4mde - Revision history

OCA at 12:25, 1 March 2024

OCA — Fri, 01 Mar 2024 12:25:50 GMT

←Older revision		Revision as of 12:25, 1 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4mde]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Acetivibrio_thermocellus_ATCC_27405 Acetivibrio thermocellus ATCC 27405]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MDE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4MDE FirstGlance]. <br>		<table><tr><td colspan='2'>[[4mde]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Acetivibrio_thermocellus_ATCC_27405 Acetivibrio thermocellus ATCC 27405]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MDE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4MDE FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 1.8Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=4mde FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mde OCA], [https://pdbe.org/4mde PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4mde RCSB], [https://www.ebi.ac.uk/pdbsum/4mde PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4mde 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=4mde FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mde OCA], [https://pdbe.org/4mde PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4mde RCSB], [https://www.ebi.ac.uk/pdbsum/4mde PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4mde ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/A3DJ38_ACET2 A3DJ38_ACET2]		[https://www.uniprot.org/uniprot/A3DJ38_ACET2 A3DJ38_ACET2]
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Clostridium thermocellum polynucleotide kinase (CthPnk), the 5' end-healing module of a bacterial RNA repair system, catalyzes reversible phosphoryl transfer from an NTP donor to a 5'-OH polynucleotide acceptor. Here we report the crystal structures of CthPnk-D38N in a Michaelis complex with GTPMg2+ and a 5'-OH oligonucleotide and a product complex with GDPMg2+ and a 5'-PO4 oligonucleotide. The O5' nucleophile is situated 3.0 A from the GTP gamma phosphorus in the Michaelis complex, where it is coordinated by Asn38 and is apical to the bridging beta phosphate oxygen of the GDP leaving group. In the product complex, the transferred phosphate has undergone stereochemical inversion and Asn38 coordinates the 5'-bridging phosphate oxygen of the oligonucleotide. The D38N enzyme is poised for catalysis, but cannot execute because it lacks Asp38-hereby implicated as the essential general base catalyst that abstracts a proton from the 5'-OH during the kinase reaction. Asp38 serves as a general acid catalyst during the 'reverse kinase' reaction by donating a proton to the O5' leaving group of the 5'-PO4 strand. The acceptor strand binding mode of CthPnk is distinct from that of bacteriophage T4 Pnk.
-
-	Structures of bacterial polynucleotide kinase in a Michaelis complex with GTPMg2+ and 5'-OH oligonucleotide and a product complex with GDPMg2+ and 5'-PO4 oligonucleotide reveal a mechanism of general acid-base catalysis and the determinants of phosphoacceptor recognition.,Das U, Wang LK, Smith P, Jacewicz A, Shuman S Nucleic Acids Res. 2013 Oct 22. PMID:24150947<ref>PMID:24150947</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 4mde" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 11:10, 21 December 2022

OCA — Wed, 21 Dec 2022 11:10:52 GMT

←Older revision		Revision as of 11:10, 21 December 2022
Line 1:		Line 1:

	==Structure of bacterial polynucleotide kinase product complex bound to GDP and DNA==		==Structure of bacterial polynucleotide kinase product complex bound to GDP and DNA==
-	<StructureSection load='4mde' size='340' side='right' caption='[[4mde]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='4mde' size='340' side='right'caption='[[4mde]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4mde]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Cloth Cloth~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MDE OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4MDE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4mde]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Acetivibrio_thermocellus_ATCC_27405 Acetivibrio thermocellus ATCC 27405]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MDE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4MDE FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4jsy\|4jsy]], [[4jt2\|4jt2]], [[4jt4\|4jt4]], [[4jst\|4jst]], [[4gp6\|4gp6]], [[4gp7\|4gp7]], [[4mdf\|4mdf]]</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=4mde FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mde OCA], [https://pdbe.org/4mde PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4mde RCSB], [https://www.ebi.ac.uk/pdbsum/4mde PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4mde ProSAT]</span></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Cthe_2768 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=203119 CLOTH])~~</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=4mde FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mde OCA], [~~http~~://pdbe.org/4mde PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4mde RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4mde PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4mde ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A3DJ38_ACET2 A3DJ38_ACET2]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Cloth~~]]	+	[[Category: Acetivibrio thermocellus ATCC 27405]]
-	[[Category: Das, U]]	+	[[Category: Large Structures]]
-	[[Category: Jacewicz, A]]	+	[[Category: Das U]]
-	[[Category: Shuman, S]]	+	[[Category: Jacewicz A]]
-	[[Category: Smith, P]]	+	[[Category: Shuman S]]
-	[[Category: Wang~~, L K]]~~	+	[[Category: Smith P]]
-	~~[[Category: Hydrolase-dna complex]]~~	+	[[Category: Wang LK]]
-	~~[[Category: P-loop phosphotransferase]]~~	+
-	~~[[Category: Rna repair]]~~	+
-	~~[[Category: Transferase]]~~	+
-	~~[[Category: Transferase-dna complex~~]]	+

