5lgw - Revision history

OCA at 18:24, 18 October 2023

OCA — Wed, 18 Oct 2023 18:24:48 GMT

←Older revision		Revision as of 18:24, 18 October 2023
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	<StructureSection load='5lgw' size='340' side='right'caption='[[5lgw]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='5lgw' size='340' side='right'caption='[[5lgw]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5lgw]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"actinomyces_coelicolor"_(muller_1908)_lieske_1921 "actinomyces~~ coelicolor~~" (muller 1908) lieske 1921~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LGW OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5LGW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5lgw]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_coelicolor Streptomyces coelicolor]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LGW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5LGW FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</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]] 1.95Å</td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">glgE1~~, ~~pep1, pep1A, pep1I, SCO5443, SC6A11.19c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1902 "Actinomyces coelicolor" (Muller 1908) Lieske 1921])~~<~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=PRD_900018:beta-maltose'>PRD_900018</scene>, <scene name='pdbligand=PRD_900030:alpha-maltopentaose'>PRD_900030</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>[http://en.wikipedia.org/wiki/Starch_synthase_(maltosyl-transferring) Starch synthase (maltosyl-transferring)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.99.16 2.4.99.16] </~~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=5lgw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5lgw OCA], [https://pdbe.org/5lgw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5lgw RCSB], [https://www.ebi.ac.uk/pdbsum/5lgw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5lgw 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=5lgw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5lgw OCA], [~~http~~://pdbe.org/5lgw PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5lgw RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5lgw PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5lgw ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/GLGE1_STRCO GLGE1_STRCO]] Maltosyltransferase that uses maltose 1-phosphate (M1P) as the sugar donor to elongate linear or branched alpha-(1->4)-glucans. Maltooligosaccharides with a degree of polymerization (DP) superior or equal to 4 are efficient acceptors, with DP6 being optimal in the GlgE-catalyzed polymerization with M1P. Is specific for the alpha-anomer of M1P as substrate, since the beta-anomer of M1P gives no activity. Alpha-D-glucose 1-phosphate cannot serve as a donor substrate, but alpha-maltosyl fluoride is an efficient donor in vitro. Exhibits an alpha-retaining catalytic mechanism, with evidence that maltooligosaccharide acceptors are extended at their non-reducing ends. Is also able to catalyze the reverse reaction in vitro, releasing M1P from glycogen or maltoheptaose in the presence of inorganic phosphate. Also catalyzes disproportionation reactions through maltosyl transfer between maltooligosaccharides. Is probably involved in a branched alpha-glucan biosynthetic pathway from trehalose, together with TreS, Mak and GlgB.<ref>PMID:21914799</ref>	+	[https://www.uniprot.org/uniprot/GLGE1_STRCO GLGE1_STRCO] Maltosyltransferase that uses maltose 1-phosphate (M1P) as the sugar donor to elongate linear or branched alpha-(1->4)-glucans. Maltooligosaccharides with a degree of polymerization (DP) superior or equal to 4 are efficient acceptors, with DP6 being optimal in the GlgE-catalyzed polymerization with M1P. Is specific for the alpha-anomer of M1P as substrate, since the beta-anomer of M1P gives no activity. Alpha-D-glucose 1-phosphate cannot serve as a donor substrate, but alpha-maltosyl fluoride is an efficient donor in vitro. Exhibits an alpha-retaining catalytic mechanism, with evidence that maltooligosaccharide acceptors are extended at their non-reducing ends. Is also able to catalyze the reverse reaction in vitro, releasing M1P from glycogen or maltoheptaose in the presence of inorganic phosphate. Also catalyzes disproportionation reactions through maltosyl transfer between maltooligosaccharides. Is probably involved in a branched alpha-glucan biosynthetic pathway from trehalose, together with TreS, Mak and GlgB.<ref>PMID:21914799</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Barclay~~, J E~~]]	+	[[Category: Streptomyces coelicolor]]
-	[[Category: Bornemann, S]]	+	[[Category: Barclay JE]]
-	[[Category: Gorelik, A]]	+	[[Category: Bornemann S]]
-	[[Category: Lawson~~, D M~~]]	+	[[Category: Gorelik A]]
-	[[Category: Mia, F]]	+	[[Category: Lawson DM]]
-	[[Category: Rashid~~, A M~~]]	+	[[Category: Mia F]]
-	[[Category: Stevenson~~, C E.M~~]]	+	[[Category: Rashid AM]]
-	[[Category: Syson, K]]	+	[[Category: Stevenson CEM]]
-	[[Category: Tang, M]]	+	[[Category: Syson K]]
-	~~[[Category: Alpha-glucan biosynthesis]]~~	+	[[Category: Tang M]]
-	~~[[Category: Glycoside hydrolase family 13_3]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 10:37, 12 August 2020

