5t2s: Difference between revisions

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'''Unreleased structure'''


The entry 5t2s is ON HOLD until Paper Publication
==Structure of the FHA1 domain of Rad53 bound simultaneously to the BRCT domain of Dbf4 and a phosphopeptide.==
<StructureSection load='5t2s' size='340' side='right' caption='[[5t2s]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5t2s]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5T2S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5T2S FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=TPO:PHOSPHOTHREONINE'>TPO</scene></td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5t2f|5t2f]]</td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Dual-specificity_kinase Dual-specificity kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.12.1 2.7.12.1] </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=5t2s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t2s OCA], [http://pdbe.org/5t2s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5t2s RCSB], [http://www.ebi.ac.uk/pdbsum/5t2s PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5t2s ProSAT]</span></td></tr>
</table>
== Function ==
[[http://www.uniprot.org/uniprot/DBF4_YEAST DBF4_YEAST]] Regulatory subunit of the CDC7-DBF4 kinase, also called DBF4-dependent kinase (DDK), which is involved in cell cycle regulation of premitotic and premeiotic chromosome replication and in chromosome segregation. DDK plays an essential role in initiating DNA replication at replication origins by phosphorylating the MCM2 and MCM4 subunits of the MCM2-7 helicase complex. DBF4 recruits the catalytic subunit CDC7 to MCM2 and to origins of replication. DDK has also postreplicative functions in meiosis. DDK phosphorylates the meiosis-specific double-strand break protein MER2 for initiation of meiotic recombination. Interacts with CDC5 during meiosis to promote double-strand breaks and monopolar spindle orientation. Inhibits CDC5 activity during mitosis through direct binding to its PBD.<ref>PMID:8066465</ref> <ref>PMID:12441400</ref> <ref>PMID:16319063</ref> <ref>PMID:17018296</ref> <ref>PMID:19013276</ref> <ref>PMID:18245450</ref> <ref>PMID:19692334</ref> <ref>PMID:19478884</ref> <ref>PMID:20436286</ref> <ref>PMID:21036905</ref> <ref>PMID:20170732</ref> <ref>PMID:20054399</ref>  
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Forkhead-associated (FHA) domains are phosphopeptide recognition modules found in many signaling proteins. The Saccharomyces cerevisiae protein kinase Rad53 is a key regulator of the DNA damage checkpoint and uses its two FHA domains to interact with multiple binding partners during the checkpoint response. One of these binding partners is the Dbf4-dependent kinase (DDK), a heterodimer composed of the Cdc7 kinase and its regulatory subunit Dbf4. Binding of Rad53 to DDK, through its N-terminal FHA (FHA1) domain, ultimately inhibits DDK kinase activity, thereby preventing firing of late origins. We have previously found that the FHA1 domain of Rad53 binds simultaneously to Dbf4 and a phosphoepitope, suggesting that this domain functions as an 'AND' logic gate. Here, we present the crystal structures of the FHA1 domain of Rad53 bound to Dbf4, in the presence and absence of a Cdc7 phosphorylated peptide. Our results reveal how the FHA1 uses a canonical binding interface to recognize the Cdc7 phosphopeptide and a non-canonical interface to bind Dbf4. Based on these data we propose a mechanism to explain how Rad53 enhances the specificity of FHA1-mediated transient interactions.


Authors: Guarne, A., Almawi, A., Matthews, L.
'AND' logic gates at work: Crystal structure of Rad53 bound to Dbf4 and Cdc7.,Almawi AW, Matthews LA, Larasati, Myrox P, Boulton S, Lai C, Moraes T, Melacini G, Ghirlando R, Duncker BP, Guarne A Sci Rep. 2016 Sep 29;6:34237. doi: 10.1038/srep34237. PMID:27681475<ref>PMID:27681475</ref>