OCA at 13:38, 11 August 2016

OCA — Thu, 11 Aug 2016 13:38:58 GMT

←Older revision		Revision as of 13:38, 11 August 2016
Line 1:		Line 1:
-	{{STRUCTURE_4mde\| PDB=4mde \| SCENE= }}
-	===Structure of bacterial polynucleotide kinase product complex bound to GDP and DNA===
-	{{ABSTRACT_PUBMED_24150947}}

-	==~~About this~~ Structure==	+	==Structure of bacterial polynucleotide kinase product complex bound to GDP and DNA==
-	[[4mde]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Cloth Cloth]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MDE OCA].	+	<StructureSection load='4mde' size='340' side='right' caption='[[4mde]], [[Resolution\|resolution]] 1.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4mde]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Cloth Cloth]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MDE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4MDE FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4jsy\|4jsy]], [[4jt2\|4jt2]], [[4jt4\|4jt4]], [[4jst\|4jst]], [[4gp6\|4gp6]], [[4gp7\|4gp7]], [[4mdf\|4mdf]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Cthe_2768 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=203119 CLOTH])</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=4mde FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mde OCA], [http://pdbe.org/4mde PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4mde RCSB], [http://www.ebi.ac.uk/pdbsum/4mde PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4mde ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Clostridium thermocellum polynucleotide kinase (CthPnk), the 5' end-healing module of a bacterial RNA repair system, catalyzes reversible phosphoryl transfer from an NTP donor to a 5'-OH polynucleotide acceptor. Here we report the crystal structures of CthPnk-D38N in a Michaelis complex with GTPMg2+ and a 5'-OH oligonucleotide and a product complex with GDPMg2+ and a 5'-PO4 oligonucleotide. The O5' nucleophile is situated 3.0 A from the GTP gamma phosphorus in the Michaelis complex, where it is coordinated by Asn38 and is apical to the bridging beta phosphate oxygen of the GDP leaving group. In the product complex, the transferred phosphate has undergone stereochemical inversion and Asn38 coordinates the 5'-bridging phosphate oxygen of the oligonucleotide. The D38N enzyme is poised for catalysis, but cannot execute because it lacks Asp38-hereby implicated as the essential general base catalyst that abstracts a proton from the 5'-OH during the kinase reaction. Asp38 serves as a general acid catalyst during the 'reverse kinase' reaction by donating a proton to the O5' leaving group of the 5'-PO4 strand. The acceptor strand binding mode of CthPnk is distinct from that of bacteriophage T4 Pnk.

-	~~==Reference==~~	+	Structures of bacterial polynucleotide kinase in a Michaelis complex with GTPMg2+ and 5'-OH oligonucleotide and a product complex with GDPMg2+ and 5'-PO4 oligonucleotide reveal a mechanism of general acid-base catalysis and the determinants of phosphoacceptor recognition.,Das U, Wang LK, Smith P, Jacewicz A, Shuman S Nucleic Acids Res. 2013 Oct 22. PMID:24150947<ref>PMID:24150947</ref>
-	<ref ~~group="xtra"~~>PMID:~~024150947~~</ref><~~references group~~="~~xtra~~"/><references/>	+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 4mde" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Cloth]]		[[Category: Cloth]]
-	[[Category: Das, U.]]	+	[[Category: Das, U]]
-	[[Category: Jacewicz, A.]]	+	[[Category: Jacewicz, A]]
-	[[Category: Shuman, S.]]	+	[[Category: Shuman, S]]
-	[[Category: Smith, P.]]	+	[[Category: Smith, P]]
-	[[Category: Wang, L K.]]	+	[[Category: Wang, L K]]
	[[Category: Hydrolase-dna complex]]		[[Category: Hydrolase-dna complex]]
	[[Category: P-loop phosphotransferase]]		[[Category: P-loop phosphotransferase]]

OCA at 04:34, 13 February 2014

OCA — Thu, 13 Feb 2014 04:34:55 GMT

←Older revision		Revision as of 04:34, 13 February 2014
Line 4:		Line 4:

	==About this Structure==		==About this Structure==
-	[[4mde]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Clostridium_thermocellum_atcc_27405 Clostridium thermocellum atcc 27405~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MDE OCA].	+	[[4mde]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Cloth Cloth]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MDE OCA].

