5meb: Difference between revisions

Latest revision as of 18:40, 1 November 2023

Crystal structure of yeast Cdt1 C-terminal domain

Structural highlights

5meb is a 2 chain structure with sequence from Saccharomyces cerevisiae. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.8Å
Ligands:	MSE, SO4
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

CDT1_YEAST DNA replication licensing factor, required for pre-replication complex assembly. Faithful duplication of the genetic material requires 'once per cell cycle' DNA replication initiation and elongation. Central to this control is the tightly regulated formation of prereplicative complexes (preRCs) at future origins of DNA replication. Required for the recruitment of the MCM2-7 helicase complex to the replication origins.^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7]

Publication Abstract from PubMed

ORC, Cdc6 and Cdt1 act together to load hexameric MCM, the motor of the eukaryotic replicative helicase, into double hexamers at replication origins. Here we show that Cdt1 interacts with MCM subunits Mcm2, 4 and 6, which both destabilizes the Mcm2-5 interface and inhibits MCM ATPase activity. Using X-ray crystallography, we show that Cdt1 contains two winged-helix domains in the C-terminal half of the protein and a catalytically inactive dioxygenase-related N-terminal domain, which is important for MCM loading, but not for subsequent replication. We used these structures together with single-particle electron microscopy to generate three-dimensional models of MCM complexes. These show that Cdt1 stabilizes MCM in a left-handed spiral open at the Mcm2-5 gate. We propose that Cdt1 acts as a brace, holding MCM open for DNA entry and bound to ATP until ORC-Cdc6 triggers ATP hydrolysis by MCM, promoting both Cdt1 ejection and MCM ring closure.

Cdt1 stabilizes an open MCM ring for helicase loading.,Frigola J, He J, Kinkelin K, Pye VE, Renault L, Douglas ME, Remus D, Cherepanov P, Costa A, Diffley JFX Nat Commun. 2017 Jun 23;8:15720. doi: 10.1038/ncomms15720. PMID:28643783^[8]

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

References

↑ Jacobson MD, Munoz CX, Knox KS, Williams BE, Lu LL, Cross FR, Vallen EA. Mutations in SID2, a novel gene in Saccharomyces cerevisiae, cause synthetic lethality with sic1 deletion and may cause a defect during S phase. Genetics. 2001 Sep;159(1):17-33. PMID:11560884
↑ Devault A, Vallen EA, Yuan T, Green S, Bensimon A, Schwob E. Identification of Tah11/Sid2 as the ortholog of the replication licensing factor Cdt1 in Saccharomyces cerevisiae. Curr Biol. 2002 Apr 16;12(8):689-94. PMID:11967159
↑ Randell JC, Bowers JL, Rodriguez HK, Bell SP. Sequential ATP hydrolysis by Cdc6 and ORC directs loading of the Mcm2-7 helicase. Mol Cell. 2006 Jan 6;21(1):29-39. PMID:16387651 doi:https://dx.doi.org/10.1016/j.molcel.2005.11.023
↑ Kawasaki Y, Kim HD, Kojima A, Seki T, Sugino A. Reconstitution of Saccharomyces cerevisiae prereplicative complex assembly in vitro. Genes Cells. 2006 Jul;11(7):745-56. PMID:16824194 doi:https://dx.doi.org/10.1111/j.1365-2443.2006.00975.x
↑ Asano T, Makise M, Takehara M, Mizushima T. Interaction between ORC and Cdt1p of Saccharomyces cerevisiae. FEMS Yeast Res. 2007 Dec;7(8):1256-62. Epub 2007 Sep 6. PMID:17825064 doi:https://dx.doi.org/10.1111/j.1567-1364.2007.00299.x
↑ Chen S, de Vries MA, Bell SP. Orc6 is required for dynamic recruitment of Cdt1 during repeated Mcm2-7 loading. Genes Dev. 2007 Nov 15;21(22):2897-907. PMID:18006685 doi:https://dx.doi.org/10.1101/gad.1596807
↑ Remus D, Beuron F, Tolun G, Griffith JD, Morris EP, Diffley JF. Concerted loading of Mcm2-7 double hexamers around DNA during DNA replication origin licensing. Cell. 2009 Nov 13;139(4):719-30. doi: 10.1016/j.cell.2009.10.015. Epub 2009 Nov, 5. PMID:19896182 doi:https://dx.doi.org/10.1016/j.cell.2009.10.015
↑ Frigola J, He J, Kinkelin K, Pye VE, Renault L, Douglas ME, Remus D, Cherepanov P, Costa A, Diffley JFX. Cdt1 stabilizes an open MCM ring for helicase loading. Nat Commun. 2017 Jun 23;8:15720. doi: 10.1038/ncomms15720. PMID:28643783 doi:https://dx.doi.org/10.1038/ncomms15720

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OCA

[1] Jacobson MD, Munoz CX, Knox KS, Williams BE, Lu LL, Cross FR, Vallen EA. Mutations in SID2, a novel gene in Saccharomyces cerevisiae, cause synthetic lethality with sic1 deletion and may cause a defect during S phase. Genetics. 2001 Sep;159(1):17-33. PMID:11560884

