6e49

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Pif1 peptide bound to PCNA trimerPif1 peptide bound to PCNA trimer

Structural highlights

6e49 is a 6 chain structure. This structure supersedes the now removed PDB entry 6b8i. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[PCNA_YEAST] This protein is an auxiliary protein of DNA polymerase delta and is involved in the control of eukaryotic DNA replication by increasing the polymerase's processibility during elongation of the leading strand. Involved in DNA repair.[1] [2] [PIF1_YEAST] DNA-dependent ATPase and 5'-3' DNA helicase required for the maintenance of both mitochondrial and nuclear genome stability. Efficiently unwinds G-quadruplex (G4) DNA structures and forked RNA-DNA hybrids. Appears to move along DNA in single nucleotide or base pair steps, powered by hydrolysis of 1 molecule of ATP. Processes at an unwinding rate of about 75 bp/s. Resolves G4 structures, preventing replication pausing and double-strand breaks (DSBs) at G4 motifs. Involved in the maintenance of telomeric DNA. Inhibits telomere elongation, de novo telomere formation and telomere addition to DSBs via catalytic inhibition of telomerase. Reduces the processivity of telomerase by displacing active telomerase from DNA ends. Releases telomerase by unwinding the short telomerase RNA/telomeric DNA hybrid that is the intermediate in the telomerase reaction. Involved in the maintenance of ribosomal (rDNA). Required for efficient fork arrest at the replication fork barrier within rDNA. Involved in the maintenance of mitochondrial (mtDNA). Required to maintain mtDNA under conditions that introduce dsDNA breaks in mtDNA, either preventing or repairing dsDNA breaks. May inhibit replication progression to allow time for repair. May have a general role in chromosomal replication by affecting Okazaki fragment maturation. May have a role in conjunction with DNA2 helicase/nuclease in 5'-flap extension during Okazaki fragment processing.[HAMAP-Rule:MF_03176][3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] [24] [25]

Publication Abstract from PubMed

The S. cerevisiae Pif1 helicase functions with DNA polymerase (Pol) delta in DNA synthesis during break-induced replication (BIR), a conserved pathway responsible for replication fork repair and telomere recombination. Pif1 interacts with the DNA polymerase processivity clamp PCNA, but the functional significance of the Pif1-PCNA complex remains to be elucidated. Here, we solve the crystal structure of PCNA in complex with a non-canonical PCNA-interacting motif in Pif1. The structure guides the construction of a Pif1 mutant that is deficient in PCNA interaction. This mutation impairs the ability of Pif1 to enhance DNA strand displacement synthesis by Pol delta in vitro and also the efficiency of BIR in cells. These results provide insights into the role of the Pif1-PCNA-Pol delta ensemble during DNA break repair by homologous recombination.

Role of the Pif1-PCNA Complex in Pol delta-Dependent Strand Displacement DNA Synthesis and Break-Induced Replication.,Buzovetsky O, Kwon Y, Pham NT, Kim C, Ira G, Sung P, Xiong Y Cell Rep. 2017 Nov 14;21(7):1707-1714. doi: 10.1016/j.celrep.2017.10.079. PMID:29141206[26]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

