5jdk - Revision history

OCA at 09:17, 20 March 2024

OCA — Wed, 20 Mar 2024 09:17:28 GMT

←Older revision		Revision as of 09:17, 20 March 2024
Line 10:		Line 10:
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/SAP1_SCHPO SAP1_SCHPO] Binds to sequences required for mating-type switching. Makes a simultaneous contact with both the alpha and beta domains of the switch-activating site SAS1. Also binds to replication fork barrier 1 (RFB1) located within a 78 base pair sequence near the 3' end of the rRNA coding region. This leads to replication fork blockage. It binds the consensus sequence 5'-TA[AG]GCAGNTN[CT]AACG[AC]G-3'. Has a role in chromosome organization and integrity where it is involved in chromosome segregation. Has a role in sister chromatid cohesion and condensation.		[https://www.uniprot.org/uniprot/SAP1_SCHPO SAP1_SCHPO] Binds to sequences required for mating-type switching. Makes a simultaneous contact with both the alpha and beta domains of the switch-activating site SAS1. Also binds to replication fork barrier 1 (RFB1) located within a 78 base pair sequence near the 3' end of the rRNA coding region. This leads to replication fork blockage. It binds the consensus sequence 5'-TA[AG]GCAGNTN[CT]AACG[AC]G-3'. Has a role in chromosome organization and integrity where it is involved in chromosome segregation. Has a role in sister chromatid cohesion and condensation.
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	A central step in the initiation of chromosomal DNA replication in eukaryotes is the assembly of pre-replicative complex (pre-RC) at late M and early G1 phase of the cell cycles. Since 1973, four proteins or protein complexes, including cell division control protein 6 (Cdc6)/Cdc18, minichromosome maintenance protein complex, origin recognition complex (ORC), and Cdt1, are known components of the pre-RC. Previously, we reported that a non-ORC protein binds to the essential element Delta9 of the Schizosaccharomyces pombe DNA-replication origin ARS3001. In this study, we identified that the non-ORC protein is Sap1. Like ORC, Sap1 binds to DNA origins during cell growth cycles. But unlike ORC, which binds to asymmetric AT-rich sequences through its nine AT-hook motifs, Sap1 preferentially binds to a DNA sequence of 5'-(A/T) n (C/G)(A/T)9-10(G/C)(A/T) n -3' (n >/= 1). We also found that Sap1 and ORC physically interact. We further demonstrated that Sap1 is required for the assembly of the pre-RC because of its essential role in recruiting Cdc18 to DNA origins. Thus, we conclude that Sap1 is a replication-initiation factor that directly participates in the assembly of the pre-RC. DNA-replication origins in fission yeast are defined by possessing two essential elements with one bound by ORC and the other by Sap1.
-
-	Sap1 is a replication-initiation factor essential for the assembly of pre-replicative complex in the fission yeast Schizosaccharomyces pombe.,Guan L, He P, Yang F, Zhang Y, Hu Y, Ding J, Hua Y, Zhang Y, Ye Q, Hu J, Wang T, Jin C, Kong D J Biol Chem. 2017 Apr 14;292(15):6056-6075. doi: 10.1074/jbc.M116.767806. Epub, 2017 Feb 21. PMID:28223353<ref>PMID:28223353</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 5jdk" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 11:00, 6 September 2023

OCA — Wed, 06 Sep 2023 11:00:18 GMT

←Older revision		Revision as of 11:00, 6 September 2023
Line 1:		Line 1:

	==Crystal structure of the DNA binding domain of Sap1 in fission yeast S.pombe==		==Crystal structure of the DNA binding domain of Sap1 in fission yeast S.pombe==
-	<StructureSection load='5jdk' size='340' side='right' caption='[[5jdk]], [[Resolution\|resolution]] 1.00Å' scene=''>	+	<StructureSection load='5jdk' size='340' side='right'caption='[[5jdk]], [[Resolution\|resolution]] 1.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5jdk]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Fission_yeast Fission yeast~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JDK OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5JDK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5jdk]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Schizosaccharomyces_pombe_972h- Schizosaccharomyces pombe 972h-]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JDK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5JDK 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>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 0.998Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~sap1, SPCC1672.02c ([http~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=284812 Fission yeast])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></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=5jdk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jdk OCA], [~~http~~://pdbe.org/5jdk PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5jdk RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5jdk PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5jdk ProSAT]</span></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=5jdk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jdk OCA], [https://pdbe.org/5jdk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5jdk RCSB], [https://www.ebi.ac.uk/pdbsum/5jdk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5jdk ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/SAP1_SCHPO SAP1_SCHPO]] Binds to sequences required for mating-type switching. Makes a simultaneous contact with both the alpha and beta domains of the switch-activating site SAS1. Also binds to replication fork barrier 1 (RFB1) located within a 78 base pair sequence near the 3' end of the rRNA coding region. This leads to replication fork blockage. It binds the consensus sequence 5'-TA[AG]GCAGNTN[CT]AACG[AC]G-3'. Has a role in chromosome organization and integrity where it is involved in chromosome segregation. Has a role in sister chromatid cohesion and condensation.	+	[https://www.uniprot.org/uniprot/SAP1_SCHPO SAP1_SCHPO] Binds to sequences required for mating-type switching. Makes a simultaneous contact with both the alpha and beta domains of the switch-activating site SAS1. Also binds to replication fork barrier 1 (RFB1) located within a 78 base pair sequence near the 3' end of the rRNA coding region. This leads to replication fork blockage. It binds the consensus sequence 5'-TA[AG]GCAGNTN[CT]AACG[AC]G-3'. Has a role in chromosome organization and integrity where it is involved in chromosome segregation. Has a role in sister chromatid cohesion and condensation.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Fission yeast~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~He, P]]~~	+	[[Category: Schizosaccharomyces pombe 972h-]]
-	~~[[Category: Wang, T]]~~	+	[[Category: He P]]
-	~~[[Category: Alpha~~-~~helix~~]]	+	[[Category: Wang T]]
-	[[Category: ~~Dna binding protein~~]]	+
-	[[Category: ~~Dna replication~~]]	+

OCA at 20:37, 24 January 2018

OCA — Wed, 24 Jan 2018 20:37:29 GMT

←Older revision		Revision as of 20:37, 24 January 2018
Line 3:		Line 3:
	<StructureSection load='5jdk' size='340' side='right' caption='[[5jdk]], [[Resolution\|resolution]] 1.00Å' scene=''>		<StructureSection load='5jdk' size='340' side='right' caption='[[5jdk]], [[Resolution\|resolution]] 1.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5jdk]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JDK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JDK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5jdk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Fission_yeast Fission yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JDK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JDK 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>		</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='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">sap1, SPCC1672.02c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=284812 Fission yeast])</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=5jdk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jdk OCA], [http://pdbe.org/5jdk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jdk RCSB], [http://www.ebi.ac.uk/pdbsum/5jdk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jdk 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=5jdk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jdk OCA], [http://pdbe.org/5jdk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jdk RCSB], [http://www.ebi.ac.uk/pdbsum/5jdk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jdk ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/SAP1_SCHPO SAP1_SCHPO]] Binds to sequences required for mating-type switching. Makes a simultaneous contact with both the alpha and beta domains of the switch-activating site SAS1. Also binds to replication fork barrier 1 (RFB1) located within a 78 base pair sequence near the 3' end of the rRNA coding region. This leads to replication fork blockage. It binds the consensus sequence 5'-TA[AG]GCAGNTN[CT]AACG[AC]G-3'. Has a role in chromosome organization and integrity where it is involved in chromosome segregation. Has a role in sister chromatid cohesion and condensation.		[[http://www.uniprot.org/uniprot/SAP1_SCHPO SAP1_SCHPO]] Binds to sequences required for mating-type switching. Makes a simultaneous contact with both the alpha and beta domains of the switch-activating site SAS1. Also binds to replication fork barrier 1 (RFB1) located within a 78 base pair sequence near the 3' end of the rRNA coding region. This leads to replication fork blockage. It binds the consensus sequence 5'-TA[AG]GCAGNTN[CT]AACG[AC]G-3'. Has a role in chromosome organization and integrity where it is involved in chromosome segregation. Has a role in sister chromatid cohesion and condensation.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	A central step in the initiation of chromosomal DNA replication in eukaryotes is the assembly of pre-replicative complex (pre-RC) at late M and early G1 phase of the cell cycles. Since 1973, four proteins or protein complexes, including cell division control protein 6 (Cdc6)/Cdc18, minichromosome maintenance protein complex, origin recognition complex (ORC), and Cdt1, are known components of the pre-RC. Previously, we reported that a non-ORC protein binds to the essential element Delta9 of the Schizosaccharomyces pombe DNA-replication origin ARS3001. In this study, we identified that the non-ORC protein is Sap1. Like ORC, Sap1 binds to DNA origins during cell growth cycles. But unlike ORC, which binds to asymmetric AT-rich sequences through its nine AT-hook motifs, Sap1 preferentially binds to a DNA sequence of 5'-(A/T) n (C/G)(A/T)9-10(G/C)(A/T) n -3' (n >/= 1). We also found that Sap1 and ORC physically interact. We further demonstrated that Sap1 is required for the assembly of the pre-RC because of its essential role in recruiting Cdc18 to DNA origins. Thus, we conclude that Sap1 is a replication-initiation factor that directly participates in the assembly of the pre-RC. DNA-replication origins in fission yeast are defined by possessing two essential elements with one bound by ORC and the other by Sap1.
		+
		+	Sap1 is a replication-initiation factor essential for the assembly of pre-replicative complex in the fission yeast Schizosaccharomyces pombe.,Guan L, He P, Yang F, Zhang Y, Hu Y, Ding J, Hua Y, Zhang Y, Ye Q, Hu J, Wang T, Jin C, Kong D J Biol Chem. 2017 Apr 14;292(15):6056-6075. doi: 10.1074/jbc.M116.767806. Epub, 2017 Feb 21. PMID:28223353<ref>PMID:28223353</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5jdk" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Fission yeast]]
	[[Category: He, P]]		[[Category: He, P]]
	[[Category: Wang, T]]		[[Category: Wang, T]]

