2qby: Difference between revisions

Latest revision as of 11:28, 30 August 2023

Crystal structure of a heterodimer of Cdc6/Orc1 initiators bound to origin DNA (from S. solfataricus)

Structural highlights

2qby is a 4 chain structure with sequence from Saccharolobus solfataricus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 3.35Å
Ligands:	ADP, K, MG, SPD
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

CDC61_SACS2 Involved in regulation of DNA replication. May play essential roles in origin recognition and cell cycle control of replication. Binds to DNA, with a preference for molecules that contain a bubble, a fork, or a tail. Inhibits the binding of the MCM helicase to the origin DNA and strongly inhibits its DNA helicase activity. Also regulates the DNA polymerase and the nuclease activities of PolB1. Stimulates the DNA-binding activity of Cdc6-3.[HAMAP-Rule:MF_01407]^[1] ^[2] ^[3] ^[4]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

The faithful duplication of genetic material depends on essential DNA replication initiation factors. Cellular initiators form higher-order assemblies on replication origins, using adenosine triphosphate (ATP) to locally remodel duplex DNA and facilitate proper loading of synthetic replisomal components. To better understand initiator function, we determined the 3.4 angstrom-resolution structure of an archaeal Cdc6/Orc1 heterodimer bound to origin DNA. The structure demonstrates that, in addition to conventional DNA binding elements, initiators use their AAA+ ATPase domains to recognize origin DNA. Together these interactions establish the polarity of initiator assembly on the origin and induce substantial distortions into origin DNA strands. Biochemical and comparative analyses indicate that AAA+/DNA contacts observed in the structure are dynamic and evolutionarily conserved, suggesting that the complex forms a core component of the basal initiation machinery.

Replication origin recognition and deformation by a heterodimeric archaeal Orc1 complex.,Dueber EL, Corn JE, Bell SD, Berger JM Science. 2007 Aug 31;317(5842):1210-3. PMID:17761879^[5]

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

References

↑ De Felice M, Esposito L, Rossi M, Pisani FM. Biochemical characterization of two Cdc6/ORC1-like proteins from the crenarchaeon Sulfolobus solfataricus. Extremophiles. 2006 Feb;10(1):61-70. Epub 2005 Sep 23. PMID:16179962 doi:https://dx.doi.org/10.1007/s00792-005-0473-0
↑ Jiang PX, Wang J, Feng Y, He ZG. Divergent functions of multiple eukaryote-like Orc1/Cdc6 proteins on modulating the loading of the MCM helicase onto the origins of the hyperthermophilic archaeon Sulfolobus solfataricus P2. Biochem Biophys Res Commun. 2007 Sep 28;361(3):651-8. Epub 2007 Jul 25. PMID:17673179 doi:https://dx.doi.org/10.1016/j.bbrc.2007.07.073
↑ Wang J, Jiang PX, Feng H, Feng Y, He ZG. Three eukaryote-like Orc1/Cdc6 proteins functionally interact and mutually regulate their activities of binding to the replication origin in the hyperthermophilic archaeon Sulfolobus solfataricus P2. Biochem Biophys Res Commun. 2007 Nov 9;363(1):63-70. Epub 2007 Aug 31. PMID:17825793 doi:https://dx.doi.org/10.1016/j.bbrc.2007.08.125
↑ Zhang L, Zhang L, Liu Y, Yang S, Gao C, Gong H, Feng Y, He ZG. Archaeal eukaryote-like Orc1/Cdc6 initiators physically interact with DNA polymerase B1 and regulate its functions. Proc Natl Acad Sci U S A. 2009 May 12;106(19):7792-7. doi:, 10.1073/pnas.0813056106. Epub 2009 Apr 29. PMID:19416914 doi:https://dx.doi.org/10.1073/pnas.0813056106
↑ Dueber EL, Corn JE, Bell SD, Berger JM. Replication origin recognition and deformation by a heterodimeric archaeal Orc1 complex. Science. 2007 Aug 31;317(5842):1210-3. PMID:17761879 doi:https://dx.doi.org/317/5842/1210

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OCA

[1] De Felice M, Esposito L, Rossi M, Pisani FM. Biochemical characterization of two Cdc6/ORC1-like proteins from the crenarchaeon Sulfolobus solfataricus. Extremophiles. 2006 Feb;10(1):61-70. Epub 2005 Sep 23. PMID:16179962 doi:https://dx.doi.org/10.1007/s00792-005-0473-0

[2] Jiang PX, Wang J, Feng Y, He ZG. Divergent functions of multiple eukaryote-like Orc1/Cdc6 proteins on modulating the loading of the MCM helicase onto the origins of the hyperthermophilic archaeon Sulfolobus solfataricus P2. Biochem Biophys Res Commun. 2007 Sep 28;361(3):651-8. Epub 2007 Jul 25. PMID:17673179 doi:https://dx.doi.org/10.1016/j.bbrc.2007.07.073

