3w7u - Revision history

OCA at 05:26, 3 August 2022

OCA — Wed, 03 Aug 2022 05:26:15 GMT

←Older revision		Revision as of 05:26, 3 August 2022
Line 1:		Line 1:

	==Escherichia coli K12 YgjK complexed with galactose==		==Escherichia coli K12 YgjK complexed with galactose==
-	<StructureSection load='3w7u' size='340' side='right' caption='[[3w7u]], [[Resolution\|resolution]] 1.99Å' scene=''>	+	<StructureSection load='3w7u' size='340' side='right'caption='[[3w7u]], [[Resolution\|resolution]] 1.99Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3w7u]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Ecoli Ecoli]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3c69 3c69]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3W7U OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3W7U FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3w7u]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Ecoli Ecoli]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3c69 3c69]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3W7U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3W7U FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GLA:ALPHA+D-GALACTOSE'>GLA</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GLA:ALPHA+D-GALACTOSE'>GLA</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3d3i\|3d3i]], [[3w7s\|3w7s]], [[3w7t\|3w7t]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3d3i\|3d3i]], [[3w7s\|3w7s]], [[3w7t\|3w7t]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b3080, JW3051, ygjK ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b3080, JW3051, ygjK ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=3w7u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3w7u OCA], [~~http~~://pdbe.org/3w7u PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3w7u RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3w7u PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3w7u 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=3w7u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3w7u OCA], [https://pdbe.org/3w7u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3w7u RCSB], [https://www.ebi.ac.uk/pdbsum/3w7u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3w7u ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/YGJK_ECOLI YGJK_ECOLI]] Glucoside hydrolase that cleaves the alpha-1,3-glucosidic linkage in nigerose. Has very low activity towards maltooligosaccharides, soluble starch, nigerotriose, kojibiose and trehalose.	+	[[https://www.uniprot.org/uniprot/YGJK_ECOLI YGJK_ECOLI]] Glucoside hydrolase that cleaves the alpha-1,3-glucosidic linkage in nigerose. Has very low activity towards maltooligosaccharides, soluble starch, nigerotriose, kojibiose and trehalose.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 25:		Line 25:
	</StructureSection>		</StructureSection>
	[[Category: Ecoli]]		[[Category: Ecoli]]
		+	[[Category: Large Structures]]
	[[Category: Kamitori, S]]		[[Category: Kamitori, S]]
	[[Category: Kurakata, Y]]		[[Category: Kurakata, Y]]

OCA at 16:39, 5 August 2016

OCA — Fri, 05 Aug 2016 16:39:15 GMT

←Older revision		Revision as of 16:39, 5 August 2016
Line 1:		Line 1:
		+
	==Escherichia coli K12 YgjK complexed with galactose==		==Escherichia coli K12 YgjK complexed with galactose==
	<StructureSection load='3w7u' size='340' side='right' caption='[[3w7u]], [[Resolution\|resolution]] 1.99Å' scene=''>		<StructureSection load='3w7u' size='340' side='right' caption='[[3w7u]], [[Resolution\|resolution]] 1.99Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3w7u]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Escherichia_coli_k-12 Escherichia coli k-12~~]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3c69 3c69]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3W7U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3W7U FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3w7u]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3c69 3c69]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3W7U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3W7U FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GLA:ALPHA+D-GALACTOSE'>GLA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GLA:ALPHA+D-GALACTOSE'>GLA</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3d3i\|3d3i]], [[3w7s\|3w7s]], [[3w7t\|3w7t]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3d3i\|3d3i]], [[3w7s\|3w7s]], [[3w7t\|3w7t]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b3080, JW3051, ygjK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ~~Escherichia coli K-12~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b3080, JW3051, ygjK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=3w7u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3w7u OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3w7u RCSB], [http://www.ebi.ac.uk/pdbsum/3w7u 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=3w7u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3w7u OCA], [http://pdbe.org/3w7u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3w7u RCSB], [http://www.ebi.ac.uk/pdbsum/3w7u PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3w7u ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/YGJK_ECOLI YGJK_ECOLI]] Glucoside hydrolase that cleaves the alpha-1,3-glucosidic linkage in nigerose. Has very low activity towards maltooligosaccharides, soluble starch, nigerotriose, kojibiose and trehalose.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 16:		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 3w7u" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Escherichia coli k-12~~]]	+	[[Category: Ecoli]]
	[[Category: Kamitori, S]]		[[Category: Kamitori, S]]
	[[Category: Kurakata, Y]]		[[Category: Kurakata, Y]]

