5omd

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of S. cerevisiae Ddc2 N-terminal coiled-coil domain

Structural highlights

5omd is a 1 chain structure with sequence from 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 2.1Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

LCD1_YEAST Forms a complex with the serine/threonine kinase MEC1 which activates checkpoint signaling upon genotoxic stresses. The MEC1-LCD1 complex is recruited by the single-strand-binding protein complex RPA to DNA lesions in order to initiate the DNA repair by homologous recombination, after the MRX-complex and TEL1 are displaced. Required for the recruitment of MEC1 to DNA lesions, the activation of CHK1 and RAD53 kinases and phosphorylation of RAD9 in response to DNA damage. Required for cell growth and meiotic recombination.^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8] ^[9]

Publication Abstract from PubMed

Mec1-Ddc2 (ATR-ATRIP) is a key DNA-damage-sensing kinase that is recruited through the single-stranded (ss) DNA-binding replication protein A (RPA) to initiate the DNA damage checkpoint response. Activation of ATR-ATRIP in the absence of DNA damage is lethal. Therefore, it is important that damage-specific recruitment precedes kinase activation, which is achieved at least in part by Mec1-Ddc2 homodimerization. Here, we report a structural, biochemical, and functional characterization of the yeast Mec1-Ddc2-RPA assembly. High-resolution co-crystal structures of Ddc2-Rfa1 and Ddc2-Rfa1-t11 (K45E mutant) N termini and of the Ddc2 coiled-coil domain (CCD) provide insight into Mec1-Ddc2 homodimerization and damage-site targeting. Based on our structural and functional findings, we present a Mec1-Ddc2-RPA-ssDNA composite structural model. By way of validation, we show that RPA-dependent recruitment of Mec1-Ddc2 is crucial for maintaining its homodimeric state at ssDNA and that Ddc2's recruitment domain and CCD are important for Mec1-dependent survival of UV-light-induced DNA damage.

Structural Basis of Mec1-Ddc2-RPA Assembly and Activation on Single-Stranded DNA at Sites of Damage.,Deshpande I, Seeber A, Shimada K, Keusch JJ, Gut H, Gasser SM Mol Cell. 2017 Oct 19;68(2):431-445.e5. doi: 10.1016/j.molcel.2017.09.019. Epub, 2017 Oct 12. PMID:29033322^[10]

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

References

↑ Paciotti V, Clerici M, Lucchini G, Longhese MP. The checkpoint protein Ddc2, functionally related to S. pombe Rad26, interacts with Mec1 and is regulated by Mec1-dependent phosphorylation in budding yeast. Genes Dev. 2000 Aug 15;14(16):2046-59. PMID:10950868
↑ Rouse J, Jackson SP. LCD1: an essential gene involved in checkpoint control and regulation of the MEC1 signalling pathway in Saccharomyces cerevisiae. EMBO J. 2000 Nov 1;19(21):5801-12. PMID:11060031 doi:http://dx.doi.org/10.1093/emboj/19.21.5801
↑ Wakayama T, Kondo T, Ando S, Matsumoto K, Sugimoto K. Pie1, a protein interacting with Mec1, controls cell growth and checkpoint responses in Saccharomyces cerevisiae. Mol Cell Biol. 2001 Feb;21(3):755-64. PMID:11154263 doi:http://dx.doi.org/10.1128/MCB.21.3.755-764.2001
↑ Clerici M, Paciotti V, Baldo V, Romano M, Lucchini G, Longhese MP. Hyperactivation of the yeast DNA damage checkpoint by TEL1 and DDC2 overexpression. EMBO J. 2001 Nov 15;20(22):6485-98. PMID:11707419 doi:http://dx.doi.org/10.1093/emboj/20.22.6485
↑ Rouse J, Jackson SP. Lcd1p recruits Mec1p to DNA lesions in vitro and in vivo. Mol Cell. 2002 Apr;9(4):857-69. PMID:11983176
↑ Enomoto S, Glowczewski L, Berman J. MEC3, MEC1, and DDC2 are essential components of a telomere checkpoint pathway required for cell cycle arrest during senescence in Saccharomyces cerevisiae. Mol Biol Cell. 2002 Aug;13(8):2626-38. PMID:12181334 doi:http://dx.doi.org/10.1091/mbc.02-02-0012
↑ Lisby M, Barlow JH, Burgess RC, Rothstein R. Choreography of the DNA damage response: spatiotemporal relationships among checkpoint and repair proteins. Cell. 2004 Sep 17;118(6):699-713. PMID:15369670 doi:http://dx.doi.org/10.1016/j.cell.2004.08.015
↑ Nakada D, Hirano Y, Tanaka Y, Sugimoto K. Role of the C terminus of Mec1 checkpoint kinase in its localization to sites of DNA damage. Mol Biol Cell. 2005 Nov;16(11):5227-35. Epub 2005 Sep 7. PMID:16148046 doi:http://dx.doi.org/E05-05-0405
↑ Ma JL, Lee SJ, Duong JK, Stern DF. Activation of the checkpoint kinase Rad53 by the phosphatidyl inositol kinase-like kinase Mec1. J Biol Chem. 2006 Feb 17;281(7):3954-63. Epub 2005 Dec 19. PMID:16365046 doi:http://dx.doi.org/M507508200
↑ Deshpande I, Seeber A, Shimada K, Keusch JJ, Gut H, Gasser SM. Structural Basis of Mec1-Ddc2-RPA Assembly and Activation on Single-Stranded DNA at Sites of Damage. Mol Cell. 2017 Oct 19;68(2):431-445.e5. doi: 10.1016/j.molcel.2017.09.019. Epub, 2017 Oct 12. PMID:29033322 doi:http://dx.doi.org/10.1016/j.molcel.2017.09.019

