5o6e: Difference between revisions

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New page: '''Unreleased structure''' The entry 5o6e is ON HOLD Authors: LU, K.Y., CHEN, W.F., RETY, S., LIU, N.N., XU, X.G. Description: Structure of ScPif1 in complex with TTTGGGTT and ADP-AlF4...
 
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'''Unreleased structure'''


The entry 5o6e is ON HOLD
==Structure of ScPif1 in complex with TTTGGGTT and ADP-AlF4==
<StructureSection load='5o6e' size='340' side='right'caption='[[5o6e]], [[Resolution|resolution]] 3.34&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5o6e]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae] and [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5O6E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5O6E FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.345&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=ALF:TETRAFLUOROALUMINATE+ION'>ALF</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5o6e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o6e OCA], [https://pdbe.org/5o6e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5o6e RCSB], [https://www.ebi.ac.uk/pdbsum/5o6e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5o6e ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/PIF1_YEAST 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]<ref>PMID:10693764</ref> <ref>PMID:10926538</ref> <ref>PMID:11429610</ref> <ref>PMID:12024022</ref> <ref>PMID:15907372</ref> <ref>PMID:15923634</ref> <ref>PMID:16121131</ref> <ref>PMID:16537895</ref> <ref>PMID:16816432</ref> <ref>PMID:16878131</ref> <ref>PMID:17257907</ref> <ref>PMID:17590086</ref> <ref>PMID:17720711</ref> <ref>PMID:1849081</ref> <ref>PMID:19424434</ref> <ref>PMID:20225162</ref> <ref>PMID:21620135</ref> <ref>PMID:23175612</ref> <ref>PMID:23446274</ref> <ref>PMID:23596008</ref> <ref>PMID:23657261</ref> <ref>PMID:3038524</ref> <ref>PMID:8287473</ref>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The Saccharomyces cerevisiae Pif1 protein (ScPif1p) is the prototypical member of the Pif1 family of DNA helicases. ScPif1p is involved in the maintenance of mitochondrial, ribosomal and telomeric DNA and suppresses genome instability at G-quadruplex motifs. Here, we report the crystal structures of a truncated ScPif1p (ScPif1p237-780) in complex with different ssDNAs. Our results have revealed that a yeast-specific insertion domain protruding from the 2B domain folds as a bundle bearing an alpha-helix, alpha16. The alpha16 helix regulates the helicase activities of ScPif1p through interactions with the previously identified loop3. Furthermore, a biologically relevant dimeric structure has been identified, which can be further specifically stabilized by G-quadruplex DNA. Basing on structural analyses and mutational studies with DNA binding and unwinding assays, a potential G-quadruplex DNA binding site in ScPif1p monomers is suggested. Our results also show that ScPif1p uses the Q-motif to preferentially hydrolyze ATP, and a G-rich tract is preferentially recognized by more residues, consistent with previous biochemical observations. These findings provide a structural and mechanistic basis for understanding the multifunctional ScPif1p.


Authors: LU, K.Y., CHEN, W.F., RETY, S., LIU, N.N., XU, X.G.
Insights into the structural and mechanistic basis of multifunctional S. cerevisiae Pif1p helicase.,Lu KY, Chen WF, Rety S, Liu NN, Wu WQ, Dai YX, Li D, Ma HY, Dou SX, Xi XG Nucleic Acids Res. 2017 Nov 30. pii: 4675318. doi: 10.1093/nar/gkx1217. PMID:29202194<ref>PMID:29202194</ref>


Description: Structure of ScPif1 in complex with TTTGGGTT and ADP-AlF4
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
[[Category: Unreleased Structures]]
</div>
[[Category: Chen, W.F]]
<div class="pdbe-citations 5o6e" style="background-color:#fffaf0;"></div>
[[Category: Xu, X.G]]
 
[[Category: Rety, S]]
==See Also==
[[Category: Lu, K.Y]]
*[[Helicase 3D structures|Helicase 3D structures]]
[[Category: Liu, N.N]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Saccharomyces cerevisiae]]
[[Category: Saccharomyces cerevisiae S288C]]
[[Category: Chen WF]]
[[Category: Liu NN]]
[[Category: Lu KY]]
[[Category: Rety S]]
[[Category: Xu XG]]

Latest revision as of 22:09, 29 November 2023

Structure of ScPif1 in complex with TTTGGGTT and ADP-AlF4Structure of ScPif1 in complex with TTTGGGTT and ADP-AlF4

Structural highlights

5o6e is a 4 chain structure with sequence from Saccharomyces cerevisiae and Saccharomyces cerevisiae S288C. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 3.345Å
Ligands:, , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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][1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23]

Publication Abstract from PubMed

The Saccharomyces cerevisiae Pif1 protein (ScPif1p) is the prototypical member of the Pif1 family of DNA helicases. ScPif1p is involved in the maintenance of mitochondrial, ribosomal and telomeric DNA and suppresses genome instability at G-quadruplex motifs. Here, we report the crystal structures of a truncated ScPif1p (ScPif1p237-780) in complex with different ssDNAs. Our results have revealed that a yeast-specific insertion domain protruding from the 2B domain folds as a bundle bearing an alpha-helix, alpha16. The alpha16 helix regulates the helicase activities of ScPif1p through interactions with the previously identified loop3. Furthermore, a biologically relevant dimeric structure has been identified, which can be further specifically stabilized by G-quadruplex DNA. Basing on structural analyses and mutational studies with DNA binding and unwinding assays, a potential G-quadruplex DNA binding site in ScPif1p monomers is suggested. Our results also show that ScPif1p uses the Q-motif to preferentially hydrolyze ATP, and a G-rich tract is preferentially recognized by more residues, consistent with previous biochemical observations. These findings provide a structural and mechanistic basis for understanding the multifunctional ScPif1p.

Insights into the structural and mechanistic basis of multifunctional S. cerevisiae Pif1p helicase.,Lu KY, Chen WF, Rety S, Liu NN, Wu WQ, Dai YX, Li D, Ma HY, Dou SX, Xi XG Nucleic Acids Res. 2017 Nov 30. pii: 4675318. doi: 10.1093/nar/gkx1217. PMID:29202194[24]

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

See Also

References

  1. ↑ 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
  2. ↑ 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
  3. ↑ 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
  4. ↑ 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
  5. ↑ 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
  6. ↑ 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
  7. ↑ 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
  8. ↑ 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
  9. ↑ 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
  10. ↑ 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
  11. ↑ 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
  12. ↑ 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
  13. ↑ 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
  14. ↑ 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
  15. ↑ 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
  16. ↑ 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
  17. ↑ 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
  18. ↑ 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
  19. ↑ 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
  20. ↑ 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
  21. ↑ 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
  22. ↑ 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
  23. ↑ 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
  24. ↑ Lu KY, Chen WF, Rety S, Liu NN, Wu WQ, Dai YX, Li D, Ma HY, Dou SX, Xi XG. Insights into the structural and mechanistic basis of multifunctional S. cerevisiae Pif1p helicase. Nucleic Acids Res. 2017 Nov 30. pii: 4675318. doi: 10.1093/nar/gkx1217. PMID:29202194 doi:http://dx.doi.org/10.1093/nar/gkx1217

5o6e, resolution 3.34Å

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