1xv5 - Revision history

OCA at 07:12, 9 August 2023

OCA — Wed, 09 Aug 2023 07:12:32 GMT

←Older revision		Revision as of 07:12, 9 August 2023
Line 3:		Line 3:
	<StructureSection load='1xv5' size='340' side='right'caption='[[1xv5]], [[Resolution\|resolution]] 1.73Å' scene=''>		<StructureSection load='1xv5' size='340' side='right'caption='[[1xv5]], [[Resolution\|resolution]] 1.73Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1xv5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Bpt4 Bpt4~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XV5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XV5 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1xv5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_virus_T4 Escherichia virus T4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XV5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XV5 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>~~, ~~<scene name='pdbligand=EDO:~~1~~,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</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]] 1.73Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=CME:S,S-(2-HYDROXYETHYL)THIOCYSTEINE'>CME</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CME:S,S-(2-HYDROXYETHYL)THIOCYSTEINE'>CME</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></td></tr>
-	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b></td><td class="sblockDat"><div style='overflow: auto; max~~-~~height: 3em;~~'>~~[[1y6f\|1y6f]], [[1y6g\|1y6g]], [[1y8z\|1y8z]], [[1ya6\|1ya6]]~~</~~div~~><~~/td></tr>~~	+
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks'>[https~~:~~//en.wikipedia.org/wiki/DNA_alpha~~-~~glucosyltransferase DNA alpha~~-~~glucosyltransferase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.26 2.4.1.26]~~ </~~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=1xv5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xv5 OCA], [https://pdbe.org/1xv5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xv5 RCSB], [https://www.ebi.ac.uk/pdbsum/1xv5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xv5 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=1xv5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xv5 OCA], [https://pdbe.org/1xv5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xv5 RCSB], [https://www.ebi.ac.uk/pdbsum/1xv5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xv5 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/GSTA_BPT4 GSTA_BPT4]] Is involved in a DNA modification process to protect the phage genome against its own nucleases and the host restriction endonuclease system.	+	[https://www.uniprot.org/uniprot/GSTA_BPT4 GSTA_BPT4] Is involved in a DNA modification process to protect the phage genome against its own nucleases and the host restriction endonuclease system.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 25:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bpt4]]~~	+	[[Category: Escherichia virus T4]]
-	~~[[Category: DNA alpha-glucosyltransferase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Lariviere, L]]	+	[[Category: Lariviere L]]
-	[[Category: Morera, S]]	+	[[Category: Morera S]]
-	[[Category: Sommer, N]]	+	[[Category: Sommer N]]
-	~~[[Category: Transferase~~]]	+

OCA at 16:20, 3 November 2021

OCA — Wed, 03 Nov 2021 16:20:14 GMT

OCA at 17:14, 29 January 2020

OCA — Wed, 29 Jan 2020 17:14:51 GMT

←Older revision		Revision as of 17:14, 29 January 2020
Line 1:		Line 1:

	==alpha-glucosyltransferase (AGT) in complex with UDP==		==alpha-glucosyltransferase (AGT) in complex with UDP==
-	<StructureSection load='1xv5' size='340' side='right' caption='[[1xv5]], [[Resolution\|resolution]] 1.73Å' scene=''>	+	<StructureSection load='1xv5' size='340' side='right'caption='[[1xv5]], [[Resolution\|resolution]] 1.73Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1xv5]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpt4 Bpt4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XV5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XV5 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1xv5]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpt4 Bpt4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XV5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XV5 FirstGlance]. <br>
Line 27:		Line 27:
	[[Category: Bpt4]]		[[Category: Bpt4]]
	[[Category: DNA alpha-glucosyltransferase]]		[[Category: DNA alpha-glucosyltransferase]]
		+	[[Category: Large Structures]]
	[[Category: Lariviere, L]]		[[Category: Lariviere, L]]
	[[Category: Morera, S]]		[[Category: Morera, S]]
	[[Category: Sommer, N]]		[[Category: Sommer, N]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 07:29, 18 April 2018