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5omd"

@@ Line 3: / Line 3: @@
 <StructureSection load='5omd' size='340' side='right'caption='[[5omd]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5omd]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OMD OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5OMD FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5omd]] is a 1 chain structure with sequence from [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=5OMD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5OMD FirstGlance]. <br>
-</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5omd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5omd OCA], [http://pdbe.org/5omd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5omd RCSB], [http://www.ebi.ac.uk/pdbsum/5omd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5omd ProSAT]</span></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]] 2.1&#8491;</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=5omd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5omd OCA], [https://pdbe.org/5omd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5omd RCSB], [https://www.ebi.ac.uk/pdbsum/5omd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5omd ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/LCD1_YEAST LCD1_YEAST]] Forms a complex with the serine/threonine kinase MEC1 which activates checkpoint signaling upon genotoxic stresses. The MEC1-LCD1 complex is recruited by the single-strand-binding protein complex RPA to DNA lesions in order to initiate the DNA repair by homologous recombination, after the MRX-complex and TEL1 are displaced. Required for the recruitment of MEC1 to DNA lesions, the activation of CHK1 and RAD53 kinases and phosphorylation of RAD9 in response to DNA damage. Required for cell growth and meiotic recombination.<ref>PMID:10950868</ref> <ref>PMID:11060031</ref> <ref>PMID:11154263</ref> <ref>PMID:11707419</ref> <ref>PMID:11983176</ref> <ref>PMID:12181334</ref> <ref>PMID:15369670</ref> <ref>PMID:16148046</ref> <ref>PMID:16365046</ref>
+[https://www.uniprot.org/uniprot/LCD1_YEAST LCD1_YEAST] Forms a complex with the serine/threonine kinase MEC1 which activates checkpoint signaling upon genotoxic stresses. The MEC1-LCD1 complex is recruited by the single-strand-binding protein complex RPA to DNA lesions in order to initiate the DNA repair by homologous recombination, after the MRX-complex and TEL1 are displaced. Required for the recruitment of MEC1 to DNA lesions, the activation of CHK1 and RAD53 kinases and phosphorylation of RAD9 in response to DNA damage. Required for cell growth and meiotic recombination.<ref>PMID:10950868</ref> <ref>PMID:11060031</ref> <ref>PMID:11154263</ref> <ref>PMID:11707419</ref> <ref>PMID:11983176</ref> <ref>PMID:12181334</ref> <ref>PMID:15369670</ref> <ref>PMID:16148046</ref> <ref>PMID:16365046</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 25: / Line 26: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Deshpande, I]]
+[[Category: Saccharomyces cerevisiae S288C]]
-[[Category: Gasser, S M]]
+[[Category: Deshpande I]]
-[[Category: Gut, H]]
+[[Category: Gasser SM]]
-[[Category: Keusch, J J]]
+[[Category: Gut H]]
-[[Category: Seeber, A]]
+[[Category: Keusch JJ]]
-[[Category: Shimada, K]]
+[[Category: Seeber A]]
-[[Category: Coiled-coil]]
+[[Category: Shimada K]]
-[[Category: Dimerization]]
-[[Category: Protein binding]]

5omd

From Proteopedia

Current revision

Crystal structure of S. cerevisiae Ddc2 N-terminal coiled-coil domain

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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