6vdc - Revision history

OCA at 08:09, 11 October 2023

OCA — Wed, 11 Oct 2023 08:09:33 GMT

←Older revision		Revision as of 08:09, 11 October 2023
Line 3:		Line 3:
	<StructureSection load='6vdc' size='340' side='right'caption='[[6vdc]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='6vdc' size='340' side='right'caption='[[6vdc]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6vdc]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_smegmatis"_trevisan_1889 "bacillus~~ smegmatis~~" trevisan 1889~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VDC OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6VDC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6vdc]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycolicibacterium_smegmatis Mycolicibacterium smegmatis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VDC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6VDC FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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]] 2.402Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>polA, MSMEI_3749 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~1772~~ "~~Bacillus smegmatis~~" ~~Trevisan 1889])</td~~><~~/tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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=6vdc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vdc OCA], [https://pdbe.org/6vdc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6vdc RCSB], [https://www.ebi.ac.uk/pdbsum/6vdc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6vdc 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=6vdc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vdc OCA], [~~http~~://pdbe.org/6vdc PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6vdc RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6vdc PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6vdc ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~I7G3P9_MYCS2 I7G3P9_MYCS2]~~] In addition to polymerase activity, this DNA polymerase exhibits 5'-3' exonuclease activity.[RuleBase:RU004460]	+	[https://www.uniprot.org/uniprot/A0QYZ2_MYCS2 A0QYZ2_MYCS2] In addition to polymerase activity, this DNA polymerase exhibits 5'-3' exonuclease activity.[RuleBase:RU004460]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 20:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 6vdc" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6vdc" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Bacillus smegmatis trevisan 1889]]
-	[[Category: DNA-directed DNA polymerase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Ghosh, S~~]]	+	[[Category: Mycolicibacterium smegmatis]]
-	[[Category: ~~Goldgur, Y]]~~	+	[[Category: Ghosh S]]
-	~~[[Category: Shuman,~~ S]]	+	[[Category: Goldgur Y]]
-	[[Category: ~~Apoenzyme~~]]	+	[[Category: Shuman S]]
-	[[Category: ~~Dna polymerase]]~~	+
-	~~[[Category: Mycobacteria]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 07:20, 15 April 2020

OCA — Wed, 15 Apr 2020 07:20:39 GMT

←Older revision		Revision as of 07:20, 15 April 2020
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	<StructureSection load='6vdc' size='340' side='right'caption='[[6vdc]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='6vdc' size='340' side='right'caption='[[6vdc]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6vdc]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_smegmatis"_trevisan_1889 "bacillus smegmatis" trevisan 1889]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VDC OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6VDC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6vdc]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_smegmatis"_trevisan_1889 "bacillus smegmatis" trevisan 1889]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VDC OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6VDC FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">polA, MSMEI_3749 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1772 "Bacillus smegmatis" Trevisan 1889])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">polA, MSMEI_3749 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1772 "Bacillus smegmatis" Trevisan 1889])</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=6vdc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vdc OCA], [http://pdbe.org/6vdc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6vdc RCSB], [http://www.ebi.ac.uk/pdbsum/6vdc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6vdc 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=6vdc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vdc OCA], [http://pdbe.org/6vdc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6vdc RCSB], [http://www.ebi.ac.uk/pdbsum/6vdc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6vdc ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 07:45, 19 February 2020