OCA — Wed, 12 Aug 2020 10:37:01 GMT

←Older revision		Revision as of 10:37, 12 August 2020
Line 1:		Line 1:

	==GlgE isoform 1 from Streptomyces coelicolor D394A mutant co-crystallised with maltodextrin==		==GlgE isoform 1 from Streptomyces coelicolor D394A mutant co-crystallised with maltodextrin==
-	<StructureSection load='5lgw' size='340' side='right' caption='[[5lgw]], [[Resolution\|resolution]] 1.95Å' scene=''>	+	<StructureSection load='5lgw' size='340' side='right'caption='[[5lgw]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5lgw]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LGW OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5LGW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5lgw]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"actinomyces_coelicolor"_(muller_1908)_lieske_1921 "actinomyces coelicolor" (muller 1908) lieske 1921]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LGW OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5LGW FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <~~scene name~~='~~pdbligand~~=~~N9S~~:~~4-O-ALPHA-D-GLUCOPYRANOSYL-BETA-D-GLUCOPYRANOSE'~~>~~N9S~~</~~scene~~></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">glgE1, pep1, pep1A, pep1I, SCO5443, SC6A11.19c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1902 "Actinomyces coelicolor" (Muller 1908) Lieske 1921])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Starch_synthase_(maltosyl-transferring) Starch synthase (maltosyl-transferring)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.99.16 2.4.99.16] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Starch_synthase_(maltosyl-transferring) Starch synthase (maltosyl-transferring)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.99.16 2.4.99.16] </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=5lgw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5lgw OCA], [http://pdbe.org/5lgw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5lgw RCSB], [http://www.ebi.ac.uk/pdbsum/5lgw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5lgw 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=5lgw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5lgw OCA], [http://pdbe.org/5lgw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5lgw RCSB], [http://www.ebi.ac.uk/pdbsum/5lgw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5lgw ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 23:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Barclay, J E]]		[[Category: Barclay, J E]]
	[[Category: Bornemann, S]]		[[Category: Bornemann, S]]

