6s1n Citations

Structure of the processive human Pol δ holoenzyme.

Abstract

In eukaryotes, DNA polymerase δ (Pol δ) bound to the proliferating cell nuclear antigen (PCNA) replicates the lagging strand and cooperates with flap endonuclease 1 (FEN1) to process the Okazaki fragments for their ligation. We present the high-resolution cryo-EM structure of the human processive Pol δ-DNA-PCNA complex in the absence and presence of FEN1. Pol δ is anchored to one of the three PCNA monomers through the C-terminal domain of the catalytic subunit. The catalytic core sits on top of PCNA in an open configuration while the regulatory subunits project laterally. This arrangement allows PCNA to thread and stabilize the DNA exiting the catalytic cleft and recruit FEN1 to one unoccupied monomer in a toolbelt fashion. Alternative holoenzyme conformations reveal important functional interactions that maintain PCNA orientation during synthesis. This work sheds light on the structural basis of Pol δ's activity in replicating the human genome.

Articles - 6s1n mentioned but not cited (1)

  1. Resveratrol Mediates the Apoptosis of Triple Negative Breast Cancer Cells by Reducing POLD1 Expression. Liang ZJ, Wan Y, Zhu DD, Wang MX, Jiang HM, Huang DL, Luo LF, Chen MJ, Yang WP, Li HM, Wei CY. Front Oncol 11 569295 (2021)


Reviews citing this publication (14)

  1. Human PCNA Structure, Function and Interactions. González-Magaña A, Blanco FJ. Biomolecules 10 E570 (2020)
  2. Karyopherin-mediated nucleocytoplasmic transport. Wing CE, Fung HYJ, Chook YM. Nat Rev Mol Cell Biol 23 307-328 (2022)
  3. Diversity and evolution of B-family DNA polymerases. Kazlauskas D, Krupovic M, Guglielmini J, Forterre P, Venclovas Č. Nucleic Acids Res 48 10142-10156 (2020)
  4. Strand discrimination in DNA mismatch repair. Putnam CD. DNA Repair (Amst) 105 103161 (2021)
  5. DNA Polymerases at the Eukaryotic Replication Fork Thirty Years after: Connection to Cancer. Pavlov YI, Zhuk AS, Stepchenkova EI. Cancers (Basel) 12 E3489 (2020)
  6. Iron-sulfur clusters as inhibitors and catalysts of viral replication. Honarmand Ebrahimi K, Ciofi-Baffoni S, Hagedoorn PL, Nicolet Y, Le Brun NE, Hagen WR, Armstrong FA. Nat Chem 14 253-266 (2022)
  7. The Interplay of Cohesin and the Replisome at Processive and Stressed DNA Replication Forks. van Schie JJM, de Lange J. Cells 10 3455 (2021)
  8. Mechanisms for Maintaining Eukaryotic Replisome Progression in the Presence of DNA Damage. Guilliam TA. Front Mol Biosci 8 712971 (2021)
  9. Post-Translational Modifications of PCNA: Guiding for the Best DNA Damage Tolerance Choice. Bellí G, Colomina N, Castells-Roca L, Lorite NP. J Fungi (Basel) 8 621 (2022)
  10. Structural and Molecular Kinetic Features of Activities of DNA Polymerases. Kuznetsova AA, Fedorova OS, Kuznetsov NA. Int J Mol Sci 23 6373 (2022)
  11. Water skating: How polymerase sliding clamps move on DNA. Li H, Zheng F, O'Donnell M. FEBS J 288 7256-7262 (2021)
  12. Implementing fluorescence enhancement, quenching, and FRET for investigating flap endonuclease 1 enzymatic reaction at the single-molecule level. Sobhy MA, Tehseen M, Takahashi M, Bralić A, De Biasio A, Hamdan SM. Comput Struct Biotechnol J 19 4456-4471 (2021)
  13. Beyond the Lesion: Back to High Fidelity DNA Synthesis. Kaszubowski JD, Trakselis MA. Front Mol Biosci 8 811540 (2021)
  14. Repair and tolerance of DNA damage at the replication fork: A structural perspective. Eichman BF. Curr Opin Struct Biol 81 102618 (2023)

