4wvb - Revision history

OCA at 15:23, 8 November 2023

2023-11-08T15:23:59Z

← Older revision		Revision as of 15:23, 8 November 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4wvb]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4WVB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4WVB FirstGlance]. <br>		<table><tr><td colspan='2'>[[4wvb]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4WVB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4WVB 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=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</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]] 1.77Å</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=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</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=4wvb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wvb OCA], [https://pdbe.org/4wvb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4wvb RCSB], [https://www.ebi.ac.uk/pdbsum/4wvb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4wvb 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=4wvb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wvb OCA], [https://pdbe.org/4wvb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4wvb RCSB], [https://www.ebi.ac.uk/pdbsum/4wvb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4wvb ProSAT]</span></td></tr>
	</table>		</table>

OCA at 20:59, 12 April 2023

2023-04-12T20:59:09Z

← Older revision		Revision as of 20:59, 12 April 2023
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	<StructureSection load='4wvb' size='340' side='right'caption='[[4wvb]], [[Resolution\|resolution]] 1.77Å' scene=''>		<StructureSection load='4wvb' size='340' side='right'caption='[[4wvb]], [[Resolution\|resolution]] 1.77Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4wvb]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Thet8 Thet8~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4WVB OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4WVB FirstGlance]. <br>		<table><tr><td colspan='2'>[[4wvb]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4WVB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4WVB 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=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</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=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></td></tr>
	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2z07\|2z07]], [[4wva\|4wva]], [[4wvc\|4wvc]]</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=4wvb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wvb OCA], [https://pdbe.org/4wvb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4wvb RCSB], [https://www.ebi.ac.uk/pdbsum/4wvb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4wvb ProSAT]</span></td></tr>
	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TTHA0978 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 THET8])~~</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=4wvb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wvb OCA], [~~http~~://pdbe.org/4wvb PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4wvb RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4wvb PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4wvb ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[https://www.uniprot.org/uniprot/Q5SJN0_THET8 Q5SJN0_THET8]
	<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: ~~Thet8~~]]		[[Category: Thermus thermophilus HB8]]
	[[Category: Ichikawa, M]]		[[Category: Ichikawa M]]
	[[Category: Miyazaki, T]]		[[Category: Miyazaki T]]
	[[Category: Nishikawa, A]]		[[Category: Nishikawa A]]
	[[Category: Tonozuka, T]]		[[Category: Tonozuka T]]
	~~[[Category: Gh63]]~~
	~~[[Category: Hydrolase~~]]

OCA at 08:56, 23 May 2019

2019-05-23T08:56:07Z

← Older revision		Revision as of 08:56, 23 May 2019
Line 1:		Line 1:

	==Crystal structure of GH63 mannosylglycerate hydrolase from Thermus thermophilus HB8 in complex with glucose==		==Crystal structure of GH63 mannosylglycerate hydrolase from Thermus thermophilus HB8 in complex with glucose==
	<StructureSection load='4wvb' size='340' side='right' caption='[[4wvb]], [[Resolution\|resolution]] 1.77Å' scene=''>		<StructureSection load='4wvb' size='340' side='right'caption='[[4wvb]], [[Resolution\|resolution]] 1.77Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4wvb]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4WVB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4WVB FirstGlance]. <br>		<table><tr><td colspan='2'>[[4wvb]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Thet8 Thet8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4WVB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4WVB 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=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</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=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2z07\|2z07]], [[4wva\|4wva]], [[4wvc\|4wvc]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2z07\|2z07]], [[4wva\|4wva]], [[4wvc\|4wvc]]</td></tr>
			<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TTHA0978 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 THET8])</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=4wvb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wvb OCA], [http://pdbe.org/4wvb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4wvb RCSB], [http://www.ebi.ac.uk/pdbsum/4wvb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4wvb 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=4wvb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wvb OCA], [http://pdbe.org/4wvb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4wvb RCSB], [http://www.ebi.ac.uk/pdbsum/4wvb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4wvb ProSAT]</span></td></tr>
	</table>		</table>
Line 21:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Large Structures]]
			[[Category: Thet8]]
	[[Category: Ichikawa, M]]		[[Category: Ichikawa, M]]
	[[Category: Miyazaki, T]]		[[Category: Miyazaki, T]]

OCA at 00:19, 26 January 2017

2017-01-26T00:19:13Z

← Older revision		Revision as of 00:19, 26 January 2017
Line 1:		Line 1:

	==Crystal structure of GH63 mannosylglycerate hydrolase from Thermus thermophilus HB8 in complex with glucose==		==Crystal structure of GH63 mannosylglycerate hydrolase from Thermus thermophilus HB8 in complex with glucose==
	<StructureSection load='4wvb' size='340' side='right' caption='[[4wvb]], [[Resolution\|resolution]] 1.77Å' scene=''>		<StructureSection load='4wvb' size='340' side='right' caption='[[4wvb]], [[Resolution\|resolution]] 1.77Å' scene=''>
Line 5:		Line 6:
	</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=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</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=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2z07\|2z07]], [[4wva\|4wva]], [[4wvc\|4wvc]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2z07\|2z07]], [[4wva\|4wva]], [[4wvc\|4wvc]]</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=4wvb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wvb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4wvb RCSB], [http://www.ebi.ac.uk/pdbsum/4wvb 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=4wvb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wvb OCA], [http://pdbe.org/4wvb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4wvb RCSB], [http://www.ebi.ac.uk/pdbsum/4wvb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4wvb ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	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 4wvb" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 11:44, 11 March 2015

