Quaternary structural diversity in eukaryotic DNA polymerases: monomeric to multimeric form

Acharya, Narottam; Khandagale, Prashant; Thakur, Shilpa; Sahu, Jugal Kishor; Utkalaja, Bhabasha Gyanadeep

doi:10.1007/s00294-020-01071-1

Cited by 14 publications

(16 citation statements)

References 213 publications

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“…The bacteriophage T7 replicase, T7 DNAP, is a member of the wellstudied family-A of polymerases. The structures of seven DNAPs from this family have been determined: DNAPs I from Escherichia coli, Bacillus, and Thermus aquaticus (Taq), T7 DNAP, and human DNAPs , , and  [5][6][7][8][9][10][11][12][13]. All those polymerases harbor a conserved DNA polymerization domain that is subdivided into three subdomains dubbed: palm, fingers, and thumb, and a 3'-5' exonuclease domain that in the case of Bacillus and Taq DNAPs is inactive [14].…”

Section: Introductionmentioning

confidence: 99%

Structure of an open conformation of T7 DNA polymerase reveals novel structural features regulating primer-template stabilization at the polymerization active site

Juarez-Quintero¹,

Peralta-Castro²,

Cardoza

et al. 2021

Biochemical Journal

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The crystal structure of full-length T7 DNA polymerase in complex with its processivity factor thioredoxin and double-stranded DNA in the polymerization active site exhibits two novel structural motifs in family-A DNA polymerases: an extended b-hairpin at the fingers subdomain, that interacts with the DNA template strand downstream the primer-terminus, and a helix-loop-helix motif (insertion1) located between residues 102 to 122 in the exonuclease domain. The extended b-hairpin is involved in nucleotide incorporation on substrates with 5'-overhangs longer than 2 nucleotides, suggesting a role in stabilizing the template strand into the polymerization domain. Our biochemical data reveal that insertion1 of the exonuclease domain makes stabilizing interactions that facilitate proofreading by shuttling the primer strand into the exonuclease active site. Overall, our studies evidence conservation of the 3'-5' exonuclease domain fold between family-A DNA polymerases and highlight the modular architecture of T7 DNA polymerase. Our data suggest that the intercalating b-hairpin guides the template-strand into the polymerization active site after the T7 primase-helicase unwinds the DNA double helix ameliorating the formation of secondary structures and decreasing the appearance of indels

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Section: Introductionmentioning

confidence: 99%

Structure of an open conformation of T7 DNA polymerase reveals novel structural features regulating primer-template stabilization at the polymerization active site

Juarez-Quintero¹,

Peralta-Castro²,

Cardoza

et al. 2021

Biochemical Journal

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“…Chromosomal DNA replication requires continuous polymerisation of thousands of nucleotides by replicative DNA polymerases during the S‐phase of a cell cycle [1,2]. The DNA sliding clamp, proliferating cell nuclear antigen (PCNA), plays an essential role in this efficient and processive DNA synthesis.…”

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confidence: 99%

Structural analyses of PCNA from the fungal pathogen Candida albicans identify three regions with species‐specific conformations

et al. 2021

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An assembly of multiprotein complexes achieves chromosomal DNA replication at the replication fork. In eukaryotes, proliferating cell nuclear antigen (PCNA) plays a vital role in the assembly of multiprotein complexes at the replication fork and is essential for cell viability. PCNA from several organisms, including Saccharomyces cerevisiae, has been structurally characterised. However, the structural analyses of PCNA from fungal pathogens are limited. Recently, we have reported that PCNA from the opportunistic fungal pathogen Candida albicans complements the essential functions of ScPCNA in S. cerevisiae. Still, it only partially rescues the loss of ScPCNA when the yeast cells are under genotoxic stress. To understand this further, herein, we have determined the crystal structure of CaPCNA and compared that with the existing structures of other fungal and human PCNA. Our comparative structural and in‐solution small‐angle X‐ray scattering (SAXS) analyses reveal that CaPCNA forms a stable homotrimer, both in crystal and in solution. It displays noticeable structural alterations in the oligomerisation interface, P‐loop and hydrophobic pocket regions, suggesting its differential function in a heterologous system and avenues for developing specific therapeutics. Databases The PDB and SASBDB accession codes for CaPCNA are https://doi.org/10.2210/pdb7BUP/pdb and SASDHQ9, respectively.

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“…Biochemical analyses suggested that these two ScPCNA mutants inhibited translesion DNA synthesis by ScPol and ScPol, and cells harbouring these PCNA mutants exhibited DNA damaging agent sensitivity and enhanced mutagenesis compared to wild type (12,13). Pol and Pol are specialized DNA polymerases involved in translesion DNA synthesis and damage tolerance pathways (19)(20)(21).…”

Section: Discussionmentioning

confidence: 99%

Interdomain connecting loop and J loop structures determine cross-species compatibility of PCNA

Kumari

Sundaram

Manohar

et al. 2021

Journal of Biological Chemistry

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Quaternary structural diversity in eukaryotic DNA polymerases: monomeric to multimeric form

Cited by 14 publications

References 213 publications

Structure of an open conformation of T7 DNA polymerase reveals novel structural features regulating primer-template stabilization at the polymerization active site

Structure of an open conformation of T7 DNA polymerase reveals novel structural features regulating primer-template stabilization at the polymerization active site

Structural analyses of PCNA from the fungal pathogen Candida albicans identify three regions with species‐specific conformations

Interdomain connecting loop and J loop structures determine cross-species compatibility of PCNA

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