OCA — Wed, 19 Feb 2020 07:45:21 GMT

←Older revision		Revision as of 07:45, 19 February 2020
Line 3:		Line 3:
	<StructureSection load='6vdc' size='340' side='right'caption='[[6vdc]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='6vdc' size='340' side='right'caption='[[6vdc]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6vdc]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VDC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6VDC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6vdc]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_smegmatis"_trevisan_1889 "bacillus smegmatis" trevisan 1889]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VDC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6VDC FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">polA, MSMEI_3749 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1772 "Bacillus smegmatis" Trevisan 1889])</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=6vdc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vdc OCA], [http://pdbe.org/6vdc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6vdc RCSB], [http://www.ebi.ac.uk/pdbsum/6vdc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6vdc 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=6vdc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vdc OCA], [http://pdbe.org/6vdc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6vdc RCSB], [http://www.ebi.ac.uk/pdbsum/6vdc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6vdc ProSAT]</span></td></tr>
Line 10:		Line 11:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/I7G3P9_MYCS2 I7G3P9_MYCS2]] In addition to polymerase activity, this DNA polymerase exhibits 5'-3' exonuclease activity.[RuleBase:RU004460]		[[http://www.uniprot.org/uniprot/I7G3P9_MYCS2 I7G3P9_MYCS2]] In addition to polymerase activity, this DNA polymerase exhibits 5'-3' exonuclease activity.[RuleBase:RU004460]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Mycobacterial Pol1 is a bifunctional enzyme composed of an N-terminal DNA flap endonuclease/5' exonuclease domain (FEN/EXO) and a C-terminal DNA polymerase domain (POL). Here we document additional functions of Pol1: FEN activity on the flap RNA strand of an RNA:DNA hybrid and reverse transcriptase activity on a DNA-primed RNA template. We report crystal structures of the POL domain, as apoenzyme and as ternary complex with 3'-dideoxy-terminated DNA primer-template and dNTP. The thumb, palm, and fingers subdomains of POL form an extensive interface with the primer-template and the triphosphate of the incoming dNTP. Progression from an open conformation of the apoenzyme to a nearly closed conformation of the ternary complex entails a disordered-to-ordered transition of several segments of the thumb and fingers modules and an inward motion of the fingers subdomain-especially the O helix-to engage the primer-template and dNTP triphosphate. Distinctive structural features of mycobacterial Pol1 POL include a manganese binding site in the vestigial 3' exonuclease subdomain and a non-catalytic water-bridged magnesium complex at the protein-DNA interface. We report a crystal structure of the bifunctional FEN/EXO-POL apoenzyme that reveals the positions of two active site metals in the FEN/EXO domain.
		+
		+	Mycobacterial DNA polymerase I: activities and crystal structures of the POL domain as apoenzyme and in complex with a DNA primer-template and of the full-length FEN/EXO-POL enzyme.,Ghosh S, Goldgur Y, Shuman S Nucleic Acids Res. 2020 Feb 8. pii: 5730378. doi: 10.1093/nar/gkaa075. PMID:32034423<ref>PMID:32034423</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6vdc" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus smegmatis trevisan 1889]]
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]

OCA at 04:30, 13 February 2020

OCA — Thu, 13 Feb 2020 04:30:56 GMT

←Older revision		Revision as of 04:30, 13 February 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6vdc is ~~ON HOLD until Paper Publication~~	+	==POL domain of Pol1 from M. smegmatis==
-		+	<StructureSection load='6vdc' size='340' side='right'caption='[[6vdc]], [[Resolution\|resolution]] 2.40Å' scene=''>
-	~~Authors~~: ~~Shuman~~, S., ~~Goldgur~~, Y., ~~Ghosh~~, S.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6vdc]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VDC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6VDC FirstGlance]. <br>
-	~~Description~~: ~~POL domain of Pol1 from M~~. ~~smegmatis~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<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=6vdc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vdc OCA], [http://pdbe.org/6vdc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6vdc RCSB], [http://www.ebi.ac.uk/pdbsum/6vdc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6vdc ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/I7G3P9_MYCS2 I7G3P9_MYCS2]] In addition to polymerase activity, this DNA polymerase exhibits 5'-3' exonuclease activity.[RuleBase:RU004460]
		+	__TOC__
		+	</StructureSection>
		+	[[Category: DNA-directed DNA polymerase]]
		+	[[Category: Large Structures]]
		+	[[Category: Ghosh, S]]
	[[Category: Goldgur, Y]]		[[Category: Goldgur, Y]]
	[[Category: Shuman, S]]		[[Category: Shuman, S]]
-	[[Category: ~~Ghosh, S~~]]	+	[[Category: Apoenzyme]]
		+	[[Category: Dna polymerase]]
		+	[[Category: Mycobacteria]]
		+	[[Category: Transferase]]

OCA at 06:10, 8 January 2020

OCA — Wed, 08 Jan 2020 06:10:20 GMT

←Older revision		Revision as of 06:10, 8 January 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6vdc is ON HOLD	+	The entry 6vdc is ON HOLD until Paper Publication

	Authors: Shuman, S., Goldgur, Y., Ghosh, S.		Authors: Shuman, S., Goldgur, Y., Ghosh, S.

OCA: Protected "6vdc" [edit=sysop:move=sysop]

OCA — Wed, 01 Jan 2020 06:52:54 GMT

Protected "6vdc" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:52, 1 January 2020

OCA: New page: '''Unreleased structure''' The entry 6vdc is ON HOLD Authors: Shuman, S., Goldgur, Y., Ghosh, S. Description: POL domain of Pol1 from M. smegmatis Category: Unreleased Structures [...

OCA — Wed, 01 Jan 2020 06:52:52 GMT

New page: '''Unreleased structure''' The entry 6vdc is ON HOLD Authors: Shuman, S., Goldgur, Y., Ghosh, S. Description: POL domain of Pol1 from M. smegmatis Category: Unreleased Structures [...

New page

'''Unreleased structure'''

The entry 6vdc is ON HOLD

Authors: Shuman, S., Goldgur, Y., Ghosh, S.

Description: POL domain of Pol1 from M. smegmatis
[[Category: Unreleased Structures]]
[[Category: Goldgur, Y]]
[[Category: Shuman, S]]
[[Category: Ghosh, S]]