5vbn - Revision history

OCA at 14:32, 6 March 2024

2024-03-06T14:32:05Z

←Older revision		Revision as of 14:32, 6 March 2024
Line 3:		Line 3:
	<StructureSection load='5vbn' size='340' side='right'caption='[[5vbn]], [[Resolution\|resolution]] 2.35Å' scene=''>		<StructureSection load='5vbn' size='340' side='right'caption='[[5vbn]], [[Resolution\|resolution]] 2.35Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5vbn]] is a 4 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=5VBN OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5VBN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5vbn]] is a 4 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=5VBN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5VBN FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.35Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>POLE2, DPE2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~9606 HUMAN]), POLE, POLE1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td~~><~~/tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7]~~ </~~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=5vbn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vbn OCA], [https://pdbe.org/5vbn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5vbn RCSB], [https://www.ebi.ac.uk/pdbsum/5vbn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5vbn 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=5vbn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vbn OCA], [~~http~~://pdbe.org/5vbn PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5vbn RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5vbn PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5vbn ProSAT]</span></td></tr>	+
	</table>		</table>
-	== Disease ==
-	[[http://www.uniprot.org/uniprot/DPOE1_HUMAN DPOE1_HUMAN]] Facial dysmorphism - immunodeficiency - livedo - short stature. Disease susceptibility is associated with variations affecting the gene represented in this entry. The disease is caused by mutations affecting the gene represented in this entry.
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/DPOE2_HUMAN DPOE2_HUMAN]] Participates in DNA repair and in chromosomal DNA replication. ~~[[http://www.uniprot.org/uniprot/DPOE1_HUMAN DPOE1_HUMAN]] Participates in DNA repair and in chromosomal DNA replication.~~	+	[https://www.uniprot.org/uniprot/DPOE2_HUMAN DPOE2_HUMAN] Participates in DNA repair and in chromosomal DNA replication.
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	The eukaryotic B-family DNA polymerases include four members, Polalpha, Poldelta, Pol, and Polzeta, which share common architectural features, such as the exonuclease/polymerase and C-terminal domains (CTDs) of catalytic subunits bound to indispensable B-subunits, which serve as scaffolds that mediate interactions with other components of the replication machinery. Crystal structures for the B-subunits of Polalpha and Poldelta/Polzeta have been reported; the former within the primosome and separately with CTD, and the latter with the N-terminal domain (NTD) of the C-subunit. Here we present the crystal structure of the human Pol B-subunit (p59) in complex with CTD of the catalytic subunit (p261C). The structure revealed a well-defined electron density for p261C and the phosphodiesterase (PDE) and oligonucleotide/oligosaccharide-binding domains of p59. However, electron density was missing for the p59 NTD and for the linker connecting it to the PDE domain. Similar to Polalpha, p261C contains a three-helix bundle in the middle and zinc-binding modules (Zn1 and Zn2) on each side. Intersubunit interactions involving 11 hydrogen bonds and numerous hydrophobic contacts account for stable complex formation with a buried surface area of 3094 A2 Comparative structural analysis of p59-p261C with the corresponding Polalpha complex revealed significant differences between the B-subunits and CTDs as well as their interaction interfaces. The B-subunit of Poldelta/Polzeta also substantially differs from B-subunits of either Polalpha or Pol. This work provides a structural basis to explain biochemical and genetic data on the importance of B-subunit integrity in replisome function in vivo.	+
-		+
-	Crystal structure of the human Pol B-subunit in complex with the C-terminal domain of the catalytic subunit.,Baranovskiy AG, Gu J, Babayeva ND, Kurinov I, Pavlov YI, Tahirov TH J Biol Chem. 2017 Jul 26. pii: jbc.M117.792705. doi: 10.1074/jbc.M117.792705. PMID:28747437<ref>PMID:28747437</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 5vbn" style="background-color:#fffaf0;"></div>~~	+

	==See Also==		==See Also==
	*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]		*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~DNA-directed DNA polymerase]]~~	+	[[Category: Homo sapiens]]
-	~~[[Category: Human~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Babayeva~~, N D~~]]	+	[[Category: Babayeva ND]]
-	[[Category: Baranovskiy~~, A G~~]]	+	[[Category: Baranovskiy AG]]
-	[[Category: Gu, J]]	+	[[Category: Gu J]]
-	[[Category: Suwa, Y]]	+	[[Category: Suwa Y]]
-	[[Category: Tahirov~~, T H]]~~	+	[[Category: Tahirov TH]]
-	~~[[Category: B-subunit]]~~	+
-	~~[[Category: Catalytic subunit]]~~	+
-	~~[[Category: Dna polymerase]]~~	+
-	~~[[Category: Dna polymerase epsilon]]~~	+
-	~~[[Category: Dna replication]]~~	+
-	~~[[Category: Polymerase]]~~	+
-	~~[[Category: Replication]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 09:35, 4 December 2019

2019-12-04T09:35:48Z

←Older revision		Revision as of 09:35, 4 December 2019
Line 1:		Line 1:

	==Crystal Structure of human DNA polymerase epsilon B-subunit in complex with C-terminal domain of catalytic subunit==		==Crystal Structure of human DNA polymerase epsilon B-subunit in complex with C-terminal domain of catalytic subunit==
-	<StructureSection load='5vbn' size='340' side='right' caption='[[5vbn]], [[Resolution\|resolution]] 2.35Å' scene=''>	+	<StructureSection load='5vbn' size='340' side='right'caption='[[5vbn]], [[Resolution\|resolution]] 2.35Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5vbn]] is a 4 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=5VBN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VBN FirstGlance]. <br>		<table><tr><td colspan='2'>[[5vbn]] is a 4 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=5VBN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VBN FirstGlance]. <br>
Line 22:		Line 22:
	</div>		</div>
	<div class="pdbe-citations 5vbn" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5vbn" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 28:		Line 31:
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Babayeva, N D]]		[[Category: Babayeva, N D]]
	[[Category: Baranovskiy, A G]]		[[Category: Baranovskiy, A G]]

