3e2d - Revision history

OCA at 08:24, 20 March 2024

2024-03-20T08:24:36Z

← Older revision		Revision as of 08:24, 20 March 2024
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	<StructureSection load='3e2d' size='340' side='right'caption='[[3e2d]], [[Resolution\|resolution]] 1.40Å' scene=''>		<StructureSection load='3e2d' size='340' side='right'caption='[[3e2d]], [[Resolution\|resolution]] 1.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3e2d]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Vibrio_sp.~~_g15~~-21 Vibrio sp. ~~g15~~-21]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E2D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3E2D FirstGlance]. <br>		<table><tr><td colspan='2'>[[3e2d]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Vibrio_sp._G15-21 Vibrio sp. G15-21]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E2D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3E2D FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.4Å</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Alkaline_phosphatase Alkaline phosphatase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.1 3.1.3.1] </span></td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=3e2d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e2d OCA], [https://pdbe.org/3e2d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3e2d RCSB], [https://www.ebi.ac.uk/pdbsum/3e2d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3e2d 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=3e2d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e2d OCA], [https://pdbe.org/3e2d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3e2d RCSB], [https://www.ebi.ac.uk/pdbsum/3e2d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3e2d ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[https://www.uniprot.org/uniprot/Q93P54_9VIBR Q93P54_9VIBR]
	== 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=3e2d 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=3e2d ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	Alkaline phosphatase (AP) from the cold-adapted Vibrio strain G15-21 is among the AP variants with the highest known k(cat) value. Here the structure of the enzyme at 1.4 A resolution is reported and compared to APs from E. coli, human placenta, shrimp and the Antarctic bacterium strain TAB5. The Vibrio AP is a dimer although its monomers are without the long N-terminal helix that embraces the other subunit in many other APs. The long insertion loop, previously noted as a special feature of the Vibrio AP, serves a similar function. The surface does not have the high negative charge density as observed in shrimp AP, but a positively charged patch is observed around the active site that may be favourable for substrate binding. The dimer interface has a similar number of non-covalent interactions as other APs and the "crown"-domain is the largest observed in known APs. Part of it slopes over the catalytic site suggesting that the substrates may be small molecules. The catalytic serines are refined with multiple conformations in both monomers. One of the ligands to the catalytic zinc ion in binding site M1 is directly connected to the crown-domain and is closest to the dimer interface. Subtle movements in metal ligands may help in the release of the product and/or facilitate prior dephosphorylation of the covalent intermediate. Intersubunit interactions may be a major factor for promoting active site geometries that lead to the high catalytic activity of Vibrio AP at low temperatures.

	The 1.4 A crystal structure of the large and cold-active Vibrio sp. alkaline phosphatase.,Helland R, Larsen RL, Asgeirsson B Biochim Biophys Acta. 2009 Feb;1794(2):297-308. Epub 2008 Oct 15. PMID:18977465<ref>PMID:18977465</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 3e2d" style="background-color:#fffaf0;"></div>~~

	==See Also==		==See Also==
	*[[Alkaline phosphatase 3D structures\|Alkaline phosphatase 3D structures]]		*[[Alkaline phosphatase 3D structures\|Alkaline phosphatase 3D structures]]
	~~== References ==~~
	~~<references/>~~
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	~~[[Category: Alkaline phosphatase]]~~
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Vibrio sp. ~~g15~~-21]]		[[Category: Vibrio sp. G15-21]]
	[[Category: Asgeirsson, B]]		[[Category: Asgeirsson B]]
	[[Category: Helland, R]]		[[Category: Helland R]]
	[[Category: Larsen~~, R L]]~~		[[Category: Larsen RL]]
	~~[[Category: Cold-adaptation]]~~
	~~[[Category: Dimer]]~~
	~~[[Category: Hydrolase]]~~
	~~[[Category: Metalloenzyme]]~~
	~~[[Category: Psychrophilic bacteria~~]]

OCA at 08:13, 9 February 2022

2022-02-09T08:13:44Z

← Older revision		Revision as of 08:13, 9 February 2022
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	<StructureSection load='3e2d' size='340' side='right'caption='[[3e2d]], [[Resolution\|resolution]] 1.40Å' scene=''>		<StructureSection load='3e2d' size='340' side='right'caption='[[3e2d]], [[Resolution\|resolution]] 1.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3e2d]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Vibrio_sp._g15-21 Vibrio sp. g15-21]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E2D OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3E2D FirstGlance]. <br>		<table><tr><td colspan='2'>[[3e2d]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Vibrio_sp._g15-21 Vibrio sp. g15-21]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E2D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3E2D FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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/Alkaline_phosphatase Alkaline phosphatase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.1 3.1.3.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Alkaline_phosphatase Alkaline phosphatase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.1 3.1.3.1] </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=3e2d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e2d OCA], [~~http~~://pdbe.org/3e2d PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3e2d RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3e2d PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3e2d 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=3e2d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e2d OCA], [https://pdbe.org/3e2d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3e2d RCSB], [https://www.ebi.ac.uk/pdbsum/3e2d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3e2d ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 08:04, 31 July 2019