OCA — Wed, 18 Apr 2018 07:29:06 GMT

←Older revision		Revision as of 07:29, 18 April 2018
Line 1:		Line 1:
		+
	==alpha-glucosyltransferase (AGT) in complex with UDP==		==alpha-glucosyltransferase (AGT) in complex with UDP==
	<StructureSection load='1xv5' size='340' side='right' caption='[[1xv5]], [[Resolution\|resolution]] 1.73Å' scene=''>		<StructureSection load='1xv5' size='340' side='right' caption='[[1xv5]], [[Resolution\|resolution]] 1.73Å' scene=''>
Line 7:		Line 8:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1y6f\|1y6f]], [[1y6g\|1y6g]], [[1y8z\|1y8z]], [[1ya6\|1ya6]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1y6f\|1y6f]], [[1y6g\|1y6g]], [[1y8z\|1y8z]], [[1ya6\|1ya6]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA_alpha-glucosyltransferase DNA alpha-glucosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.26 2.4.1.26] </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_alpha-glucosyltransferase DNA alpha-glucosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.26 2.4.1.26] </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=1xv5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xv5 OCA], [http://pdbe.org/1xv5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1xv5 RCSB], [http://www.ebi.ac.uk/pdbsum/1xv5 PDBsum]</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=1xv5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xv5 OCA], [http://pdbe.org/1xv5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1xv5 RCSB], [http://www.ebi.ac.uk/pdbsum/1xv5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1xv5 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 06:33, 10 September 2015

OCA — Thu, 10 Sep 2015 06:33:16 GMT

←Older revision		Revision as of 06:33, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1xv5' size='340' side='right' caption='[[1xv5]], [[Resolution\|resolution]] 1.73Å' scene=''>		<StructureSection load='1xv5' size='340' side='right' caption='[[1xv5]], [[Resolution\|resolution]] 1.73Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1xv5]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Enterobacteria_phage_t4 Enterobacteria phage t4~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XV5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XV5 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1xv5]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpt4 Bpt4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XV5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XV5 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CME:S,S-(2-HYDROXYETHYL)THIOCYSTEINE'>CME</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CME:S,S-(2-HYDROXYETHYL)THIOCYSTEINE'>CME</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1y6f\|1y6f]], [[1y6g\|1y6g]], [[1y8z\|1y8z]], [[1ya6\|1ya6]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1y6f\|1y6f]], [[1y6g\|1y6g]], [[1y8z\|1y8z]], [[1ya6\|1ya6]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA_alpha-glucosyltransferase DNA alpha-glucosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.26 2.4.1.26] </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_alpha-glucosyltransferase DNA alpha-glucosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.26 2.4.1.26] </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=1xv5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xv5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1xv5 RCSB], [http://www.ebi.ac.uk/pdbsum/1xv5 PDBsum]</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=1xv5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xv5 OCA], [http://pdbe.org/1xv5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1xv5 RCSB], [http://www.ebi.ac.uk/pdbsum/1xv5 PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 19:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 1xv5" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bpt4]]
	[[Category: DNA alpha-glucosyltransferase]]		[[Category: DNA alpha-glucosyltransferase]]
-	[[Category: Enterobacteria phage t4]]
	[[Category: Lariviere, L]]		[[Category: Lariviere, L]]
	[[Category: Morera, S]]		[[Category: Morera, S]]
	[[Category: Sommer, N]]		[[Category: Sommer, N]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 19:31, 24 December 2014

OCA — Wed, 24 Dec 2014 19:31:37 GMT

←Older revision		Revision as of 19:31, 24 December 2014
Line 9:		Line 9:
	<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=1xv5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xv5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1xv5 RCSB], [http://www.ebi.ac.uk/pdbsum/1xv5 PDBsum]</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=1xv5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xv5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1xv5 RCSB], [http://www.ebi.ac.uk/pdbsum/1xv5 PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/GSTA_BPT4 GSTA_BPT4]] Is involved in a DNA modification process to protect the phage genome against its own nucleases and the host restriction endonuclease system.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 25:
	[[Category: DNA alpha-glucosyltransferase]]		[[Category: DNA alpha-glucosyltransferase]]
	[[Category: Enterobacteria phage t4]]		[[Category: Enterobacteria phage t4]]
-	[[Category: Lariviere, L.]]	+	[[Category: Lariviere, L]]
-	[[Category: Morera, S.]]	+	[[Category: Morera, S]]
-	[[Category: Sommer, N.]]	+	[[Category: Sommer, N]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 08:25, 8 October 2014

