of the Human Pol α B subunit in complex with the C-terminal domain of the catalytic subunit. In: Journal of Biological Chemistry. 2015 ; Vol. 290, No. 23. pp. 14328-14337.
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abstract = "In eukaryotic DNA replication, short RNA-DNA hybrid primers synthesized by primase-DNA polymerase α (Prim-Pol α) are needed to start DNA replication by the replicative DNA polymerases, Pol S and Pol e. The C terminus of the Pol α catalytic subunit (p180C) in complex with the B subunit (p70) regulates the RNA priming and DNA polymerizing activities of Prim-Pol α. It tethers Pol α and primase, facilitating RNA primer handover from primase to Pol α. To understand these regulatory mechanisms and to reveal the details of human Pol α organization, we determined the crystal structure of p70 in complex with p180C. The structured portion of p70 includes a phosphodiesterase (PDE) domain and an oligonucleotide/oligosaccharide binding (OB) domain. The N-terminal domain and the linker connecting it to the PDE domain are disordered in the reported crystal structure. The p180C adopts an elongated asymmetric saddle shape, with a three-helix bundle in the middle and zinc-binding modules (Zn1 and Zn2) on each side. The extensive p180C-p70 interactions involve 20 hydrogen bonds and a number of hydrophobic interactions resulting in an extended buried surface of 4080 {\aa}2. Importantly, in the structure of the p180C-p70 complex with full-length p70, the residues from the N-terminal to the OB domain contribute to interactions with p180C. The comparative structural analysis revealed both the conserved features and the differences between the human and yeast Pol α complexes.",
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