OCA at 05:10, 9 September 2016

OCA — Fri, 09 Sep 2016 05:10:19 GMT

←Older revision		Revision as of 05:10, 9 September 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5lgw is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==GlgE isoform 1 from Streptomyces coelicolor D394A mutant co-crystallised with maltodextrin==
		+	<StructureSection load='5lgw' size='340' side='right' caption='[[5lgw]], [[Resolution\|resolution]] 1.95Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5lgw]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LGW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5LGW FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=N9S:4-O-ALPHA-D-GLUCOPYRANOSYL-BETA-D-GLUCOPYRANOSE'>N9S</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Starch_synthase_(maltosyl-transferring) Starch synthase (maltosyl-transferring)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.99.16 2.4.99.16] </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=5lgw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5lgw OCA], [http://pdbe.org/5lgw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5lgw RCSB], [http://www.ebi.ac.uk/pdbsum/5lgw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5lgw ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/GLGE1_STRCO GLGE1_STRCO]] Maltosyltransferase that uses maltose 1-phosphate (M1P) as the sugar donor to elongate linear or branched alpha-(1->4)-glucans. Maltooligosaccharides with a degree of polymerization (DP) superior or equal to 4 are efficient acceptors, with DP6 being optimal in the GlgE-catalyzed polymerization with M1P. Is specific for the alpha-anomer of M1P as substrate, since the beta-anomer of M1P gives no activity. Alpha-D-glucose 1-phosphate cannot serve as a donor substrate, but alpha-maltosyl fluoride is an efficient donor in vitro. Exhibits an alpha-retaining catalytic mechanism, with evidence that maltooligosaccharide acceptors are extended at their non-reducing ends. Is also able to catalyze the reverse reaction in vitro, releasing M1P from glycogen or maltoheptaose in the presence of inorganic phosphate. Also catalyzes disproportionation reactions through maltosyl transfer between maltooligosaccharides. Is probably involved in a branched alpha-glucan biosynthetic pathway from trehalose, together with TreS, Mak and GlgB.<ref>PMID:21914799</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	GlgE is a maltosyltranferase involved in alpha-glucan biosynthesis in bacteria that has been genetically validated as a target for tuberculosis therapies. Crystals of the Mycobacterium tuberculosis enzyme diffract at low resolution so most structural studies have been with the very similar Streptomyces coelicolor GlgE isoform 1. Although the donor binding site for alpha-1-phosphate had been previously structurally defined, the acceptor site had not. Using mutagenesis, kinetics and protein crystallography of the S. coelicolor enzyme, we have now identified the +1 to +6 sub-sites of the acceptor/product, which overlap with the known cyclodextrin binding site. The sugar residues in the acceptor sub-sites +1 to +5 are oriented such that they disfavour the binding of malto-oligosaccharides that bear branches at their 6 positions, consistent with the known acceptor chain specificity of GlgE. A secondary binding site remote from the catalytic centre was identified that is distinct from one reported for the M. tuberculosis enzyme. This new site is capable of binding a branched alpha-glucan, and is most likely involved in guiding acceptors towards the donor site because its disruption kinetically compromises the ability of GlgE to extend polymeric substrates. However, disruption of this site, which is conserved in the S. venezuelae GlgE enzyme, did not affect the growth of S. venezuelae or the structure of the polymeric product. The acceptor sub-sites +1 to +4 in the S. coelicolor enzyme are well conserved in the M. tuberculosis enzyme so their identification could help inform the design of inhibitors with therapeutic potential.

-	~~Authors~~:	+	Ligand-bound structures and site-directed mutagenesis identify the acceptor and secondary binding sites of Streptomyces coelicolor maltosyltransferase GlgE.,Syson K, Stevenson CE, Miah F, Barclay JE, Tang M, Gorelik A, Rashid AM, Lawson DM, Bornemann S J Biol Chem. 2016 Aug 16. pii: jbc.M116.748160. PMID:27531751<ref>PMID:27531751</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5lgw" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Barclay, J E]]
		+	[[Category: Bornemann, S]]
		+	[[Category: Gorelik, A]]
		+	[[Category: Lawson, D M]]
		+	[[Category: Mia, F]]
		+	[[Category: Rashid, A M]]
		+	[[Category: Stevenson, C E.M]]
		+	[[Category: Syson, K]]
		+	[[Category: Tang, M]]
		+	[[Category: Alpha-glucan biosynthesis]]
		+	[[Category: Glycoside hydrolase family 13_3]]
		+	[[Category: Hydrolase]]
		+	[[Category: Transferase]]

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

OCA — Tue, 26 Jul 2016 13:29:46 GMT

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

←Older revision

Revision as of 13:29, 26 July 2016

OCA: New page: '''Unreleased structure''' The entry 5lgw is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

OCA — Tue, 26 Jul 2016 13:29:44 GMT

New page: '''Unreleased structure''' The entry 5lgw is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5lgw is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]