OCA — Wed, 08 Oct 2014 08:25:04 GMT

←Older revision		Revision as of 08:25, 8 October 2014
Line 1:		Line 1:
-	[[~~Image:~~1xv5.~~png~~\|~~left~~\|~~200px~~]]	+	==alpha-glucosyltransferase (AGT) in complex with UDP==
		+	<StructureSection load='1xv5' size='340' side='right' caption='[[1xv5]], [[Resolution\|resolution]] 1.73Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1xv5]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t4 Enterobacteria phage t4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XV5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XV5 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CME:S,S-(2-HYDROXYETHYL)THIOCYSTEINE'>CME</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1y6f\|1y6f]], [[1y6g\|1y6g]], [[1y8z\|1y8z]], [[1ya6\|1ya6]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA_alpha-glucosyltransferase DNA alpha-glucosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.26 2.4.1.26] </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=1xv5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xv5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1xv5 RCSB], [http://www.ebi.ac.uk/pdbsum/1xv5 PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The Escherichia coli T4 bacteriophage uses two glycosyltransferases to glucosylate and thus protect its DNA: the retaining alpha-glucosyltransferase (AGT) and the inverting beta-glucosyltransferase (BGT). They glucosylate 5-hydroxymethyl cytosine (5-HMC) bases of duplex DNA using UDP-glucose as the sugar donor to form an alpha-glucosidic linkage and a beta-glucosidic linkage, respectively. Five structures of AGT have been determined: a binary complex with the UDP product and four ternary complexes with UDP or UDP-glucose and oligonucleotides containing an A:G, HMU:G (hydroxymethyl uracyl) or AP:G (apurinic/apyrimidinic) mismatch at the target base-pair. AGT adopts the GT-B fold, one of the two folds known for GTs. However, while the sugar donor binding mode is classical for a GT-B enzyme, the sugar acceptor binding mode is unexpected and breaks the established consensus: AGT is the first GT-B enzyme that predominantly binds both the sugar donor and acceptor to the C-terminal domain. Its active site pocket is highly similar to four retaining GT-B glycosyltransferases (trehalose-6-phosphate synthase, glycogen synthase, glycogen and maltodextrin phosphorylases) strongly suggesting a common evolutionary origin and catalytic mechanism for these enzymes. Structure-guided mutagenesis and kinetic analysis do not permit identification of a nucleophile residue responsible for a glycosyl-enzyme intermediate for the classical double displacement mechanism. Interestingly, the DNA structures reveal partially flipped-out bases. They provide evidence for a passive role of AGT in the base-flipping mechanism and for its specific recognition of the acceptor base.

-	~~{{STRUCTURE_1xv5\| PDB=1xv5 \| SCENE= }}~~	+	Structural evidence of a passive base-flipping mechanism for AGT, an unusual GT-B glycosyltransferase.,Lariviere L, Sommer N, Morera S J Mol Biol. 2005 Sep 9;352(1):139-50. PMID:16081100<ref>PMID:16081100</ref>

-	~~===alpha-glucosyltransferase (AGT) in complex with UDP===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_16081100}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1xv5]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Enterobacteria_phage_t4 Enterobacteria phage t4]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1XV5 OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:016081100<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: DNA alpha-glucosyltransferase]]		[[Category: DNA alpha-glucosyltransferase]]
	[[Category: Enterobacteria phage t4]]		[[Category: Enterobacteria phage t4]]

OCA: Protected "1xv5" [edit=sysop:move=sysop]

OCA — Sat, 05 Jan 2013 13:40:29 GMT

Protected "1xv5" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:40, 5 January 2013

OCA at 13:40, 5 January 2013

OCA — Sat, 05 Jan 2013 13:40:27 GMT

←Older revision		Revision as of 13:40, 5 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1xv5.png\|left\|200px]]		[[Image:1xv5.png\|left\|200px]]

-	<!--
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	{{STRUCTURE_1xv5\| PDB=1xv5 \| SCENE= }}		{{STRUCTURE_1xv5\| PDB=1xv5 \| SCENE= }}

	===alpha-glucosyltransferase (AGT) in complex with UDP===		===alpha-glucosyltransferase (AGT) in complex with UDP===

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	{{ABSTRACT_PUBMED_16081100}}		{{ABSTRACT_PUBMED_16081100}}

	==About this Structure==		==About this Structure==
-	~~1XV5 is a~~ [[~~Single protein~~]] structure of sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t4 Enterobacteria phage t4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XV5 OCA].	+	[[1xv5]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t4 Enterobacteria phage t4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XV5 OCA].

	==Reference==		==Reference==
-	~~Structural evidence of a passive base-flipping mechanism for AGT, an unusual GT-B glycosyltransferase., Lariviere L, Sommer N, Morera S, J Mol Biol. 2005 Sep 9;352(1):139-50.~~ PMID:~~[http://www.ncbi.nlm.nih.gov~~/~~pubmed~~/~~16081100 16081100]~~	+	<ref group="xtra">PMID:016081100</ref><references group="xtra"/>
	[[Category: DNA alpha-glucosyltransferase]]		[[Category: DNA alpha-glucosyltransferase]]
	[[Category: Enterobacteria phage t4]]		[[Category: Enterobacteria phage t4]]
-	[[Category: Single protein]]
	[[Category: Lariviere, L.]]		[[Category: Lariviere, L.]]
	[[Category: Morera, S.]]		[[Category: Morera, S.]]
	[[Category: Sommer, N.]]		[[Category: Sommer, N.]]
	[[Category: Transferase]]		[[Category: Transferase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Jul 27 21:14:50 2008''