Articles citing this publication (55)

  1. Structure of the polymerase ε holoenzyme and atomic model of the leading strand replisome. Yuan Z, Georgescu R, Schauer GD, O'Donnell ME, Li H. Nat Commun 11 3156 (2020)
  2. An atomistic model of the coronavirus replication-transcription complex as a hexamer assembled around nsp15. Perry JK, Appleby TC, Bilello JP, Feng JY, Schmitz U, Campbell EA. J Biol Chem 297 101218 (2021)
  3. Structure of eukaryotic DNA polymerase δ bound to the PCNA clamp while encircling DNA. Zheng F, Georgescu RE, Li H, O'Donnell ME. Proc Natl Acad Sci U S A 117 30344-30353 (2020)
  4. Structural basis for the increased processivity of D-family DNA polymerases in complex with PCNA. Madru C, Henneke G, Raia P, Hugonneau-Beaufet I, Pehau-Arnaudet G, England P, Lindahl E, Delarue M, Carroni M, Sauguet L. Nat Commun 11 1591 (2020)
  5. Cryo-EM structure of the deltaretroviral intasome in complex with the PP2A regulatory subunit B56γ. Barski MS, Minnell JJ, Hodakova Z, Pye VE, Nans A, Cherepanov P, Maertens GN. Nat Commun 11 5043 (2020)
  6. DNA is loaded through the 9-1-1 DNA checkpoint clamp in the opposite direction of the PCNA clamp. Zheng F, Georgescu RE, Yao NY, O'Donnell ME, Li H. Nat Struct Mol Biol 29 376-385 (2022)
  7. Cryo-EM structure of human Pol κ bound to DNA and mono-ubiquitylated PCNA. Lancey C, Tehseen M, Bakshi S, Percival M, Takahashi M, Sobhy MA, Raducanu VS, Blair K, Muskett FW, Ragan TJ, Crehuet R, Hamdan SM, De Biasio A. Nat Commun 12 6095 (2021)
  8. Cryo-EM structures reveal that RFC recognizes both the 3'- and 5'-DNA ends to load PCNA onto gaps for DNA repair. Zheng F, Georgescu R, Yao NY, Li H, O'Donnell ME. Elife 11 e77469 (2022)
  9. Dynamic DNA-bound PCNA complexes co-ordinate Okazaki fragment synthesis, processing and ligation. Matsumoto Y, Brooks RC, Sverzhinsky A, Pascal JM, Tomkinson AE. J Mol Biol 432 166698 (2020)
  10. Rad27 and Exo1 function in different excision pathways for mismatch repair in Saccharomyces cerevisiae. Calil FA, Li BZ, Torres KA, Nguyen K, Bowen N, Putnam CD, Kolodner RD. Nat Commun 12 5568 (2021)
  11. Rapid genome editing by CRISPR-Cas9-POLD3 fusion. Reint G, Li Z, Labun K, Keskitalo S, Soppa I, Mamia K, Tolo E, Szymanska M, Meza-Zepeda LA, Lorenz S, Cieslar-Pobuda A, Hu X, Bordin DL, Staerk J, Valen E, Schmierer B, Varjosalo M, Taipale J, Haapaniemi E. Elife 10 e75415 (2021)
  12. Mechanism of human Lig1 regulation by PCNA in Okazaki fragment sealing. Blair K, Tehseen M, Raducanu VS, Shahid T, Lancey C, Rashid F, Crehuet R, Hamdan SM, De Biasio A. Nat Commun 13 7833 (2022)
  13. Molecular mechanisms of eukaryotic origin initiation, replication fork progression, and chromatin maintenance. Yuan Z, Li H. Biochem J 477 3499-3525 (2020)
  14. What Are the Molecular Requirements for Protein Sliding along DNA? Bigman LS, Greenblatt HM, Levy Y. J Phys Chem B 125 3119-3131 (2021)
  15. Kinetic investigation of the polymerase and exonuclease activities of human DNA polymerase ε holoenzyme. Zahurancik WJ, Suo Z. J Biol Chem 295 17251-17264 (2020)
