Crystal structure of the human Polε B-subunit in complex with the C-terminal domain of the catalytic subunit

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

Research output: Contribution to journalArticle

6 Citations (Scopus)

Abstract

The eukaryotic B-family DNA polymerases include four members: Polα, Polδ, Polε, and Polζ, which share common architectural features, such as the exonuclease/polymerase and C-terminal domains (CTDs) of catalytic subunits bound to indispensable B-subunits, which serve as scaffolds that mediate interactions with other components of the replication machinery. Crystal structures for the B-subunits of Polα and Polδ/Polζ have been reported: the former within the primosome and separately with CTD and the latter with the N-terminal domain of the C-subunit. Here we present the crystal structure of the human Polε B-subunit (p59) in complex with CTD of the catalytic subunit (p261C). The structure revealed a well defined electron density for p261C and the phosphodiesterase and oligonucleotide/oligosaccharide-binding domains of p59. However, electron density was missing for the p59 N-terminal domain and for the linker connecting it to the phosphodiesterase domain. Similar to Polα, p261C of Polε contains a three-helix bundle in the middle and zinc-binding modules on each side. Intersubunit interactions involving 11 hydrogen bonds and numerous hydrophobic contacts account for stable complex formation with a buried surface area of 3094 Å2. Comparative structural analysis of p59 –p261C with the corresponding Polα complex revealed significant differences between the B-subunits and CTDs, as well as their interaction interfaces. The B-subunit of Polδ/Polζ also substantially differs from B-subunits of either Polα or Polε. This work provides a structural basis to explain biochemical and genetic data on the importance of B-subunit integrity in replisome function in vivo.

Original languageEnglish (US)
Pages (from-to)15717-15730
Number of pages14
JournalJournal of Biological Chemistry
Volume292
Issue number38
DOIs
StatePublished - Sep 22 2017

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Phosphoric Diester Hydrolases
Carrier concentration
Catalytic Domain
Crystal structure
Electrons
Exonucleases
DNA-Directed DNA Polymerase
Oligosaccharides
Scaffolds
Structural analysis
Oligonucleotides
Machinery
Zinc
Molecular Biology
Hydrogen
Hydrogen bonds

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Cell Biology

Cite this

Crystal structure of the human Polε B-subunit in complex with the C-terminal domain of the catalytic subunit. / Baranovskiy, Andrey G.; Gu, Jianyou; Babayeva, Nigar D.; Kurinov, Igor; Pavlov, Youri I; Tahirov, Tahir H.

In: Journal of Biological Chemistry, Vol. 292, No. 38, 22.09.2017, p. 15717-15730.

Research output: Contribution to journalArticle

Baranovskiy, Andrey G. ; Gu, Jianyou ; Babayeva, Nigar D. ; Kurinov, Igor ; Pavlov, Youri I ; Tahirov, Tahir H. / Crystal structure of the human Polε B-subunit in complex with the C-terminal domain of the catalytic subunit. In: Journal of Biological Chemistry. 2017 ; Vol. 292, No. 38. pp. 15717-15730.
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abstract = "The eukaryotic B-family DNA polymerases include four members: Polα, Polδ, Polε, and Polζ, which share common architectural features, such as the exonuclease/polymerase and C-terminal domains (CTDs) of catalytic subunits bound to indispensable B-subunits, which serve as scaffolds that mediate interactions with other components of the replication machinery. Crystal structures for the B-subunits of Polα and Polδ/Polζ have been reported: the former within the primosome and separately with CTD and the latter with the N-terminal domain of the C-subunit. Here we present the crystal structure of the human Polε B-subunit (p59) in complex with CTD of the catalytic subunit (p261C). The structure revealed a well defined electron density for p261C and the phosphodiesterase and oligonucleotide/oligosaccharide-binding domains of p59. However, electron density was missing for the p59 N-terminal domain and for the linker connecting it to the phosphodiesterase domain. Similar to Polα, p261C of Polε contains a three-helix bundle in the middle and zinc-binding modules on each side. Intersubunit interactions involving 11 hydrogen bonds and numerous hydrophobic contacts account for stable complex formation with a buried surface area of 3094 {\AA}2. Comparative structural analysis of p59 –p261C with the corresponding Polα complex revealed significant differences between the B-subunits and CTDs, as well as their interaction interfaces. The B-subunit of Polδ/Polζ also substantially differs from B-subunits of either Polα or Polε. This work provides a structural basis to explain biochemical and genetic data on the importance of B-subunit integrity in replisome function in vivo.",
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T1 - Crystal structure of the human Polε B-subunit in complex with the C-terminal domain of the catalytic subunit

