5frq - Revision history

OCA at 13:20, 26 July 2023

2023-07-26T13:20:26Z

←Older revision		Revision as of 13:20, 26 July 2023
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	<StructureSection load='5frq' size='340' side='right'caption='[[5frq]], [[Resolution\|resolution]] 2.90Å' scene=''>		<StructureSection load='5frq' size='340' side='right'caption='[[5frq]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5frq]] is a 6 chain structure with sequence from [~~http://en.wikipedia.org/wiki/Campylobacter_pylori Campylobacter pylori] and [http~~://en.wikipedia.org/wiki/~~Helicobacter_pylori~~ Helicobacter pylori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FRQ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5FRQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5frq]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Helicobacter_pylori_26695 Helicobacter pylori 26695]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FRQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5FRQ FirstGlance]. <br>
-	</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>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.9Å</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=5frq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5frq OCA], [~~http~~://pdbe.org/5frq PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5frq RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5frq PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5frq 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=5frq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5frq OCA], [https://pdbe.org/5frq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5frq RCSB], [https://www.ebi.ac.uk/pdbsum/5frq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5frq ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/DPO3B_HELPY DPO3B_HELPY]] DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. This DNA polymerase also exhibits 3' to 5' exonuclease activity. The beta chain is required for initiation of replication once it is clamped onto DNA, it slides freely (bidirectional and ATP-independent) along duplex DNA (By similarity).	+	[https://www.uniprot.org/uniprot/DPO3B_HELPY DPO3B_HELPY] DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. This DNA polymerase also exhibits 3' to 5' exonuclease activity. The beta chain is required for initiation of replication once it is clamped onto DNA, it slides freely (bidirectional and ATP-independent) along duplex DNA (By similarity).
	<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: Campylobacter pylori]]~~	+	[[Category: Helicobacter pylori 26695]]
-	~~[[Category: DNA-directed DNA polymerase]]~~	+
-	[[Category: Helicobacter pylori]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Gourinath, S]]	+	[[Category: Gourinath S]]
-	[[Category: Pandey, P]]	+	[[Category: Pandey P]]
-	~~[[Category: Transferase~~]]	+

OCA at 16:10, 11 December 2019

2019-12-11T16:10:15Z

←Older revision		Revision as of 16:10, 11 December 2019
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	==Crystal Structure of Helicobacter pylori beta clamp bound to DNA ligase peptide==		==Crystal Structure of Helicobacter pylori beta clamp bound to DNA ligase peptide==
-	<StructureSection load='5frq' size='340' side='right' caption='[[5frq]], [[Resolution\|resolution]] 2.90Å' scene=''>	+	<StructureSection load='5frq' size='340' side='right'caption='[[5frq]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5frq]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Helicobacter_pylori Helicobacter pylori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FRQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5FRQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5frq]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Campylobacter_pylori Campylobacter pylori] and [http://en.wikipedia.org/wiki/Helicobacter_pylori Helicobacter pylori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FRQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5FRQ FirstGlance]. <br>
	</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>		</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=5frq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5frq OCA], [http://pdbe.org/5frq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5frq RCSB], [http://www.ebi.ac.uk/pdbsum/5frq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5frq 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=5frq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5frq OCA], [http://pdbe.org/5frq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5frq RCSB], [http://www.ebi.ac.uk/pdbsum/5frq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5frq ProSAT]</span></td></tr>
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	</div>		</div>
	<div class="pdbe-citations 5frq" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5frq" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[DNA ligase 3D structures\|DNA ligase 3D structures]]
		+	*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Campylobacter pylori]]
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Helicobacter pylori]]		[[Category: Helicobacter pylori]]
		+	[[Category: Large Structures]]
	[[Category: Gourinath, S]]		[[Category: Gourinath, S]]
	[[Category: Pandey, P]]		[[Category: Pandey, P]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 00:02, 10 September 2016

2016-09-10T00:02:20Z

←Older revision		Revision as of 00:02, 10 September 2016
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-	'''Unreleased structure'''

