1kwg - Revision history

OCA at 13:26, 13 March 2024

OCA — Wed, 13 Mar 2024 13:26:10 GMT

←Older revision		Revision as of 13:26, 13 March 2024
Line 3:		Line 3:
	<StructureSection load='1kwg' size='340' side='right'caption='[[1kwg]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='1kwg' size='340' side='right'caption='[[1kwg]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1kwg]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KWG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KWG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1kwg]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KWG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KWG FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.6Å</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Beta-galactosidase Beta-galactosidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.23 3.2.1.23] </span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=1kwg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kwg OCA], [https://pdbe.org/1kwg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kwg RCSB], [https://www.ebi.ac.uk/pdbsum/1kwg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kwg 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=1kwg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kwg OCA], [https://pdbe.org/1kwg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kwg RCSB], [https://www.ebi.ac.uk/pdbsum/1kwg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kwg ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/BGAL_THETH BGAL_THETH]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1kwg ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1kwg ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The beta-galactosidase from an extreme thermophile, Thermus thermophilus A4 (A4-beta-Gal), is thermostable and belongs to the glycoside hydrolase family 42 (GH-42). As the first known structures of a GH-42 enzyme, we determined the crystal structures of free and galactose-bound A4-beta-Gal at 1.6A and 2.2A resolution, respectively. A4-beta-Gal forms a homotrimeric structure resembling a flowerpot. Each monomer has an active site located inside a large central tunnel. The N-terminal domain of A4-beta-Gal has a TIM barrel fold, as predicted from hydrophobic cluster analysis. The putative catalytic residues of A4-beta-Gal (Glu141 and Glu312) superimpose well with the catalytic residues of Escherichia coli beta-galactosidase. The environment around the catalytic nucleophile (Glu312) is similar to that in the case of E.coli beta-galactosidase, but the recognition mechanism for a substrate is different. Trp182 of the next subunit of the trimer constitutes a part of the active-site pocket, indicating that the trimeric structure is essential for the enzyme activity. Structural comparison with other glycoside hydrolases revealed that many features of the 4/7 superfamily are conserved in the A4-beta-Gal structure. On the basis of the results of 1H NMR spectroscopy, A4-beta-Gal was determined to be a "retaining" enzyme. Interestingly, the active site was similar with those of retaining enzymes, but the overall fold of the TIM barrel domain was very similar to that of an inverting enzyme, beta-amylase.
-
-	Trimeric crystal structure of the glycoside hydrolase family 42 beta-galactosidase from Thermus thermophilus A4 and the structure of its complex with galactose.,Hidaka M, Fushinobu S, Ohtsu N, Motoshima H, Matsuzawa H, Shoun H, Wakagi T J Mol Biol. 2002 Sep 6;322(1):79-91. PMID:12215416<ref>PMID:12215416</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1kwg" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Galactosidase 3D structures\|Galactosidase 3D structures]]		*[[Galactosidase 3D structures\|Galactosidase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]
-	[[Category: Beta-galactosidase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Fushinobu, S]]	+	[[Category: Thermus thermophilus]]
-	[[Category: Hidaka, M]]	+	[[Category: Fushinobu S]]
-	[[Category: Matsuzawa, H]]	+	[[Category: Hidaka M]]
-	[[Category: Motoshima, H]]	+	[[Category: Matsuzawa H]]
-	[[Category: Ohtsu, N]]	+	[[Category: Motoshima H]]
-	[[Category: Shoun, H]]	+	[[Category: Ohtsu N]]
-	[[Category: Wakagi, T]]	+	[[Category: Shoun H]]
-	~~[[Category: Glycoside hydrolase family 42]]~~	+	[[Category: Wakagi T]]
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Tim barrel]]~~	+
-	~~[[Category: Trimer~~]]	+

OCA at 06:36, 18 August 2021

OCA — Wed, 18 Aug 2021 06:36:31 GMT

←Older revision		Revision as of 06:36, 18 August 2021
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	<StructureSection load='1kwg' size='340' side='right'caption='[[1kwg]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='1kwg' size='340' side='right'caption='[[1kwg]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1kwg]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KWG OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1KWG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1kwg]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KWG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KWG FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Beta-galactosidase Beta-galactosidase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.23 3.2.1.23] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Beta-galactosidase Beta-galactosidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.23 3.2.1.23] </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=1kwg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kwg OCA], [~~http~~://pdbe.org/1kwg PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1kwg RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1kwg PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1kwg 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=1kwg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kwg OCA], [https://pdbe.org/1kwg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kwg RCSB], [https://www.ebi.ac.uk/pdbsum/1kwg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kwg ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 12:38, 13 November 2019