  16. Simplified detection of polyhistidine-tagged proteins in gels and membranes using a UV-excitable dye and a multiple chelator head pair. Raducanu VS, Isaioglou I, Raducanu DV, Merzaban JS, Hamdan SM. J Biol Chem 295 12214-12223 (2020)
  17. Two conformations of DNA polymerase D-PCNA-DNA, an archaeal replisome complex, revealed by cryo-electron microscopy. Mayanagi K, Oki K, Miyazaki N, Ishino S, Yamagami T, Morikawa K, Iwasaki K, Kohda D, Shirai T, Ishino Y. BMC Biol 18 152 (2020)
  18. Pol32, an accessory subunit of DNA polymerase delta, plays an essential role in genome stability and pathogenesis of Candida albicans. Patel SK, Sahu SR, Utkalaja BG, Bose S, Acharya N. Gut Microbes 15 2163840 (2023)
  19. Structure of the mammalian adenine DNA glycosylase MUTYH: insights into the base excision repair pathway and cancer. Nakamura T, Okabe K, Hirayama S, Chirifu M, Ikemizu S, Morioka H, Nakabeppu Y, Yamagata Y. Nucleic Acids Res 49 7154-7163 (2021)
  20. DNA polymerase POLD1 promotes proliferation and metastasis of bladder cancer by stabilizing MYC. Wang Y, Ju L, Wang G, Qian K, Jin W, Li M, Yu J, Shi Y, Wang Y, Zhang Y, Xiao Y, Wang X. Nat Commun 14 2421 (2023)
  21. Mechanistic investigation of human maturation of Okazaki fragments reveals slow kinetics. Raducanu VS, Tehseen M, Al-Amodi A, Joudeh LI, De Biasio A, Hamdan SM. Nat Commun 13 6973 (2022)
  22. The [4Fe4S] Cluster of Yeast DNA Polymerase ε Is Redox Active and Can Undergo DNA-Mediated Signaling. Pinto MN, Ter Beek J, Ekanger LA, Johansson E, Barton JK. J Am Chem Soc 143 16147-16153 (2021)
  23. Tracking of progressing human DNA polymerase δ holoenzymes reveals distributions of DNA lesion bypass activities. Dannenberg RL, Cardina JA, Pytko KG, Hedglin M. Nucleic Acids Res 50 9893-9908 (2022)
  24. CAF-1 deposits newly synthesized histones during DNA replication using distinct mechanisms on the leading and lagging strands. Rouillon C, Eckhardt BV, Kollenstart L, Gruss F, Verkennis AEE, Rondeel I, Krijger PHL, Ricci G, Biran A, van Laar T, Delvaux de Fenffe CM, Luppens G, Albanese P, Sato K, Scheltema RA, de Laat W, Knipscheer P, Dekker NH, Groth A, Mattiroli F. Nucleic Acids Res 51 3770-3792 (2023)
  25. Cryo-EM structures and biochemical insights into heterotrimeric PCNA regulation of DNA ligase. Sverzhinsky A, Tomkinson AE, Pascal JM. Structure 30 371-385.e5 (2022)
  26. Crystal structure of African swine fever virus pE301R reveals a ring-shaped trimeric DNA sliding clamp. Wu J, Zheng H, Gong P. J Biol Chem 299 104872 (2023)
  27. Interaction of human HelQ with DNA polymerase delta halts DNA synthesis and stimulates DNA single-strand annealing. He L, Lever R, Cubbon A, Tehseen M, Jenkins T, Nottingham AO, Horton A, Betts H, Fisher M, Hamdan SM, Soultanas P, Bolt EL. Nucleic Acids Res 51 1740-1749 (2023)
  28. Structural basis for the inhibition of HTLV-1 integration inferred from cryo-EM deltaretroviral intasome structures. Barski MS, Vanzo T, Zhao XZ, Smith SJ, Ballandras-Colas A, Cronin NB, Pye VE, Hughes SH, Burke TR, Cherepanov P, Maertens GN. Nat Commun 12 4996 (2021)