Description: Structure of the FHA1 domain of Rad53 bound simultaneously to the BRCT domain of Dbf4 and a phosphopeptide.
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
[[Category: Unreleased Structures]]
</div>
<div class="pdbe-citations 5t2s" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Dual-specificity kinase]]
[[Category: Almawi, A]]
[[Category: Guarne, A]]
[[Category: Guarne, A]]
[[Category: Almawi, A]]
[[Category: Matthews, L]]
[[Category: Matthews, L]]
[[Category: Brct]]
[[Category: Cell cycle]]
[[Category: Fha]]
[[Category: Phosphopeptide]]
[[Category: Protein chimera]]

Revision as of 12:24, 19 October 2016

Structure of the FHA1 domain of Rad53 bound simultaneously to the BRCT domain of Dbf4 and a phosphopeptide.Structure of the FHA1 domain of Rad53 bound simultaneously to the BRCT domain of Dbf4 and a phosphopeptide.

Structural highlights

5t2s is a 4 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
NonStd Res:
Activity:Dual-specificity kinase, with EC number 2.7.12.1
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[DBF4_YEAST] Regulatory subunit of the CDC7-DBF4 kinase, also called DBF4-dependent kinase (DDK), which is involved in cell cycle regulation of premitotic and premeiotic chromosome replication and in chromosome segregation. DDK plays an essential role in initiating DNA replication at replication origins by phosphorylating the MCM2 and MCM4 subunits of the MCM2-7 helicase complex. DBF4 recruits the catalytic subunit CDC7 to MCM2 and to origins of replication. DDK has also postreplicative functions in meiosis. DDK phosphorylates the meiosis-specific double-strand break protein MER2 for initiation of meiotic recombination. Interacts with CDC5 during meiosis to promote double-strand breaks and monopolar spindle orientation. Inhibits CDC5 activity during mitosis through direct binding to its PBD.[1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12]

Publication Abstract from PubMed

Forkhead-associated (FHA) domains are phosphopeptide recognition modules found in many signaling proteins. The Saccharomyces cerevisiae protein kinase Rad53 is a key regulator of the DNA damage checkpoint and uses its two FHA domains to interact with multiple binding partners during the checkpoint response. One of these binding partners is the Dbf4-dependent kinase (DDK), a heterodimer composed of the Cdc7 kinase and its regulatory subunit Dbf4. Binding of Rad53 to DDK, through its N-terminal FHA (FHA1) domain, ultimately inhibits DDK kinase activity, thereby preventing firing of late origins. We have previously found that the FHA1 domain of Rad53 binds simultaneously to Dbf4 and a phosphoepitope, suggesting that this domain functions as an 'AND' logic gate. Here, we present the crystal structures of the FHA1 domain of Rad53 bound to Dbf4, in the presence and absence of a Cdc7 phosphorylated peptide. Our results reveal how the FHA1 uses a canonical binding interface to recognize the Cdc7 phosphopeptide and a non-canonical interface to bind Dbf4. Based on these data we propose a mechanism to explain how Rad53 enhances the specificity of FHA1-mediated transient interactions.

'AND' logic gates at work: Crystal structure of Rad53 bound to Dbf4 and Cdc7.,Almawi AW, Matthews LA, Larasati, Myrox P, Boulton S, Lai C, Moraes T, Melacini G, Ghirlando R, Duncker BP, Guarne A Sci Rep. 2016 Sep 29;6:34237. doi: 10.1038/srep34237. PMID:27681475[13]