OCA — Wed, 13 Nov 2019 12:38:04 GMT

←Older revision		Revision as of 12:38, 13 November 2019
Line 1:		Line 1:

	==Crystal structure of Thermus thermophilus A4 beta-galactosidase==		==Crystal structure of Thermus thermophilus A4 beta-galactosidase==
-	<StructureSection load='1kwg' size='340' side='right' caption='[[1kwg]], [[Resolution\|resolution]] 1.60Å' scene=''>	+	<StructureSection load='1kwg' size='340' side='right'caption='[[1kwg]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1kwg]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KWG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KWG FirstGlance]. <br>		<table><tr><td colspan='2'>[[1kwg]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KWG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KWG FirstGlance]. <br>
Line 27:		Line 27:
	</div>		</div>
	<div class="pdbe-citations 1kwg" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1kwg" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Galactosidase 3D structures\|Galactosidase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 33:		Line 36:
	[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]		[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]
	[[Category: Beta-galactosidase]]		[[Category: Beta-galactosidase]]
		+	[[Category: Large Structures]]
	[[Category: Fushinobu, S]]		[[Category: Fushinobu, S]]
	[[Category: Hidaka, M]]		[[Category: Hidaka, M]]

OCA at 21:48, 24 January 2018

OCA — Wed, 24 Jan 2018 21:48:07 GMT

←Older revision		Revision as of 21:48, 24 January 2018
Line 1:		Line 1:
		+
	==Crystal structure of Thermus thermophilus A4 beta-galactosidase==		==Crystal structure of Thermus thermophilus A4 beta-galactosidase==
	<StructureSection load='1kwg' size='340' side='right' caption='[[1kwg]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='1kwg' size='340' side='right' caption='[[1kwg]], [[Resolution\|resolution]] 1.60Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-galactosidase Beta-galactosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.23 3.2.1.23] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-galactosidase Beta-galactosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.23 3.2.1.23] </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=1kwg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kwg OCA], [http://pdbe.org/1kwg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1kwg RCSB], [http://www.ebi.ac.uk/pdbsum/1kwg 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=1kwg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kwg OCA], [http://pdbe.org/1kwg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1kwg RCSB], [http://www.ebi.ac.uk/pdbsum/1kwg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1kwg ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 11:		Line 12:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kw/1kwg_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kw/1kwg_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 26:		Line 27:
	</div>		</div>
	<div class="pdbe-citations 1kwg" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1kwg" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Galactosidase\|Galactosidase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 12:18, 9 February 2016

OCA — Tue, 09 Feb 2016 12:18:45 GMT

←Older revision		Revision as of 12:18, 9 February 2016
Line 15:		Line 15:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1kwg ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 22:11, 10 September 2015

OCA — Thu, 10 Sep 2015 22:11:11 GMT

←Older revision		Revision as of 22:11, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1kwg' size='340' side='right' caption='[[1kwg]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='1kwg' size='340' side='right' caption='[[1kwg]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1kwg]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Thermus_thermophilus Thermus thermophilus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KWG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KWG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1kwg]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KWG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KWG FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-galactosidase Beta-galactosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.23 3.2.1.23] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-galactosidase Beta-galactosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.23 3.2.1.23] </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=1kwg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kwg OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1kwg RCSB], [http://www.ebi.ac.uk/pdbsum/1kwg 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=1kwg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kwg OCA], [http://pdbe.org/1kwg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1kwg RCSB], [http://www.ebi.ac.uk/pdbsum/1kwg PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 25:		Line 25:
	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 1kwg" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 32:		Line 33:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]
	[[Category: Beta-galactosidase]]		[[Category: Beta-galactosidase]]
-	[[Category: Thermus thermophilus]]
	[[Category: Fushinobu, S]]		[[Category: Fushinobu, S]]
	[[Category: Hidaka, M]]		[[Category: Hidaka, M]]

