- EMDB-22803: Cryo-EM 3D map of the Saccharomyces cerevisiae replicative polyme... -
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基本情報
登録情報
データベース: EMDB / ID: EMD-22803
タイトル
Cryo-EM 3D map of the Saccharomyces cerevisiae replicative polymerase delta in complex with a primer/template and the PCNA clamp
マップデータ
Replicative polymerase delta in complex with a primer/template and the PCNA clamp
試料
複合体: Pol delta-PCNA-DNA
複合体: dsDNA
DNA: DNA (5'-D(P*AP*TP*GP*AP*CP*CP*AP*TP*GP*AP*TP*TP*AP*CP*GP*AP*AP*TP*TP*GP*C)-3')
DNA: DNA (25-MER)
複合体: Proteins
タンパク質・ペプチド: Proliferating cell nuclear antigen
タンパク質・ペプチド: DNA polymerase
タンパク質・ペプチド: POL31 isoform 1
タンパク質・ペプチド: POL32 isoform 1
リガンド: MAGNESIUM ION
リガンド: IRON/SULFUR CLUSTER
リガンド: 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE
リガンド: ZINC ION
機能・相同性
機能・相同性情報
delta DNA polymerase complex / DNA-templated DNA replication maintenance of fidelity / DNA amplification / RNA-templated DNA biosynthetic process / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / meiotic mismatch repair / Processive synthesis on the lagging strand / Removal of the Flap Intermediate / E3 ubiquitin ligases ubiquitinate target proteins / Polymerase switching ...delta DNA polymerase complex / DNA-templated DNA replication maintenance of fidelity / DNA amplification / RNA-templated DNA biosynthetic process / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / meiotic mismatch repair / Processive synthesis on the lagging strand / Removal of the Flap Intermediate / E3 ubiquitin ligases ubiquitinate target proteins / Polymerase switching / SUMOylation of DNA replication proteins / positive regulation of DNA metabolic process / DNA replication, removal of RNA primer / maintenance of DNA trinucleotide repeats / Translesion Synthesis by POLH / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / establishment of mitotic sister chromatid cohesion / PCNA complex / Termination of translesion DNA synthesis / lagging strand elongation / double-strand break repair via break-induced replication / postreplication repair / 加水分解酵素; エステル加水分解酵素; 5'-リン酸モノエステル産生エンドデオキシリボヌクレアーゼ / silent mating-type cassette heterochromatin formation / nucleotide-excision repair, DNA gap filling / DNA replication proofreading / 3'-5'-DNA exonuclease activity / mitotic sister chromatid cohesion / DNA metabolic process / DNA strand elongation involved in DNA replication / error-free translesion synthesis / DNA polymerase processivity factor activity / leading strand elongation / regulation of DNA replication / Dual incision in TC-NER / subtelomeric heterochromatin formation / mismatch repair / translesion synthesis / positive regulation of DNA repair / base-excision repair, gap-filling / replication fork / positive regulation of DNA replication / nucleotide-excision repair / base-excision repair / DNA-templated DNA replication / mitotic cell cycle / 4 iron, 4 sulfur cluster binding / DNA replication / chromosome, telomeric region / molecular adaptor activity / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding / identical protein binding / nucleus / metal ion binding / cytosol 類似検索 - 分子機能
DNA polymerase delta subunit, OB-fold domain / DNA polymerase delta subunit 2, C-terminal domain / DNA polymerase delta subunit OB-fold domain / DNA polymerase delta/II small subunit family / C4-type zinc-finger of DNA polymerase delta / C4-type zinc-finger of DNA polymerase delta / DNA polymerase alpha/delta/epsilon, subunit B / DNA polymerase alpha/epsilon subunit B / Proliferating cell nuclear antigen signature 2. / Proliferating cell nuclear antigen, PCNA, conserved site ...DNA polymerase delta subunit, OB-fold domain / DNA polymerase delta subunit 2, C-terminal domain / DNA polymerase delta subunit OB-fold domain / DNA polymerase delta/II small subunit family / C4-type zinc-finger of DNA polymerase delta / C4-type zinc-finger of DNA polymerase delta / DNA polymerase alpha/delta/epsilon, subunit B / DNA polymerase alpha/epsilon subunit B / Proliferating cell nuclear antigen signature 2. / Proliferating cell nuclear antigen, PCNA, conserved site / Proliferating cell nuclear antigen signature 1. / Proliferating cell nuclear antigen, PCNA / Proliferating cell nuclear antigen, PCNA, N-terminal / Proliferating cell nuclear antigen, PCNA, C-terminal / Proliferating cell nuclear antigen, N-terminal domain / Proliferating cell nuclear antigen, C-terminal domain / DNA polymerase family B, thumb domain / DNA polymerase family B signature. / DNA-directed DNA polymerase, family B, conserved site / : / DNA polymerase family B / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA-directed DNA polymerase, family B, multifunctional domain / DNA polymerase, palm domain superfamily / DNA polymerase type-B family / DNA-directed DNA polymerase, family B / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily 類似検索 - ドメイン・相同性
BJ4_G0010060.mRNA.1.CDS.1 / POL31 isoform 1 / DNA polymerase / Proliferating cell nuclear antigen / DNA polymerase delta catalytic subunit / Proliferating cell nuclear antigen / DNA polymerase delta small subunit / DNA polymerase delta subunit 3 類似検索 - 構成要素
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
GM131754
米国
Howard Hughes Medical Institute (HHMI)
米国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
GM115809
米国
引用
ジャーナル: Proc Natl Acad Sci U S A / 年: 2020 タイトル: Structure of eukaryotic DNA polymerase δ bound to the PCNA clamp while encircling DNA. 著者: Fengwei Zheng / Roxana E Georgescu / Huilin Li / Michael E O'Donnell / 要旨: The DNA polymerase (Pol) δ of (S.c.) is composed of the catalytic subunit Pol3 along with two regulatory subunits, Pol31 and Pol32. Pol δ binds to proliferating cell nuclear antigen (PCNA) and ...The DNA polymerase (Pol) δ of (S.c.) is composed of the catalytic subunit Pol3 along with two regulatory subunits, Pol31 and Pol32. Pol δ binds to proliferating cell nuclear antigen (PCNA) and functions in genome replication, repair, and recombination. Unique among DNA polymerases, the Pol3 catalytic subunit contains a 4Fe-4S cluster that may sense the cellular redox state. Here we report the 3.2-Å cryo-EM structure of S.c. Pol δ in complex with primed DNA, an incoming ddTTP, and the PCNA clamp. Unexpectedly, Pol δ binds only one subunit of the PCNA trimer. This singular yet extensive interaction holds DNA such that the 2-nm-wide DNA threads through the center of the 3-nm interior channel of the clamp without directly contacting the protein. Thus, a water-mediated clamp and DNA interface enables the PCNA clamp to "waterskate" along the duplex with minimum drag. Pol31 and Pol32 are positioned off to the side of the catalytic Pol3-PCNA-DNA axis. We show here that Pol31-Pol32 binds single-stranded DNA that we propose underlies polymerase recycling during lagging strand synthesis, in analogy to replicase. Interestingly, the 4Fe-4S cluster in the C-terminal CysB domain of Pol3 forms the central interface to Pol31-Pol32, and this strategic location may explain the regulation of the oxidation state on Pol δ activity, possibly useful during cellular oxidative stress. Importantly, human cancer and other disease mutations map to nearly every domain of Pol3, suggesting that all aspects of Pol δ replication are important to human health and disease.