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

References

  1. ↑ Dowell SJ, Romanowski P, Diffley JF. Interaction of Dbf4, the Cdc7 protein kinase regulatory subunit, with yeast replication origins in vivo. Science. 1994 Aug 26;265(5176):1243-6. PMID:8066465
  2. ↑ Duncker BP, Shimada K, Tsai-Pflugfelder M, Pasero P, Gasser SM. An N-terminal domain of Dbf4p mediates interaction with both origin recognition complex (ORC) and Rad53p and can deregulate late origin firing. Proc Natl Acad Sci U S A. 2002 Dec 10;99(25):16087-92. Epub 2002 Nov 19. PMID:12441400 doi:http://dx.doi.org/10.1073/pnas.252093999
  3. ↑ Valentin G, Schwob E, Della Seta F. Dual role of the Cdc7-regulatory protein Dbf4 during yeast meiosis. J Biol Chem. 2006 Feb 3;281(5):2828-34. Epub 2005 Nov 30. PMID:16319063 doi:http://dx.doi.org/10.1074/jbc.M510626200
  4. ↑ Sheu YJ, Stillman B. Cdc7-Dbf4 phosphorylates MCM proteins via a docking site-mediated mechanism to promote S phase progression. Mol Cell. 2006 Oct 6;24(1):101-13. PMID:17018296 doi:http://dx.doi.org/10.1016/j.molcel.2006.07.033
  5. ↑ Matos J, Lipp JJ, Bogdanova A, Guillot S, Okaz E, Junqueira M, Shevchenko A, Zachariae W. Dbf4-dependent CDC7 kinase links DNA replication to the segregation of homologous chromosomes in meiosis I. Cell. 2008 Nov 14;135(4):662-78. doi: 10.1016/j.cell.2008.10.026. PMID:19013276 doi:http://dx.doi.org/10.1016/j.cell.2008.10.026
  6. ↑ Wan L, Niu H, Futcher B, Zhang C, Shokat KM, Boulton SJ, Hollingsworth NM. Cdc28-Clb5 (CDK-S) and Cdc7-Dbf4 (DDK) collaborate to initiate meiotic recombination in yeast. Genes Dev. 2008 Feb 1;22(3):386-97. doi: 10.1101/gad.1626408. PMID:18245450 doi:http://dx.doi.org/10.1101/gad.1626408
  7. ↑ Bruck I, Kaplan D. Dbf4-Cdc7 phosphorylation of Mcm2 is required for cell growth. J Biol Chem. 2009 Oct 16;284(42):28823-31. doi: 10.1074/jbc.M109.039123. Epub, 2009 Aug 18. PMID:19692334 doi:http://dx.doi.org/10.1074/jbc.M109.039123
  8. ↑ Miller CT, Gabrielse C, Chen YC, Weinreich M. Cdc7p-Dbf4p regulates mitotic exit by inhibiting Polo kinase. PLoS Genet. 2009 May;5(5):e1000498. doi: 10.1371/journal.pgen.1000498. Epub 2009 , May 29. PMID:19478884 doi:http://dx.doi.org/10.1371/journal.pgen.1000498
  9. ↑ Jones DR, Prasad AA, Chan PK, Duncker BP. The Dbf4 motif C zinc finger promotes DNA replication and mediates resistance to genotoxic stress. Cell Cycle. 2010 May 15;9(10):2018-26. Epub 2010 May 15. PMID:20436286
  10. ↑ Chen YC, Weinreich M. Dbf4 regulates the Cdc5 Polo-like kinase through a distinct non-canonical binding interaction. J Biol Chem. 2010 Dec 31;285(53):41244-54. doi: 10.1074/jbc.M110.155242. Epub, 2010 Oct 29. PMID:21036905 doi:http://dx.doi.org/10.1074/jbc.M110.155242
  11. ↑ Kaplan DL, Bruck I. Methods to study kinase regulation of the replication fork helicase. Methods. 2010 Jul;51(3):358-62. doi: 10.1016/j.ymeth.2010.02.013. Epub 2010 Feb, 17. PMID:20170732 doi:http://dx.doi.org/10.1016/j.ymeth.2010.02.013
  12. ↑ Sheu YJ, Stillman B. The Dbf4-Cdc7 kinase promotes S phase by alleviating an inhibitory activity in Mcm4. Nature. 2010 Jan 7;463(7277):113-7. doi: 10.1038/nature08647. PMID:20054399 doi:http://dx.doi.org/10.1038/nature08647
  13. ↑ Almawi AW, Matthews LA, Larasati, Myrox P, Boulton S, Lai C, Moraes T, Melacini G, Ghirlando R, Duncker BP, Guarne A. 'AND' logic gates at work: Crystal structure of Rad53 bound to Dbf4 and Cdc7. Sci Rep. 2016 Sep 29;6:34237. doi: 10.1038/srep34237. PMID:27681475 doi:http://dx.doi.org/10.1038/srep34237

5t2s, resolution 2.40Å

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