  29. Candidate variants in DNA replication and repair genes in early-onset renal cell carcinoma patients referred for germline testing. Demidova EV, Serebriiskii IG, Vlasenkova R, Kelow S, Andrake MD, Hartman TR, Kent T, Virtucio J, Rosen GL, Pomerantz RT, Dunbrack RL, Golemis EA, Hall MJ, Chen DYT, Daly MB, Arora S. BMC Genomics 24 212 (2023)
  30. Identification of probable inhibitors for the DNA polymerase of the Monkeypox virus through the virtual screening approach. Kumari S, Chakraborty S, Ahmad M, Kumar V, Tailor PB, Biswal BK. Int J Biol Macromol 229 515-528 (2023)
  31. Potential therapeutic targets for Mpox: the evidence to date. Byrareddy SN, Sharma K, Sachdev S, Reddy AS, Acharya A, Klaustermeier KM, Lorson CL, Singh K. Expert Opin Ther Targets 27 419-431 (2023)
  32. The fidelity of DNA replication, particularly on GC-rich templates, is reduced by defects of the Fe-S cluster in DNA polymerase δ. Kiktev DA, Dominska M, Zhang T, Dahl J, Stepchenkova EI, Mieczkowski P, Burgers PM, Lujan S, Burkholder A, Kunkel TA, Petes TD. Nucleic Acids Res 49 5623-5636 (2021)
  33. Top-down stepwise refinement identifies coding and noncoding RNA-associated epigenetic regulatory maps in malignant glioma. Huang Y, Gao X, Yang E, Yue K, Cao Y, Zhao B, Zhang H, Dai S, Zhang L, Luo P, Jiang X. J Cell Mol Med 26 2230-2250 (2022)
  34. Heterotrimeric PCNA increases the activity and fidelity of Dbh, a Y-family translesion DNA polymerase prone to creating single-base deletion mutations. Wu Y, Jaremko WJ, Wilson RC, Pata JD. DNA Repair (Amst) 96 102967 (2020)
  35. Human DNA polymerase α has a strong mutagenic potential at the initial steps of DNA synthesis. Lisova AE, Baranovskiy AG, Morstadt LM, Babayeva ND, Tahirov TH. Nucleic Acids Res 50 12266-12273 (2022)
  36. Mild MDPL in a patient with a novel de novo missense variant in the Cys-B region of POLD1. Chopra M, Caswell R, Barcia G, Rondeau S, Jonard L, Nitchké P, Amram D, Bellaiche ML, Abadie V, Parodi M, Denoyelle F, Hattersley A, Bole C, Lyonnet S, Marlin S. Eur J Hum Genet 30 960-966 (2022)
  37. Modification of the 4Fe-4S Cluster Charge Transport Pathway Alters RNA Synthesis by Yeast DNA Primase. Salay LE, Blee AM, Raza MK, Gallagher KS, Chen H, Dorfeuille AJ, Barton JK, Chazin WJ. Biochemistry 61 1113-1123 (2022)
  38. Non-canonical binding of the Chaetomium thermophilum PolD4 N-terminal PIP motif to PCNA involves Q-pocket and compact 2-fork plug interactions but no 310 helix. Yang D, Alphey MS, MacNeill SA. FEBS J 290 162-175 (2023)
  39. Stepwise requirements for polymerases δ and θ in theta-mediated end joining. Stroik S, Carvajal-Garcia J, Gupta D, Edwards A, Luthman A, Wyatt DW, Dannenberg RL, Feng W, Kunkel TA, Gupta GP, Hedglin M, Wood R, Doublié S, Rothenberg E, Ramsden DA. Nature 623 836-841 (2023)
  40. The Fork Protection Complex: A Regulatory Hub at the Head of the Replisome. Grabarczyk DB. Subcell Biochem 99 83-107 (2022)