[3] Wang J, Jiang PX, Feng H, Feng Y, He ZG. Three eukaryote-like Orc1/Cdc6 proteins functionally interact and mutually regulate their activities of binding to the replication origin in the hyperthermophilic archaeon Sulfolobus solfataricus P2. Biochem Biophys Res Commun. 2007 Nov 9;363(1):63-70. Epub 2007 Aug 31. PMID:17825793 doi:https://dx.doi.org/10.1016/j.bbrc.2007.08.125

[4] Zhang L, Zhang L, Liu Y, Yang S, Gao C, Gong H, Feng Y, He ZG. Archaeal eukaryote-like Orc1/Cdc6 initiators physically interact with DNA polymerase B1 and regulate its functions. Proc Natl Acad Sci U S A. 2009 May 12;106(19):7792-7. doi:, 10.1073/pnas.0813056106. Epub 2009 Apr 29. PMID:19416914 doi:https://dx.doi.org/10.1073/pnas.0813056106

[5] Dueber EL, Corn JE, Bell SD, Berger JM. Replication origin recognition and deformation by a heterodimeric archaeal Orc1 complex. Science. 2007 Aug 31;317(5842):1210-3. PMID:17761879 doi:https://dx.doi.org/317/5842/1210

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[2]

[3]

[4]

[5]

@@ Line 3: / Line 3: @@
 <StructureSection load='2qby' size='340' side='right'caption='[[2qby]], [[Resolution|resolution]] 3.35&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2qby]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/'saccharolobus_solfataricus' 'saccharolobus solfataricus']. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QBY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QBY FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2qby]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharolobus_solfataricus Saccharolobus solfataricus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QBY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QBY FirstGlance]. <br>
-</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=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SPD:SPERMIDINE'>SPD</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]] 3.35&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">cdc6-1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2287 'Saccharolobus solfataricus']), cdc6-3 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2287 'Saccharolobus solfataricus'])</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=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SPD:SPERMIDINE'>SPD</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=2qby FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qby OCA], [https://pdbe.org/2qby PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2qby RCSB], [https://www.ebi.ac.uk/pdbsum/2qby PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2qby ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/CDC63_SULSO CDC63_SULSO]] Involved in regulation of DNA replication. May play essential roles in origin recognition and cell cycle control of replication. Binds to DNA, with a preference for molecules that contain a bubble, a fork, or a tail. Inhibits the binding of the MCM helicase to the origin DNA and inhibits its DNA helicase activity. Also regulates the DNA polymerase and the nuclease activities of PolB1. Inhibits the DNA-binding activity of Cdc6-1 and Cdc6-2.<ref>PMID:16179962</ref> <ref>PMID:17673179</ref> <ref>PMID:17825793</ref> <ref>PMID:19416914</ref>  [[https://www.uniprot.org/uniprot/CDC61_SULSO CDC61_SULSO]] Involved in regulation of DNA replication. May play essential roles in origin recognition and cell cycle control of replication. Binds to DNA, with a preference for molecules that contain a bubble, a fork, or a tail. Inhibits the binding of the MCM helicase to the origin DNA and strongly inhibits its DNA helicase activity. Also regulates the DNA polymerase and the nuclease activities of PolB1. Stimulates the DNA-binding activity of Cdc6-3.<ref>PMID:16179962</ref> <ref>PMID:17673179</ref> <ref>PMID:17825793</ref> <ref>PMID:19416914</ref>
+[https://www.uniprot.org/uniprot/CDC61_SACS2 CDC61_SACS2] Involved in regulation of DNA replication. May play essential roles in origin recognition and cell cycle control of replication. Binds to DNA, with a preference for molecules that contain a bubble, a fork, or a tail. Inhibits the binding of the MCM helicase to the origin DNA and strongly inhibits its DNA helicase activity. Also regulates the DNA polymerase and the nuclease activities of PolB1. Stimulates the DNA-binding activity of Cdc6-3.[HAMAP-Rule:MF_01407]<ref>PMID:16179962</ref> <ref>PMID:17673179</ref> <ref>PMID:17825793</ref> <ref>PMID:19416914</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 33: / Line 33: @@
 __TOC__
 </StructureSection>
+[[Category: Large Structures]]
 [[Category: Saccharolobus solfataricus]]
-[[Category: Large Structures]]
+[[Category: Bell SD]]
-[[Category: Bell, S D]]
+[[Category: Berger JM]]
-[[Category: Berger, J M]]
+[[Category: Corn JE]]
-[[Category: Corn, J E]]
+[[Category: Cunningham Dueber EL]]
-[[Category: Dueber, E L.Cunningham]]
-[[Category: Aaa+ atpase domain]]
-[[Category: Double helix]]
-[[Category: Helix-turn-helix]]
-[[Category: Protein-dna complex]]
-[[Category: Replication-dna complex]]
-[[Category: Winged-helix domain]]

2qby: Difference between revisions

Latest revision as of 11:28, 30 August 2023

Crystal structure of a heterodimer of Cdc6/Orc1 initiators bound to origin DNA (from S. solfataricus)

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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