AU - Baranovskiy, Andrey G.

AU - Gu, Jianyou

AU - Babayeva, Nigar D.

AU - Kurinov, Igor

AU - Pavlov, Youri I

AU - Tahirov, Tahir H

PY - 2017/9/22

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N2 - The eukaryotic B-family DNA polymerases include four members: Polα, Polδ, Polε, and Polζ, which share common architectural features, such as the exonuclease/polymerase and C-terminal domains (CTDs) of catalytic subunits bound to indispensable B-subunits, which serve as scaffolds that mediate interactions with other components of the replication machinery. Crystal structures for the B-subunits of Polα and Polδ/Polζ have been reported: the former within the primosome and separately with CTD and the latter with the N-terminal domain of the C-subunit. Here we present the crystal structure of the human Polε B-subunit (p59) in complex with CTD of the catalytic subunit (p261C). The structure revealed a well defined electron density for p261C and the phosphodiesterase and oligonucleotide/oligosaccharide-binding domains of p59. However, electron density was missing for the p59 N-terminal domain and for the linker connecting it to the phosphodiesterase domain. Similar to Polα, p261C of Polε contains a three-helix bundle in the middle and zinc-binding modules on each side. Intersubunit interactions involving 11 hydrogen bonds and numerous hydrophobic contacts account for stable complex formation with a buried surface area of 3094 Å2. Comparative structural analysis of p59 –p261C with the corresponding Polα complex revealed significant differences between the B-subunits and CTDs, as well as their interaction interfaces. The B-subunit of Polδ/Polζ also substantially differs from B-subunits of either Polα or Polε. This work provides a structural basis to explain biochemical and genetic data on the importance of B-subunit integrity in replisome function in vivo.

AB - The eukaryotic B-family DNA polymerases include four members: Polα, Polδ, Polε, and Polζ, which share common architectural features, such as the exonuclease/polymerase and C-terminal domains (CTDs) of catalytic subunits bound to indispensable B-subunits, which serve as scaffolds that mediate interactions with other components of the replication machinery. Crystal structures for the B-subunits of Polα and Polδ/Polζ have been reported: the former within the primosome and separately with CTD and the latter with the N-terminal domain of the C-subunit. Here we present the crystal structure of the human Polε B-subunit (p59) in complex with CTD of the catalytic subunit (p261C). The structure revealed a well defined electron density for p261C and the phosphodiesterase and oligonucleotide/oligosaccharide-binding domains of p59. However, electron density was missing for the p59 N-terminal domain and for the linker connecting it to the phosphodiesterase domain. Similar to Polα, p261C of Polε contains a three-helix bundle in the middle and zinc-binding modules on each side. Intersubunit interactions involving 11 hydrogen bonds and numerous hydrophobic contacts account for stable complex formation with a buried surface area of 3094 Å2. Comparative structural analysis of p59 –p261C with the corresponding Polα complex revealed significant differences between the B-subunits and CTDs, as well as their interaction interfaces. The B-subunit of Polδ/Polζ also substantially differs from B-subunits of either Polα or Polε. This work provides a structural basis to explain biochemical and genetic data on the importance of B-subunit integrity in replisome function in vivo.

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