  41. POLD1 DEDD Motif Mutation Confers Hypermutation in Endometrial Cancer and Durable Response to Pembrolizumab. Wei CH, Wang EW, Ma L, Zhou Y, Zheng L, Hampel H, Shehayeb S, Lee S, Cohen J, Kohut A, Fan F, Rosen S, Wu X, Shen B, Zhao Y. Cancers (Basel) 15 5674 (2023)
  42. A hypomorphic mutation in Pold1 disrupts the coordination of embryo size expansion and morphogenesis during gastrulation. Chen T, Alcorn H, Devbhandari S, Remus D, Lacy E, Huangfu D, Anderson KV. Biol Open 11 bio059307 (2022)
  43. A simple bypass assay for DNA polymerases shows that cancer-associated hypermutating variants exhibit differences in vitro. Crevel G, Kearsey S, Cotterill S. FEBS J 290 5744-5758 (2023)
  44. Canonical binding of Chaetomium thermophilum DNA polymerase δ/ζ subunit PolD3 and flap endonuclease Fen1 to PCNA. Alphey MS, Wolford CB, MacNeill SA. Front Mol Biosci 10 1320648 (2023)
  45. DNA Polymerase Delta Exhibits Altered Catalytic Properties on Lysine Acetylation. Njeri C, Pepenella S, Battapadi T, Bambara RA, Balakrishnan L. Genes (Basel) 14 774 (2023)
  46. Modulation of the microhomology-mediated end joining pathway suppresses large deletions and enhances homology-directed repair following CRISPR-Cas9-induced DNA breaks. Yuan B, Bi C, Tian Y, Wang J, Jin Y, Alsayegh K, Tehseen M, Yi G, Zhou X, Shao Y, Romero FV, Fischle W, Izpisua Belmonte JC, Hamdan S, Huang Y, Li M. BMC Biol 22 101 (2024)
  47. Multiple roles of Pol epsilon in eukaryotic chromosome replication. Cvetkovic MA, Ortega E, Bellelli R, Costa A. Biochem Soc Trans 50 309-320 (2022)
  48. PCNA Ser46-Leu47 residues are crucial in preserving genomic integrity. Kim S, Kim Y, Kim Y, Yoon S, Lee KY, Lee Y, Kang S, Myung K, Oh CK. PLoS One 18 e0285337 (2023)
  49. Structure of the PCNA unloader Elg1-RFC. Zheng F, Yao NY, Georgescu RE, Li H, O'Donnell ME. Sci Adv 10 eadl1739 (2024)
  50. The Atad5 RFC-like complex is the major unloader of proliferating cell nuclear antigen in Xenopus egg extracts. Kawasoe Y, Shimokawa S, Gillespie PJ, Blow JJ, Tsurimoto T, Takahashi TS. J Biol Chem 300 105588 (2024)
  51. The DHX9 helicase interacts with human DNA polymerase δ4 and stimulates its activity in D-loop extension synthesis. Wang X, Zhang S, Zhang Z, Mazloum NA, Lee EYC, Lee MYW. DNA Repair (Amst) 128 103513 (2023)
  52. The SPATA5-SPATA5L1 ATPase complex directs replisome proteostasis to ensure genome integrity. Krishnamoorthy V, Foglizzo M, Dilley RL, Wu A, Datta A, Dutta P, Campbell LJ, Degtjarik O, Musgrove LJ, Calabrese AN, Zeqiraj E, Greenberg RA. Cell 187 2250-2268.e31 (2024)
  53. The functional significance of the RPA- and PCNA-dependent recruitment of Pif1 to DNA. Kotenko O, Makovets S. EMBO Rep 25 1734-1751 (2024)
  54. The inner side of yeast PCNA contributes to genome stability by mediating interactions with Rad18 and the replicative DNA polymerase δ. Toth R, Halmai M, Gyorfy Z, Balint E, Unk I. Sci Rep 12 5163 (2022)
  55. The stabilized Pol31-Pol3 interface counteracts Pol32 ablation with differential effects on repair. Shimada K, Tsai-Pflugfelder M, Vijeh Motlagh ND, Delgoshaie N, Fuchs J, Gut H, Gasser SM. Life Sci Alliance 4 e202101138 (2021)