	==Reference==		==Reference==
	<ref group="xtra">PMID:024150947</ref><references group="xtra"/><references/>		<ref group="xtra">PMID:024150947</ref><references group="xtra"/><references/>
-	[[Category: ~~Clostridium thermocellum atcc 27405~~]]	+	[[Category: Cloth]]
	[[Category: Das, U.]]		[[Category: Das, U.]]
	[[Category: Jacewicz, A.]]		[[Category: Jacewicz, A.]]

OCA at 07:53, 6 November 2013

OCA — Wed, 06 Nov 2013 07:53:01 GMT

←Older revision		Revision as of 07:53, 6 November 2013
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{STRUCTURE_4mde\| PDB=4mde \| SCENE= }}
		+	===Structure of bacterial polynucleotide kinase product complex bound to GDP and DNA===
		+	{{ABSTRACT_PUBMED_24150947}}

-	~~The entry~~ 4mde is ~~ON HOLD until Paper Publication~~	+	==About this Structure==
		+	[[4mde]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Clostridium_thermocellum_atcc_27405 Clostridium thermocellum atcc 27405]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MDE OCA].

-	~~Authors~~: ~~Shuman, S.,~~ Das, U., ~~Wang, L.K~~., Smith, P., ~~Jacewicz, A~~.	+	==Reference==
-		+	<ref group="xtra">PMID:024150947</ref><references group="xtra"/><references/>
-	~~Description~~: ~~Structure of bacterial polynucleotide kinase product~~ complex ~~bound to GDP and DNA~~	+	[[Category: Clostridium thermocellum atcc 27405]]
		+	[[Category: Das, U.]]
		+	[[Category: Jacewicz, A.]]
		+	[[Category: Shuman, S.]]
		+	[[Category: Smith, P.]]
		+	[[Category: Wang, L K.]]
		+	[[Category: Hydrolase-dna complex]]
		+	[[Category: P-loop phosphotransferase]]
		+	[[Category: Rna repair]]
		+	[[Category: Transferase]]
		+	[[Category: Transferase-dna complex]]

OCA at 06:48, 2 October 2013

OCA — Wed, 02 Oct 2013 06:48:15 GMT

←Older revision		Revision as of 06:48, 2 October 2013
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4mde is ON HOLD	+	The entry 4mde is ON HOLD until Paper Publication

-	Authors: Shuman, S., Das, U., Wang, L.K., Smith, P., ~~Jaciewicz~~, A.	+	Authors: Shuman, S., Das, U., Wang, L.K., Smith, P., Jacewicz, A.

	Description: Structure of bacterial polynucleotide kinase product complex bound to GDP and DNA		Description: Structure of bacterial polynucleotide kinase product complex bound to GDP and DNA

OCA: Protected "4mde" [edit=sysop:move=sysop]

OCA — Wed, 28 Aug 2013 06:59:57 GMT

Protected "4mde" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:59, 28 August 2013

OCA: New page: '''Unreleased structure''' The entry 4mde is ON HOLD Authors: Shuman, S., Das, U., Wang, L.K., Smith, P., Jaciewicz, A. Description: Structure of bacterial polynucleotide kinase produc...

OCA — Wed, 28 Aug 2013 06:59:55 GMT

New page: '''Unreleased structure''' The entry 4mde is ON HOLD Authors: Shuman, S., Das, U., Wang, L.K., Smith, P., Jaciewicz, A. Description: Structure of bacterial polynucleotide kinase produc...

New page

'''Unreleased structure'''

The entry 4mde is ON HOLD

Authors: Shuman, S., Das, U., Wang, L.K., Smith, P., Jaciewicz, A.

Description: Structure of bacterial polynucleotide kinase product complex bound to GDP and DNA