OCA at 07:27, 21 December 2014

OCA — Sun, 21 Dec 2014 07:27:17 GMT

←Older revision		Revision as of 07:27, 21 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_3w7u~~\| ~~PDB~~=3w7u \| ~~SCENE~~= }}	+	==Escherichia coli K12 YgjK complexed with galactose==
-	===Escherichia coli ~~K12 YgjK complexed with galactose~~===	+	<StructureSection load='3w7u' size='340' side='right' caption='[[3w7u]], [[Resolution\|resolution]] 1.99Å' scene=''>
-	~~{{ABSTRACT_PUBMED_18586271}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3w7u]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_k-12 Escherichia coli k-12]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3c69 3c69]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3W7U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3W7U FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GLA:ALPHA+D-GALACTOSE'>GLA</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3d3i\|3d3i]], [[3w7s\|3w7s]], [[3w7t\|3w7t]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">b3080, JW3051, ygjK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 Escherichia coli K-12])</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=3w7u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3w7u OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3w7u RCSB], [http://www.ebi.ac.uk/pdbsum/3w7u PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Proteins belonging to the glycoside hydrolase family 63 (GH63) are found in bacteria, archaea, and eukaryotes. Eukaryotic GH63 proteins are processing -glucosidase I enzymes that hydrolyze an oligosaccharide precursor of eukaryotic N-linked glycoproteins. In contrast, the functions of the bacterial and archaeal GH63 proteins are unclear. Here we determined the crystal structure of a bacterial GH63 enzyme, Escherichia coli K12 YgjK, at 1.78 A resolution and investigated some properties of the enzyme. YgjK consists of the N-domain and the A-domain, joined by a linker region. The N-domain is composed of 18 antiparallel beta-strands and is classified as a super-beta-sandwich. The A-domain contains 16 -helices, 12 of which form an (/)(6)-barrel; the remaining 4 -helices are found in an extra structural unit that we designated as the A'-region. YgjK, a member of the glycoside hydrolase clan GH-G, shares structural similarity with glucoamylase (GH15) and chitobiose phosphorylase (GH94) [corrected] both of which belong to clan GH-L or GH-L-like [corrected] In crystal structures of YgjK in complex with glucose, mannose, and galactose, all of the glucose, mannose, and galactose units were located in the catalytic cleft. YgjK showed the highest activity for the -1,3-glucosidic linkage of nigerose, but also hydrolyzed trehalose, kojibiose, and maltooligosaccharides from maltose to maltoheptaose, although the activities were low. These findings suggest that YgjK is a glucosidase with relaxed specificity for sugars.