OCA at 08:24, 10 October 2018

2018-10-10T08:24:48Z

←Older revision		Revision as of 08:24, 10 October 2018
Line 3:		Line 3:
	<StructureSection load='5vbn' size='340' side='right' caption='[[5vbn]], [[Resolution\|resolution]] 2.35Å' scene=''>		<StructureSection load='5vbn' size='340' side='right' caption='[[5vbn]], [[Resolution\|resolution]] 2.35Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5vbn]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VBN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VBN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5vbn]] is a 4 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=5VBN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VBN FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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">POLE2, DPE2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), POLE, POLE1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </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=5vbn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vbn OCA], [http://pdbe.org/5vbn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vbn RCSB], [http://www.ebi.ac.uk/pdbsum/5vbn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vbn 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=5vbn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vbn OCA], [http://pdbe.org/5vbn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vbn RCSB], [http://www.ebi.ac.uk/pdbsum/5vbn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vbn ProSAT]</span></td></tr>
Line 26:		Line 27:
	</StructureSection>		</StructureSection>
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
		+	[[Category: Human]]
	[[Category: Babayeva, N D]]		[[Category: Babayeva, N D]]
	[[Category: Baranovskiy, A G]]		[[Category: Baranovskiy, A G]]

OCA at 09:09, 9 August 2017

2017-08-09T09:09:09Z

←Older revision		Revision as of 09:09, 9 August 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5vbn is ~~ON HOLD~~	+	==Crystal Structure of human DNA polymerase epsilon B-subunit in complex with C-terminal domain of catalytic subunit==
		+	<StructureSection load='5vbn' size='340' side='right' caption='[[5vbn]], [[Resolution\|resolution]] 2.35Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5vbn]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VBN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VBN FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </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=5vbn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vbn OCA], [http://pdbe.org/5vbn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vbn RCSB], [http://www.ebi.ac.uk/pdbsum/5vbn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vbn ProSAT]</span></td></tr>
		+	</table>
		+	== Disease ==
		+	[[http://www.uniprot.org/uniprot/DPOE1_HUMAN DPOE1_HUMAN]] Facial dysmorphism - immunodeficiency - livedo - short stature. Disease susceptibility is associated with variations affecting the gene represented in this entry. The disease is caused by mutations affecting the gene represented in this entry.
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DPOE2_HUMAN DPOE2_HUMAN]] Participates in DNA repair and in chromosomal DNA replication. [[http://www.uniprot.org/uniprot/DPOE1_HUMAN DPOE1_HUMAN]] Participates in DNA repair and in chromosomal DNA replication.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The eukaryotic B-family DNA polymerases include four members, Polalpha, Poldelta, Pol, and Polzeta, which share common architectural features, such as the exonuclease/polymerase and C-terminal domains (CTDs) of catalytic subunits bound to indispensable B-subunits, which serve as scaffolds that mediate interactions with other components of the replication machinery. Crystal structures for the B-subunits of Polalpha and Poldelta/Polzeta have been reported; the former within the primosome and separately with CTD, and the latter with the N-terminal domain (NTD) of the C-subunit. Here we present the crystal structure of the human Pol B-subunit (p59) in complex with CTD of the catalytic subunit (p261C). The structure revealed a well-defined electron density for p261C and the phosphodiesterase (PDE) and oligonucleotide/oligosaccharide-binding domains of p59. However, electron density was missing for the p59 NTD and for the linker connecting it to the PDE domain. Similar to Polalpha, p261C contains a three-helix bundle in the middle and zinc-binding modules (Zn1 and Zn2) on each side. Intersubunit interactions involving 11 hydrogen bonds and numerous hydrophobic contacts account for stable complex formation with a buried surface area of 3094 A2 Comparative structural analysis of p59-p261C with the corresponding Polalpha complex revealed significant differences between the B-subunits and CTDs as well as their interaction interfaces. The B-subunit of Poldelta/Polzeta also substantially differs from B-subunits of either Polalpha or Pol. This work provides a structural basis to explain biochemical and genetic data on the importance of B-subunit integrity in replisome function in vivo.

-	~~Authors~~:	+	Crystal structure of the human Pol B-subunit in complex with the C-terminal domain of the catalytic subunit.,Baranovskiy AG, Gu J, Babayeva ND, Kurinov I, Pavlov YI, Tahirov TH J Biol Chem. 2017 Jul 26. pii: jbc.M117.792705. doi: 10.1074/jbc.M117.792705. PMID:28747437<ref>PMID:28747437</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5vbn" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: DNA-directed DNA polymerase]]
		+	[[Category: Babayeva, N D]]
		+	[[Category: Baranovskiy, A G]]
		+	[[Category: Gu, J]]
		+	[[Category: Suwa, Y]]
		+	[[Category: Tahirov, T H]]
		+	[[Category: B-subunit]]
		+	[[Category: Catalytic subunit]]
		+	[[Category: Dna polymerase]]
		+	[[Category: Dna polymerase epsilon]]
		+	[[Category: Dna replication]]
		+	[[Category: Polymerase]]
		+	[[Category: Replication]]
		+	[[Category: Transferase]]

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

2017-04-05T11:53:55Z

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

←Older revision

Revision as of 11:53, 5 April 2017

OCA: New page: '''Unreleased structure''' The entry 5vbn is ON HOLD Authors: Description: Category: Unreleased Structures

2017-04-05T11:53:54Z

New page: '''Unreleased structure''' The entry 5vbn is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5vbn is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]