OCA at 17:06, 5 January 2015

OCA — Mon, 05 Jan 2015 17:06:58 GMT

←Older revision		Revision as of 17:06, 5 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1kwg]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KWG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KWG FirstGlance]. <br>		<table><tr><td colspan='2'>[[1kwg]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KWG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KWG FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-galactosidase Beta-galactosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.23 3.2.1.23] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-galactosidase Beta-galactosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.23 3.2.1.23] </span></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1kwg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kwg OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1kwg RCSB], [http://www.ebi.ac.uk/pdbsum/1kwg 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=1kwg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kwg OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1kwg RCSB], [http://www.ebi.ac.uk/pdbsum/1kwg PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 34:
	[[Category: Beta-galactosidase]]		[[Category: Beta-galactosidase]]
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]
-	[[Category: Fushinobu, S.]]	+	[[Category: Fushinobu, S]]
-	[[Category: Hidaka, M.]]	+	[[Category: Hidaka, M]]
-	[[Category: Matsuzawa, H.]]	+	[[Category: Matsuzawa, H]]
-	[[Category: Motoshima, H.]]	+	[[Category: Motoshima, H]]
-	[[Category: Ohtsu, N.]]	+	[[Category: Ohtsu, N]]
-	[[Category: Shoun, H.]]	+	[[Category: Shoun, H]]
-	[[Category: Wakagi, T.]]	+	[[Category: Wakagi, T]]
	[[Category: Glycoside hydrolase family 42]]		[[Category: Glycoside hydrolase family 42]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Tim barrel]]		[[Category: Tim barrel]]
	[[Category: Trimer]]		[[Category: Trimer]]

OCA at 18:39, 28 September 2014

OCA — Sun, 28 Sep 2014 18:39:51 GMT

←Older revision		Revision as of 18:39, 28 September 2014
Line 1:		Line 1:
-	[[~~Image~~:1kwg.~~png\|left~~\|200px]]	+	==Crystal structure of Thermus thermophilus A4 beta-galactosidase==
		+	<StructureSection load='1kwg' size='340' side='right' caption='[[1kwg]], [[Resolution\|resolution]] 1.60Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1kwg]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KWG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KWG FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-galactosidase Beta-galactosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.23 3.2.1.23] </span></td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1kwg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kwg OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1kwg RCSB], [http://www.ebi.ac.uk/pdbsum/1kwg PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kw/1kwg_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The beta-galactosidase from an extreme thermophile, Thermus thermophilus A4 (A4-beta-Gal), is thermostable and belongs to the glycoside hydrolase family 42 (GH-42). As the first known structures of a GH-42 enzyme, we determined the crystal structures of free and galactose-bound A4-beta-Gal at 1.6A and 2.2A resolution, respectively. A4-beta-Gal forms a homotrimeric structure resembling a flowerpot. Each monomer has an active site located inside a large central tunnel. The N-terminal domain of A4-beta-Gal has a TIM barrel fold, as predicted from hydrophobic cluster analysis. The putative catalytic residues of A4-beta-Gal (Glu141 and Glu312) superimpose well with the catalytic residues of Escherichia coli beta-galactosidase. The environment around the catalytic nucleophile (Glu312) is similar to that in the case of E.coli beta-galactosidase, but the recognition mechanism for a substrate is different. Trp182 of the next subunit of the trimer constitutes a part of the active-site pocket, indicating that the trimeric structure is essential for the enzyme activity. Structural comparison with other glycoside hydrolases revealed that many features of the 4/7 superfamily are conserved in the A4-beta-Gal structure. On the basis of the results of 1H NMR spectroscopy, A4-beta-Gal was determined to be a "retaining" enzyme. Interestingly, the active site was similar with those of retaining enzymes, but the overall fold of the TIM barrel domain was very similar to that of an inverting enzyme, beta-amylase.

-	~~{{STRUCTURE_1kwg\| PDB=1kwg \| SCENE= }}~~	+	Trimeric crystal structure of the glycoside hydrolase family 42 beta-galactosidase from Thermus thermophilus A4 and the structure of its complex with galactose.,Hidaka M, Fushinobu S, Ohtsu N, Motoshima H, Matsuzawa H, Shoun H, Wakagi T J Mol Biol. 2002 Sep 6;322(1):79-91. PMID:12215416<ref>PMID:12215416</ref>

-	~~===Crystal structure~~ of ~~Thermus thermophilus A4 beta-galactosidase===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_12215416}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1kwg]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Thermus_thermophilus Thermus thermophilus]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1KWG OCA].~~	+

	==See Also==		==See Also==
	*[[Galactosidase\|Galactosidase]]		*[[Galactosidase\|Galactosidase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:012215416<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Beta-galactosidase]]		[[Category: Beta-galactosidase]]
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]

OCA at 13:48, 20 October 2012

OCA — Sat, 20 Oct 2012 13:48:55 GMT

←Older revision		Revision as of 13:48, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1kwg]] is a 1 chain structure ~~of [[Galactosidase]]~~ with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KWG OCA].	+	[[1kwg]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KWG OCA].

	==See Also==		==See Also==

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

OCA — Thu, 26 Jul 2012 13:11:40 GMT

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

←Older revision

Revision as of 13:11, 26 July 2012