-	~~==About this Structure==~~	+	Structural insights into the substrate specificity and function of Escherichia coli K12 YgjK, a glucosidase belonging to the glycoside hydrolase family 63.,Kurakata Y, Uechi A, Yoshida H, Kamitori S, Sakano Y, Nishikawa A, Tonozuka T J Mol Biol. 2008 Aug 1;381(1):116-28. Epub 2008 Jun 30. PMID:18586271<ref>PMID:18586271</ref>
-	~~[[3w7u]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_k-12~~ Escherichia coli ~~k-12]. This structure supersedes~~ the ~~now removed PDB entry [http://oca~~.~~weizmann~~.~~ac.il/oca-bin/send-pdb?obs=~~1~~&id=3c69 3c69]. Full crystallographic information is available from [http~~:~~//oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=3W7U OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:018586271</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Escherichia coli k-12]]		[[Category: Escherichia coli k-12]]
-	[[Category: Kamitori, S.]]	+	[[Category: Kamitori, S]]
-	[[Category: Kurakata, Y.]]	+	[[Category: Kurakata, Y]]
-	[[Category: Miyazaki, T.]]	+	[[Category: Miyazaki, T]]
-	[[Category: Nishikawa, A.]]	+	[[Category: Nishikawa, A]]
-	[[Category: Sakano, Y.]]	+	[[Category: Sakano, Y]]
-	[[Category: Tonozuka, T.]]	+	[[Category: Tonozuka, T]]
-	[[Category: Uechi, A.]]	+	[[Category: Uechi, A]]
-	[[Category: Yoshida, H.]]	+	[[Category: Yoshida, H]]
	[[Category: Alpha/alpha barrel]]		[[Category: Alpha/alpha barrel]]
	[[Category: Gh63]]		[[Category: Gh63]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Processing alpha-glucosidase i]]		[[Category: Processing alpha-glucosidase i]]

OCA at 01:25, 4 April 2013

OCA — Thu, 04 Apr 2013 01:25:42 GMT

←Older revision		Revision as of 01:25, 4 April 2013
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{STRUCTURE_3w7u\| PDB=3w7u \| SCENE= }}
		+	===Escherichia coli K12 YgjK complexed with galactose===
		+	{{ABSTRACT_PUBMED_18586271}}

-	~~The entry~~ 3w7u is ~~ON HOLD~~	+	==About this Structure==
		+	[[3w7u]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_k-12 Escherichia coli k-12]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3c69 3c69]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3W7U OCA].

-	~~Authors~~: ~~Miyazaki~~, T., Kurakata, Y., ~~Uechi~~, A.~~, Yoshida, H., Kamitori, S.,~~ Sakano, Y., ~~Nishikawa~~, A., ~~Tonozuka, T~~.	+	==Reference==
-		+	<ref group="xtra">PMID:018586271</ref><references group="xtra"/><references/>
-	~~Description~~: ~~Escherichia coli K12 YgjK complexed with galactose~~	+	[[Category: Escherichia coli k-12]]
		+	[[Category: Kamitori, S.]]
		+	[[Category: Kurakata, Y.]]
		+	[[Category: Miyazaki, T.]]
		+	[[Category: Nishikawa, A.]]
		+	[[Category: Sakano, Y.]]
		+	[[Category: Tonozuka, T.]]
		+	[[Category: Uechi, A.]]
		+	[[Category: Yoshida, H.]]
		+	[[Category: Alpha/alpha barrel]]
		+	[[Category: Gh63]]
		+	[[Category: Hydrolase]]
		+	[[Category: Processing alpha-glucosidase i]]

OCA: Protected "3w7u" [edit=sysop:move=sysop]

OCA — Wed, 13 Mar 2013 09:39:13 GMT

Protected "3w7u" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:39, 13 March 2013

OCA: New page: '''Unreleased structure''' The entry 3w7u is ON HOLD Authors: Miyazaki, T., Kurakata, Y., Uechi, A., Yoshida, H., Kamitori, S., Sakano, Y., Nishikawa, A., Tonozuka, T. Description: Esc...

OCA — Wed, 13 Mar 2013 09:39:12 GMT

New page: '''Unreleased structure''' The entry 3w7u is ON HOLD Authors: Miyazaki, T., Kurakata, Y., Uechi, A., Yoshida, H., Kamitori, S., Sakano, Y., Nishikawa, A., Tonozuka, T. Description: Esc...

New page

'''Unreleased structure'''

The entry 3w7u is ON HOLD

Authors: Miyazaki, T., Kurakata, Y., Uechi, A., Yoshida, H., Kamitori, S., Sakano, Y., Nishikawa, A., Tonozuka, T.

Description: Escherichia coli K12 YgjK complexed with galactose