[2] Devault A, Vallen EA, Yuan T, Green S, Bensimon A, Schwob E. Identification of Tah11/Sid2 as the ortholog of the replication licensing factor Cdt1 in Saccharomyces cerevisiae. Curr Biol. 2002 Apr 16;12(8):689-94. PMID:11967159

[3] Randell JC, Bowers JL, Rodriguez HK, Bell SP. Sequential ATP hydrolysis by Cdc6 and ORC directs loading of the Mcm2-7 helicase. Mol Cell. 2006 Jan 6;21(1):29-39. PMID:16387651 doi:https://dx.doi.org/10.1016/j.molcel.2005.11.023

[4] Kawasaki Y, Kim HD, Kojima A, Seki T, Sugino A. Reconstitution of Saccharomyces cerevisiae prereplicative complex assembly in vitro. Genes Cells. 2006 Jul;11(7):745-56. PMID:16824194 doi:https://dx.doi.org/10.1111/j.1365-2443.2006.00975.x

[5] Asano T, Makise M, Takehara M, Mizushima T. Interaction between ORC and Cdt1p of Saccharomyces cerevisiae. FEMS Yeast Res. 2007 Dec;7(8):1256-62. Epub 2007 Sep 6. PMID:17825064 doi:https://dx.doi.org/10.1111/j.1567-1364.2007.00299.x

[6] Chen S, de Vries MA, Bell SP. Orc6 is required for dynamic recruitment of Cdt1 during repeated Mcm2-7 loading. Genes Dev. 2007 Nov 15;21(22):2897-907. PMID:18006685 doi:https://dx.doi.org/10.1101/gad.1596807

[7] Remus D, Beuron F, Tolun G, Griffith JD, Morris EP, Diffley JF. Concerted loading of Mcm2-7 double hexamers around DNA during DNA replication origin licensing. Cell. 2009 Nov 13;139(4):719-30. doi: 10.1016/j.cell.2009.10.015. Epub 2009 Nov, 5. PMID:19896182 doi:https://dx.doi.org/10.1016/j.cell.2009.10.015

[8] Frigola J, He J, Kinkelin K, Pye VE, Renault L, Douglas ME, Remus D, Cherepanov P, Costa A, Diffley JFX. Cdt1 stabilizes an open MCM ring for helicase loading. Nat Commun. 2017 Jun 23;8:15720. doi: 10.1038/ncomms15720. PMID:28643783 doi:https://dx.doi.org/10.1038/ncomms15720

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@@ Line 1: / Line 1: @@
 ==Crystal structure of yeast Cdt1 C-terminal domain==
-<StructureSection load='5meb' size='340' side='right' caption='[[5meb]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
+<StructureSection load='5meb' size='340' side='right'caption='[[5meb]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5meb]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MEB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5MEB FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5meb]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MEB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5MEB FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">TAH11, CDT1, SID2, YJR046W, J1641 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</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=5meb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5meb OCA], [https://pdbe.org/5meb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5meb RCSB], [https://www.ebi.ac.uk/pdbsum/5meb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5meb ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5meb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5meb OCA], [http://pdbe.org/5meb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5meb RCSB], [http://www.ebi.ac.uk/pdbsum/5meb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5meb ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/CDT1_YEAST CDT1_YEAST]] DNA replication licensing factor, required for pre-replication complex assembly. Faithful duplication of the genetic material requires 'once per cell cycle' DNA replication initiation and elongation. Central to this control is the tightly regulated formation of prereplicative complexes (preRCs) at future origins of DNA replication. Required for the recruitment of the MCM2-7 helicase complex to the replication origins.<ref>PMID:11560884</ref> <ref>PMID:11967159</ref> <ref>PMID:16387651</ref> <ref>PMID:16824194</ref> <ref>PMID:17825064</ref> <ref>PMID:18006685</ref> <ref>PMID:19896182</ref>
+[https://www.uniprot.org/uniprot/CDT1_YEAST CDT1_YEAST] DNA replication licensing factor, required for pre-replication complex assembly. Faithful duplication of the genetic material requires 'once per cell cycle' DNA replication initiation and elongation. Central to this control is the tightly regulated formation of prereplicative complexes (preRCs) at future origins of DNA replication. Required for the recruitment of the MCM2-7 helicase complex to the replication origins.<ref>PMID:11560884</ref> <ref>PMID:11967159</ref> <ref>PMID:16387651</ref> <ref>PMID:16824194</ref> <ref>PMID:17825064</ref> <ref>PMID:18006685</ref> <ref>PMID:19896182</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 24: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Atcc 18824]]
+[[Category: Large Structures]]
-[[Category: Cherepanov, P]]
+[[Category: Saccharomyces cerevisiae]]
-[[Category: Diffley, J F.X]]
+[[Category: Cherepanov P]]
-[[Category: Frigola, J]]
+[[Category: Diffley JFX]]
-[[Category: Pye, V E]]
+[[Category: Frigola J]]
-[[Category: Cdt1]]
+[[Category: Pye VE]]
-[[Category: Cell cycle]]
-[[Category: Dna replication]]
-[[Category: Mcm]]
-[[Category: Winged helix]]
-[[Category: Yeast]]

5meb: Difference between revisions

Latest revision as of 18:40, 1 November 2023

Crystal structure of yeast Cdt1 C-terminal domain

Structural highlights

Function

Publication Abstract from PubMed

References

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