OCA at 01:35, 11 March 2017

OCA — Sat, 11 Mar 2017 01:35:28 GMT

←Older revision		Revision as of 01:35, 11 March 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5jdk is ~~ON HOLD~~ ~~until Paper Publication~~	+	==Crystal structure of the DNA binding domain of Sap1 in fission yeast S.pombe==
-		+	<StructureSection load='5jdk' size='340' side='right' caption='[[5jdk]], [[Resolution\|resolution]] 1.00Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5jdk]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JDK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JDK FirstGlance]. <br>
-	~~Description~~:	+	</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>
-	[[Category: ~~Unreleased Structures~~]]	+	<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=5jdk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jdk OCA], [http://pdbe.org/5jdk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jdk RCSB], [http://www.ebi.ac.uk/pdbsum/5jdk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jdk ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/SAP1_SCHPO SAP1_SCHPO]] Binds to sequences required for mating-type switching. Makes a simultaneous contact with both the alpha and beta domains of the switch-activating site SAS1. Also binds to replication fork barrier 1 (RFB1) located within a 78 base pair sequence near the 3' end of the rRNA coding region. This leads to replication fork blockage. It binds the consensus sequence 5'-TA[AG]GCAGNTN[CT]AACG[AC]G-3'. Has a role in chromosome organization and integrity where it is involved in chromosome segregation. Has a role in sister chromatid cohesion and condensation.
		+	__TOC__
		+	</StructureSection>
		+	[[Category: He, P]]
		+	[[Category: Wang, T]]
		+	[[Category: Alpha-helix]]
		+	[[Category: Dna binding protein]]
		+	[[Category: Dna replication]]

OCA at 11:53, 4 January 2017

OCA — Wed, 04 Jan 2017 11:53:59 GMT

←Older revision		Revision as of 11:53, 4 January 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5jdk is ON HOLD	+	The entry 5jdk is ON HOLD until Paper Publication

	Authors:		Authors:

OCA at 15:18, 15 May 2016

OCA — Sun, 15 May 2016 15:18:47 GMT

←Older revision		Revision as of 15:18, 15 May 2016
Line 3:		Line 3:
	The entry 5jdk is ON HOLD		The entry 5jdk is ON HOLD

-	Authors: ~~He, P., Wang, T.~~	+	Authors:

	Description:		Description:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: He, P]]
-	[[Category: Wang, T]]

OCA: Protected "5jdk" [edit=sysop:move=sysop]

OCA — Wed, 11 May 2016 01:53:58 GMT

Protected "5jdk" [edit=sysop:move=sysop]

←Older revision

Revision as of 01:53, 11 May 2016

OCA: New page: '''Unreleased structure''' The entry 5jdk is ON HOLD Authors: He, P., Wang, T. Description: Category: Unreleased Structures Category: He, P Category: Wang, T

OCA — Wed, 11 May 2016 01:53:56 GMT

New page: '''Unreleased structure''' The entry 5jdk is ON HOLD Authors: He, P., Wang, T. Description: Category: Unreleased Structures Category: He, P Category: Wang, T

New page

'''Unreleased structure'''

The entry 5jdk is ON HOLD

Authors: He, P., Wang, T.

Description:
[[Category: Unreleased Structures]]
[[Category: He, P]]
[[Category: Wang, T]]