  1. ↑ Haracska L, Kondratick CM, Unk I, Prakash S, Prakash L. Interaction with PCNA is essential for yeast DNA polymerase eta function. Mol Cell. 2001 Aug;8(2):407-15. PMID:11545742
  2. ↑ Hoege C, Pfander B, Moldovan GL, Pyrowolakis G, Jentsch S. RAD6-dependent DNA repair is linked to modification of PCNA by ubiquitin and SUMO. Nature. 2002 Sep 12;419(6903):135-41. PMID:12226657 doi:10.1038/nature00991
  3. ↑ Ivessa AS, Zhou JQ, Zakian VA. The Saccharomyces Pif1p DNA helicase and the highly related Rrm3p have opposite effects on replication fork progression in ribosomal DNA. Cell. 2000 Feb 18;100(4):479-89. PMID:10693764
  4. ↑ Zhou J, Monson EK, Teng SC, Schulz VP, Zakian VA. Pif1p helicase, a catalytic inhibitor of telomerase in yeast. Science. 2000 Aug 4;289(5480):771-4. PMID:10926538
  5. ↑ Myung K, Chen C, Kolodner RD. Multiple pathways cooperate in the suppression of genome instability in Saccharomyces cerevisiae. Nature. 2001 Jun 28;411(6841):1073-6. doi: 10.1038/35082608. PMID:11429610 doi:http://dx.doi.org/10.1038/35082608
  6. ↑ O'Rourke TW, Doudican NA, Mackereth MD, Doetsch PW, Shadel GS. Mitochondrial dysfunction due to oxidative mitochondrial DNA damage is reduced through cooperative actions of diverse proteins. Mol Cell Biol. 2002 Jun;22(12):4086-93. PMID:12024022
  7. ↑ O'Rourke TW, Doudican NA, Zhang H, Eaton JS, Doetsch PW, Shadel GS. Differential involvement of the related DNA helicases Pif1p and Rrm3p in mtDNA point mutagenesis and stability. Gene. 2005 Jul 18;354:86-92. PMID:15907372 doi:http://dx.doi.org/S0378-1119(05)00169-1
  8. ↑ Doudican NA, Song B, Shadel GS, Doetsch PW. Oxidative DNA damage causes mitochondrial genomic instability in Saccharomyces cerevisiae. Mol Cell Biol. 2005 Jun;25(12):5196-204. doi: 10.1128/MCB.25.12.5196-5204.2005. PMID:15923634 doi:http://dx.doi.org/10.1128/MCB.25.12.5196-5204.2005
  9. ↑ Boule JB, Vega LR, Zakian VA. The yeast Pif1p helicase removes telomerase from telomeric DNA. Nature. 2005 Nov 3;438(7064):57-61. Epub 2005 Aug 24. PMID:16121131 doi:http://dx.doi.org/nature04091
  10. ↑ Budd ME, Reis CC, Smith S, Myung K, Campbell JL. Evidence suggesting that Pif1 helicase functions in DNA replication with the Dna2 helicase/nuclease and DNA polymerase delta. Mol Cell Biol. 2006 Apr;26(7):2490-500. doi: 10.1128/MCB.26.7.2490-2500.2006. PMID:16537895 doi:http://dx.doi.org/10.1128/MCB.26.7.2490-2500.2006
  11. ↑ Wagner M, Price G, Rothstein R. The absence of Top3 reveals an interaction between the Sgs1 and Pif1 DNA helicases in Saccharomyces cerevisiae. Genetics. 2006 Oct;174(2):555-73. Epub 2006 Jul 2. PMID:16816432 doi:http://dx.doi.org/genetics.104.036905
  12. ↑ Eugster A, Lanzuolo C, Bonneton M, Luciano P, Pollice A, Pulitzer JF, Stegberg E, Berthiau AS, Forstemann K, Corda Y, Lingner J, Geli V, Gilson E. The finger subdomain of yeast telomerase cooperates with Pif1p to limit telomere elongation. Nat Struct Mol Biol. 2006 Aug;13(8):734-9. doi: 10.1038/nsmb1126. Epub 2006 Jul, 30. PMID:16878131 doi:http://dx.doi.org/10.1038/nsmb1126
  13. ↑ Cheng X, Dunaway S, Ivessa AS. The role of Pif1p, a DNA helicase in Saccharomyces cerevisiae, in maintaining mitochondrial DNA. Mitochondrion. 2007 May;7(3):211-22. doi: 10.1016/j.mito.2006.11.023. Epub 2006, Dec 9. PMID:17257907 doi:http://dx.doi.org/10.1016/j.mito.2006.11.023