2015-03-11T11:44:20Z

← Older revision		Revision as of 11:44, 11 March 2015
Line 1:		Line 1:
	'''~~Unreleased~~ structure'''		==Crystal structure of GH63 mannosylglycerate hydrolase from Thermus thermophilus HB8 in complex with glucose==
			<StructureSection load='4wvb' size='340' side='right' caption='[[4wvb]], [[Resolution\|resolution]] 1.77Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[4wvb]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4WVB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4WVB 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=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></td></tr>
			<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2z07\|2z07]], [[4wva\|4wva]], [[4wvc\|4wvc]]</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=4wvb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wvb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4wvb RCSB], [http://www.ebi.ac.uk/pdbsum/4wvb PDBsum]</span></td></tr>
			</table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Glycoside hydrolase family 63 (GH63) proteins are found in eukaryotes such as processing alpha-glucosidase I and also many bacteria and archaea. Recent studies have identified two bacterial and one plant GH63 mannosylglycerate hydrolases that act on both glucosylglycerate and mannosylglycerate, which are compatible solutes found in many thermophilic prokaryotes and some plants. Here we report the 1.67-A crystal structure of one of these GH63 mannosylglycerate hydrolases, Tt8MGH from Thermus thermophilus HB8, which is 99% homologous to mannosylglycerate hydrolase from T.thermophilus HB27. Tt8MGH consists of a single (alpha/alpha)6-barrel catalytic domain with two additional helices and two long loops which form a homotrimer. The structures of this protein in complexes with glucose or glycerate were also determined at 1.77- or 2.10-A resolution, respectively. A comparison of these structures revealed that the conformations of three flexible loops were largely different from each other. The conformational changes may be induced by ligand binding and serve to form finger-like structures for holding substrates. These findings represent the first-ever proposed substrate recognition mechanism for GH63 mannosylglycerate hydrolase.

	~~The entry 4wvb is ON HOLD until Paper Publication~~		Crystal structure and substrate-binding mode of GH63 mannosylglycerate hydrolase from Thermus thermophilus HB8.,Miyazaki T, Ichikawa M, Iino H, Nishikawa A, Tonozuka T J Struct Biol. 2015 Feb 21. pii: S1047-8477(15)00037-4. doi:, 10.1016/j.jsb.2015.02.006. PMID:25712767<ref>PMID:25712767</ref>

	~~Authors: Miyazaki~~, T.~~, Ichikawa, M~~.~~, Nishikawa, A., Tonozuka, T~~.		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~Description~~: ~~Crystal structure of GH63 glucosyl/mannosylglycerate hydrolase from Thermus thermophilus HB8 in complex with glucose~~		== References ==
	[[Category: ~~Unreleased Structures~~]]		<references/>
			__TOC__
			</StructureSection>
			[[Category: Ichikawa, M]]
			[[Category: Miyazaki, T]]
	[[Category: Nishikawa, A]]		[[Category: Nishikawa, A]]
	~~[[Category: Ichikawa, M]]~~
	[[Category: Tonozuka, T]]		[[Category: Tonozuka, T]]
	[[Category: ~~Miyazaki, T~~]]		[[Category: Gh63]]
			[[Category: Hydrolase]]

OCA at 20:03, 24 December 2014

2014-12-24T20:03:14Z

← Older revision		Revision as of 20:03, 24 December 2014
Line 6:		Line 6:

	Description: Crystal structure of GH63 glucosyl/mannosylglycerate hydrolase from Thermus thermophilus HB8 in complex with glucose		Description: Crystal structure of GH63 glucosyl/mannosylglycerate hydrolase from Thermus thermophilus HB8 in complex with glucose
			[[Category: Unreleased Structures]]
			[[Category: Nishikawa, A]]
			[[Category: Ichikawa, M]]
			[[Category: Tonozuka, T]]
			[[Category: Miyazaki, T]]

OCA at 11:36, 17 December 2014

2014-12-17T11:36:17Z

← Older revision		Revision as of 11:36, 17 December 2014
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 4wvb is ON HOLD		The entry 4wvb is ON HOLD until Paper Publication

	Authors: Miyazaki, T., Ichikawa, M., Nishikawa, A., Tonozuka, T.		Authors: Miyazaki, T., Ichikawa, M., Nishikawa, A., Tonozuka, T.

	Description: Crystal structure of GH63 glucosyl/mannosylglycerate hydrolase from Thermus thermophilus HB8 in complex with glucose		Description: Crystal structure of GH63 glucosyl/mannosylglycerate hydrolase from Thermus thermophilus HB8 in complex with glucose

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

2014-11-19T11:59:24Z

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

← Older revision	Revision as of 11:59, 19 November 2014
(No difference)

OCA: New page: '''Unreleased structure''' The entry 4wvb is ON HOLD Authors: Miyazaki, T., Ichikawa, M., Nishikawa, A., Tonozuka, T. Description: Crystal structure of GH63 glucosyl/mannosylglycerate ...

2014-11-19T11:59:23Z

New page: '''Unreleased structure''' The entry 4wvb is ON HOLD Authors: Miyazaki, T., Ichikawa, M., Nishikawa, A., Tonozuka, T. Description: Crystal structure of GH63 glucosyl/mannosylglycerate ...

New page

'''Unreleased structure'''

The entry 4wvb is ON HOLD

Authors: Miyazaki, T., Ichikawa, M., Nishikawa, A., Tonozuka, T.

Description: Crystal structure of GH63 glucosyl/mannosylglycerate hydrolase from Thermus thermophilus HB8 in complex with glucose