-	~~The entry~~ 5frq is ~~ON HOLD until Paper~~ Publication	+	==Crystal Structure of Helicobacter pylori beta clamp bound to DNA ligase peptide==
		+	<StructureSection load='5frq' size='340' side='right' caption='[[5frq]], [[Resolution\|resolution]] 2.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5frq]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Helicobacter_pylori Helicobacter pylori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FRQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5FRQ FirstGlance]. <br>
		+	</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=5frq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5frq OCA], [http://pdbe.org/5frq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5frq RCSB], [http://www.ebi.ac.uk/pdbsum/5frq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5frq ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DPO3B_HELPY DPO3B_HELPY]] DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. This DNA polymerase also exhibits 3' to 5' exonuclease activity. The beta chain is required for initiation of replication once it is clamped onto DNA, it slides freely (bidirectional and ATP-independent) along duplex DNA (By similarity).
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Helicobacter pylori, a gram-negative and microaerophilic bacterium, is the major cause of chronic gastritis, gastric ulcers and gastric cancer. Owing to its central role, DNA replication machinery has emerged as a prime target for the development of antimicrobial drugs. Here, we report 2A structure of beta-clamp from H. pylori (Hpbeta-clamp), which is one of the critical components of DNA polymerase III. Despite of similarity in the overall fold of eubacterial beta-clamp structures, some distinct features in DNA interacting loops exists that have not been reported previously. The in silico prediction identified the potential binders of beta-clamp such as alpha subunit of DNA pol III and DNA ligase with identification of beta-clamp binding regions in them and validated by SPR studies. Hpbeta-clamp interacts with DNA ligase in micromolar binding affinity. Moreover, we have successfully determined the co-crystal structure of beta-clamp with peptide from DNA ligase (not reported earlier in prokaryotes) revealing the region from ligase that interacts with beta-clamp.

-	~~Authors: Pandey~~, P., ~~Gourinath~~, S.	+	Structural insight into beta-Clamp and its interaction with DNA Ligase in Helicobacter pylori.,Pandey P, Tarique KF, Mazumder M, Rehman SA, Kumari N, Gourinath S Sci Rep. 2016 Aug 8;6:31181. doi: 10.1038/srep31181. PMID:27499105<ref>PMID:27499105</ref>

-	~~Description: Crystal Structure~~ of ~~Helicobacter pylori beta clamp bound to DNA ligase peptide~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: ~~Pandey, P~~]]	+	<div class="pdbe-citations 5frq" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: DNA-directed DNA polymerase]]
		+	[[Category: Helicobacter pylori]]
	[[Category: Gourinath, S]]		[[Category: Gourinath, S]]
		+	[[Category: Pandey, P]]
		+	[[Category: Transferase]]

OCA at 11:22, 1 June 2016

2016-06-01T11:22:41Z

←Older revision		Revision as of 11:22, 1 June 2016
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	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Pandey, P., Gourinath, S.		Authors: Pandey, P., Gourinath, S.

OCA at 23:06, 10 May 2016

2016-05-10T23:06:26Z

←Older revision		Revision as of 23:06, 10 May 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5frq is ON HOLD ~~until Paper Publication~~	+	The entry 5frq is ON HOLD

	Authors: Pandey, P., Gourinath, S.		Authors: Pandey, P., Gourinath, S.

OCA at 14:56, 20 January 2016

2016-01-20T14:56:59Z

←Older revision		Revision as of 14:56, 20 January 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Pandey, P., Gourinath, S.		Authors: Pandey, P., Gourinath, S.

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

2015-12-30T18:21:14Z

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

←Older revision

Revision as of 18:21, 30 December 2015

OCA: New page: '''Unreleased structure''' The entry 5frq is ON HOLD Authors: Pandey, P., Gourinath, S. Description: Crystal Structure of Helicobacter pylori beta clamp bound to DNA ligase peptide [[C...

2015-12-30T18:21:13Z

New page: '''Unreleased structure''' The entry 5frq is ON HOLD Authors: Pandey, P., Gourinath, S. Description: Crystal Structure of Helicobacter pylori beta clamp bound to DNA ligase peptide [[C...

New page

'''Unreleased structure'''

The entry 5frq is ON HOLD

Authors: Pandey, P., Gourinath, S.

Description: Crystal Structure of Helicobacter pylori beta clamp bound to DNA ligase peptide
[[Category: Unreleased Structures]]
[[Category: Pandey, P]]
[[Category: Gourinath, S]]