  14. ↑ Vega LR, Phillips JA, Thornton BR, Benanti JA, Onigbanjo MT, Toczyski DP, Zakian VA. Sensitivity of yeast strains with long G-tails to levels of telomere-bound telomerase. PLoS Genet. 2007 Jun;3(6):e105. doi: 10.1371/journal.pgen.0030105. PMID:17590086 doi:http://dx.doi.org/10.1371/journal.pgen.0030105
  15. ↑ Boule JB, Zakian VA. The yeast Pif1p DNA helicase preferentially unwinds RNA DNA substrates. Nucleic Acids Res. 2007;35(17):5809-18. Epub 2007 Aug 24. PMID:17720711 doi:http://dx.doi.org/gkm613
  16. ↑ Lahaye A, Stahl H, Thines-Sempoux D, Foury F. PIF1: a DNA helicase in yeast mitochondria. EMBO J. 1991 Apr;10(4):997-1007. PMID:1849081
  17. ↑ Ribeyre C, Lopes J, Boule JB, Piazza A, Guedin A, Zakian VA, Mergny JL, Nicolas A. The yeast Pif1 helicase prevents genomic instability caused by G-quadruplex-forming CEB1 sequences in vivo. PLoS Genet. 2009 May;5(5):e1000475. doi: 10.1371/journal.pgen.1000475. Epub 2009 , May 8. PMID:19424434 doi:http://dx.doi.org/10.1371/journal.pgen.1000475
  18. ↑ Boule JB, Zakian VA. Characterization of the helicase activity and anti-telomerase properties of yeast Pif1p in vitro. Methods Mol Biol. 2010;587:359-76. doi: 10.1007/978-1-60327-355-8_25. PMID:20225162 doi:http://dx.doi.org/10.1007/978-1-60327-355-8_25
  19. ↑ Paeschke K, Capra JA, Zakian VA. DNA replication through G-quadruplex motifs is promoted by the Saccharomyces cerevisiae Pif1 DNA helicase. Cell. 2011 May 27;145(5):678-91. doi: 10.1016/j.cell.2011.04.015. PMID:21620135 doi:http://dx.doi.org/10.1016/j.cell.2011.04.015
  20. ↑ Ramanagoudr-Bhojappa R, Blair LP, Tackett AJ, Raney KD. Physical and functional interaction between yeast Pif1 helicase and Rim1 single-stranded DNA binding protein. Nucleic Acids Res. 2013 Jan;41(2):1029-46. doi: 10.1093/nar/gks1088. Epub 2012, Nov 21. PMID:23175612 doi:http://dx.doi.org/10.1093/nar/gks1088
  21. ↑ Galletto R, Tomko EJ. Translocation of Saccharomyces cerevisiae Pif1 helicase monomers on single-stranded DNA. Nucleic Acids Res. 2013 Apr;41(8):4613-27. doi: 10.1093/nar/gkt117. Epub 2013 Feb, 27. PMID:23446274 doi:http://dx.doi.org/10.1093/nar/gkt117
  22. ↑ Ramanagoudr-Bhojappa R, Chib S, Byrd AK, Aarattuthodiyil S, Pandey M, Patel SS, Raney KD. Yeast Pif1 helicase exhibits a one-base-pair stepping mechanism for unwinding duplex DNA. J Biol Chem. 2013 May 31;288(22):16185-95. doi: 10.1074/jbc.M113.470013. Epub, 2013 Apr 17. PMID:23596008 doi:http://dx.doi.org/10.1074/jbc.M113.470013
  23. ↑ Paeschke K, Bochman ML, Garcia PD, Cejka P, Friedman KL, Kowalczykowski SC, Zakian VA. Pif1 family helicases suppress genome instability at G-quadruplex motifs. Nature. 2013 May 23;497(7450):458-62. doi: 10.1038/nature12149. Epub 2013 May 8. PMID:23657261 doi:http://dx.doi.org/10.1038/nature12149
  24. ↑ Foury F, Lahaye A. Cloning and sequencing of the PIF gene involved in repair and recombination of yeast mitochondrial DNA. EMBO J. 1987 May;6(5):1441-9. PMID:3038524
  25. ↑ Schulz VP, Zakian VA. The saccharomyces PIF1 DNA helicase inhibits telomere elongation and de novo telomere formation. Cell. 1994 Jan 14;76(1):145-55. PMID:8287473
  26. ↑ Buzovetsky O, Kwon Y, Pham NT, Kim C, Ira G, Sung P, Xiong Y. Role of the Pif1-PCNA Complex in Pol delta-Dependent Strand Displacement DNA Synthesis and Break-Induced Replication. Cell Rep. 2017 Nov 14;21(7):1707-1714. doi: 10.1016/j.celrep.2017.10.079. PMID:29141206 doi:http://dx.doi.org/10.1016/j.celrep.2017.10.079

6e49, resolution 2.90Å

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