OCA at 18:14, 27 July 2008

OCA — Sun, 27 Jul 2008 18:14:58 GMT

←Older revision		Revision as of 18:14, 27 July 2008
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-	[[Image:1xv5.~~gif~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:1xv5.png\|left\|200px]]

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	{{STRUCTURE_1xv5\| PDB=1xv5 \| SCENE= }}		{{STRUCTURE_1xv5\| PDB=1xv5 \| SCENE= }}

-	~~'''~~alpha-glucosyltransferase (AGT) in complex with UDP~~'''~~	+	===alpha-glucosyltransferase (AGT) in complex with UDP===


-	~~==Overview==~~	+	<!--
-	The ~~Escherichia coli T4 bacteriophage uses two glycosyltransferases~~ to ~~glucosylate and thus protect its DNA:~~ the ~~retaining alpha-glucosyltransferase~~ (~~AGT) and the inverting beta-glucosyltransferase (BGT). They glucosylate 5-hydroxymethyl cytosine (5-HMC) bases of duplex DNA using UDP-glucose~~ as ~~the sugar donor to form an alpha-glucosidic linkage and a beta-glucosidic linkage, respectively. Five structures of AGT have been determined~~: ~~a binary complex with the UDP product and four ternary complexes with UDP or UDP-glucose and oligonucleotides containing an A:G, HMU:G (hydroxymethyl uracyl) or AP:G (apurinic~~/~~apyrimidinic) mismatch at the target base-pair~~. ~~AGT adopts the GT-B fold, one of the two folds known for GTs~~. ~~However~~, ~~while the sugar donor binding mode~~ is ~~classical for a GT-B enzyme,~~ the ~~sugar acceptor binding mode is unexpected and breaks the established consensus: AGT is the first GT-B enzyme that predominantly binds both the sugar donor and acceptor to the C-terminal domain~~. ~~Its active site pocket is highly similar to four retaining GT~~-~~B glycosyltransferases (trehalose~~-6-phosphate synthase, glycogen synthase, glycogen and maltodextrin phosphorylases) strongly suggesting a common evolutionary origin and catalytic mechanism for these enzymes. Structure-guided mutagenesis and kinetic analysis do not permit identification of a nucleophile residue responsible for a glycosyl-enzyme intermediate for the classical double displacement mechanism. Interestingly, the DNA structures reveal partially flipped-out bases. They provide evidence for a passive role of AGT in the base-flipping mechanism and for its specific recognition of the acceptor base.	+	The line below this paragraph, {{ABSTRACT_PUBMED_16081100}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 16081100 is the PubMed ID number.
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		+	{{ABSTRACT_PUBMED_16081100}}

	==About this Structure==		==About this Structure==
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	[[Category: Sommer, N.]]		[[Category: Sommer, N.]]
	[[Category: Transferase]]		[[Category: Transferase]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sat May 3 15~~:32:46 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Jul 27 21:14:50 2008''

←Older revision		Revision as of 16:20, 3 November 2021
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	<StructureSection load='1xv5' size='340' side='right'caption='[[1xv5]], [[Resolution\|resolution]] 1.73Å' scene=''>		<StructureSection load='1xv5' size='340' side='right'caption='[[1xv5]], [[Resolution\|resolution]] 1.73Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1xv5]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Bpt4 Bpt4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XV5 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1XV5 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1xv5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bpt4 Bpt4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XV5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XV5 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CME:S,S-(2-HYDROXYETHYL)THIOCYSTEINE'>CME</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CME:S,S-(2-HYDROXYETHYL)THIOCYSTEINE'>CME</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1y6f\|1y6f]], [[1y6g\|1y6g]], [[1y8z\|1y8z]], [[1ya6\|1ya6]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1y6f\|1y6f]], [[1y6g\|1y6g]], [[1y8z\|1y8z]], [[1ya6\|1ya6]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/DNA_alpha-glucosyltransferase DNA alpha-glucosyltransferase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.26 2.4.1.26] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/DNA_alpha-glucosyltransferase DNA alpha-glucosyltransferase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.26 2.4.1.26] </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=1xv5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xv5 OCA], [~~http~~://pdbe.org/1xv5 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1xv5 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1xv5 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1xv5 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=1xv5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xv5 OCA], [https://pdbe.org/1xv5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xv5 RCSB], [https://www.ebi.ac.uk/pdbsum/1xv5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xv5 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/GSTA_BPT4 GSTA_BPT4]] Is involved in a DNA modification process to protect the phage genome against its own nucleases and the host restriction endonuclease system.	+	[[https://www.uniprot.org/uniprot/GSTA_BPT4 GSTA_BPT4]] Is involved in a DNA modification process to protect the phage genome against its own nucleases and the host restriction endonuclease system.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==