6ya6: Difference between revisions

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<StructureSection load='6ya6' size='340' side='right'caption='[[6ya6]], [[Resolution|resolution]] 1.44&Aring;' scene=''>
<StructureSection load='6ya6' size='340' side='right'caption='[[6ya6]], [[Resolution|resolution]] 1.44&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[6ya6]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YA6 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6YA6 FirstGlance]. <br>
<table><tr><td colspan='2'>[[6ya6]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YA6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YA6 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0SX:8-CHLORO-2-[(2S)-PYRROLIDIN-2-YL][1]BENZOFURO[3,2-D]PYRIMIDIN-4(3H)-ONE'>0SX</scene>, <scene name='pdbligand=BO3:BORIC+ACID'>BO3</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.44&#8491;</td></tr>
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=SEP:PHOSPHOSERINE'>SEP</scene></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0SX:8-CHLORO-2-[(2S)-PYRROLIDIN-2-YL][1]BENZOFURO[3,2-D]PYRIMIDIN-4(3H)-ONE'>0SX</scene>, <scene name='pdbligand=BO3:BORIC+ACID'>BO3</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=SEP:PHOSPHOSERINE'>SEP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">CDC7, CDC7L1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), DBF4, ASK, DBF4A, ZDBF1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=6ya6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ya6 OCA], [https://pdbe.org/6ya6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ya6 RCSB], [https://www.ebi.ac.uk/pdbsum/6ya6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ya6 ProSAT]</span></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=6ya6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ya6 OCA], [http://pdbe.org/6ya6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ya6 RCSB], [http://www.ebi.ac.uk/pdbsum/6ya6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ya6 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/CDC7_HUMAN CDC7_HUMAN]] Seems to phosphorylate critical substrates that regulate the G1/S phase transition and/or DNA replication. Can phosphorylates MCM2 and MCM3.<ref>PMID:12065429</ref> [[http://www.uniprot.org/uniprot/DBF4A_HUMAN DBF4A_HUMAN]] Regulatory subunit for CDC7 which activates its kinase activity thereby playing a central role in DNA replication and cell proliferation. Required for progression of S phase. The complex CDC7-DBF4A selectively phosphorylates MCM2 subunit at 'Ser-40' and 'Ser-53' and then is involved in regulating the initiation of DNA replication during cell cycle.<ref>PMID:10373557</ref> <ref>PMID:10523313</ref> <ref>PMID:17062569</ref> 
[https://www.uniprot.org/uniprot/CDC7_HUMAN CDC7_HUMAN] Seems to phosphorylate critical substrates that regulate the G1/S phase transition and/or DNA replication. Can phosphorylates MCM2 and MCM3.<ref>PMID:12065429</ref>  
<div style="background-color:#fffaf0;">
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
== Publication Abstract from PubMed ==
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Human]]
[[Category: Homo sapiens]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Cherepanov, P]]
[[Category: Cherepanov P]]
[[Category: Dick, S D]]
[[Category: Dick SD]]
[[Category: Bivalent substrate]]
[[Category: Cdc7]]
[[Category: Cell cycle]]
[[Category: Dbf4]]
[[Category: Kinase]]
[[Category: Transferase]]

Revision as of 16:22, 24 January 2024

Minimal construct of Cdc7-Dbf4 bound to XL413Minimal construct of Cdc7-Dbf4 bound to XL413

Structural highlights

6ya6 is a 2 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.44Å
Ligands:, , , , , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

CDC7_HUMAN Seems to phosphorylate critical substrates that regulate the G1/S phase transition and/or DNA replication. Can phosphorylates MCM2 and MCM3.[1]

Publication Abstract from PubMed

CDC7 is an essential Ser/Thr kinase that acts upon the replicative helicase throughout the S phase of the cell cycle and is activated by DBF4. Here, we present crystal structures of a highly active human CDC7-DBF4 construct. The structures reveal a zinc-finger domain at the end of the kinase insert 2 that pins the CDC7 activation loop to motif M of DBF4 and the C lobe of CDC7. These interactions lead to ordering of the substrate-binding platform and full opening of the kinase active site. In a co-crystal structure with a mimic of MCM2 Ser40 phosphorylation target, the invariant CDC7 residues Arg373 and Arg380 engage phospho-Ser41 at substrate P+1 position, explaining the selectivity of the S-phase kinase for Ser/Thr residues followed by a pre-phosphorylated or an acidic residue. Our results clarify the role of DBF4 in activation of CDC7 and elucidate the structural basis for recognition of its preferred substrates.

Structural Basis for the Activation and Target Site Specificity of CDC7 Kinase.,Dick SD, Federico S, Hughes SM, Pye VE, O'Reilly N, Cherepanov P Structure. 2020 Jun 5. pii: S0969-2126(20)30179-9. doi:, 10.1016/j.str.2020.05.010. PMID:32521228[2]

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

References

  1. ↑ Montagnoli A, Bosotti R, Villa F, Rialland M, Brotherton D, Mercurio C, Berthelsen J, Santocanale C. Drf1, a novel regulatory subunit for human Cdc7 kinase. EMBO J. 2002 Jun 17;21(12):3171-81. PMID:12065429 doi:http://dx.doi.org/10.1093/emboj/cdf290
  2. ↑ Dick SD, Federico S, Hughes SM, Pye VE, O'Reilly N, Cherepanov P. Structural Basis for the Activation and Target Site Specificity of CDC7 Kinase. Structure. 2020 Jun 5. pii: S0969-2126(20)30179-9. doi:, 10.1016/j.str.2020.05.010. PMID:32521228 doi:http://dx.doi.org/10.1016/j.str.2020.05.010

6ya6, resolution 1.44Å

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