2019-07-31T08:04:57Z

← Older revision		Revision as of 08:04, 31 July 2019
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	==The 1.4 A crystal structure of the large and cold-active Vibrio sp. alkaline phosphatase==		==The 1.4 A crystal structure of the large and cold-active Vibrio sp. alkaline phosphatase==
	<StructureSection load='3e2d' size='340' side='right' caption='[[3e2d]], [[Resolution\|resolution]] 1.40Å' scene=''>		<StructureSection load='3e2d' size='340' side='right'caption='[[3e2d]], [[Resolution\|resolution]] 1.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3e2d]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Vibrio_sp._g15-21 Vibrio sp. g15-21]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E2D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3E2D FirstGlance]. <br>		<table><tr><td colspan='2'>[[3e2d]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Vibrio_sp._g15-21 Vibrio sp. g15-21]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E2D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3E2D FirstGlance]. <br>
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/e2/3e2d_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/e2/3e2d_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>
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	</div>		</div>
	<div class="pdbe-citations 3e2d" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3e2d" style="background-color:#fffaf0;"></div>

			==See Also==
			*[[Alkaline phosphatase 3D structures\|Alkaline phosphatase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Alkaline phosphatase]]		[[Category: Alkaline phosphatase]]
			[[Category: Large Structures]]
	[[Category: Vibrio sp. g15-21]]		[[Category: Vibrio sp. g15-21]]
	[[Category: Asgeirsson, B]]		[[Category: Asgeirsson, B]]

OCA at 09:00, 25 October 2017

2017-10-25T09:00:53Z

← Older revision		Revision as of 09:00, 25 October 2017
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	</div>		</div>
	<div class="pdbe-citations 3e2d" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3e2d" style="background-color:#fffaf0;"></div>

	~~==See Also==~~
	*[[Alkaline phosphatase\|Alkaline phosphatase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 20:27, 11 August 2016

2016-08-11T20:27:41Z

← Older revision		Revision as of 20:27, 11 August 2016
Line 1:		Line 1:

	==The 1.4 A crystal structure of the large and cold-active Vibrio sp. alkaline phosphatase==		==The 1.4 A crystal structure of the large and cold-active Vibrio sp. alkaline phosphatase==
	<StructureSection load='3e2d' size='340' side='right' caption='[[3e2d]], [[Resolution\|resolution]] 1.40Å' scene=''>		<StructureSection load='3e2d' size='340' side='right' caption='[[3e2d]], [[Resolution\|resolution]] 1.40Å' scene=''>
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	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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/Alkaline_phosphatase Alkaline phosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.1 3.1.3.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alkaline_phosphatase Alkaline phosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.1 3.1.3.1] </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=3e2d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e2d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3e2d RCSB], [http://www.ebi.ac.uk/pdbsum/3e2d 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=3e2d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e2d OCA], [http://pdbe.org/3e2d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3e2d RCSB], [http://www.ebi.ac.uk/pdbsum/3e2d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3e2d ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	<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=3e2d ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<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 3e2d" style="background-color:#fffaf0;"></div>

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

OCA at 10:59, 20 January 2015

2015-01-20T10:59:22Z

← Older revision		Revision as of 10:59, 20 January 2015
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3e2d]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Vibrio_sp._g15-21 Vibrio sp. g15-21]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E2D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3E2D FirstGlance]. <br>		<table><tr><td colspan='2'>[[3e2d]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Vibrio_sp._g15-21 Vibrio sp. g15-21]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E2D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3E2D FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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/Alkaline_phosphatase Alkaline phosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.1 3.1.3.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alkaline_phosphatase Alkaline phosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.1 3.1.3.1] </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=3e2d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e2d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3e2d RCSB], [http://www.ebi.ac.uk/pdbsum/3e2d 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=3e2d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e2d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3e2d RCSB], [http://www.ebi.ac.uk/pdbsum/3e2d PDBsum]</span></td></tr>
	<table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	[[Category: Alkaline phosphatase]]		[[Category: Alkaline phosphatase]]
	[[Category: Vibrio sp. g15-21]]		[[Category: Vibrio sp. g15-21]]
	[[Category: Asgeirsson, B.]]		[[Category: Asgeirsson, B]]
	[[Category: Helland, R.]]		[[Category: Helland, R]]
	[[Category: Larsen, R L.]]		[[Category: Larsen, R L]]
	[[Category: Cold-adaptation]]		[[Category: Cold-adaptation]]
	[[Category: Dimer]]		[[Category: Dimer]]

OCA at 12:43, 29 September 2014

2014-09-29T12:43:00Z

← Older revision		Revision as of 12:43, 29 September 2014
Line 1:		Line 1:
	[[Image:~~3e2d~~.~~png~~\|~~left~~\|~~200px~~]]		==The 1.4 A crystal structure of the large and cold-active Vibrio sp. alkaline phosphatase==
			<StructureSection load='3e2d' size='340' side='right' caption='[[3e2d]], [[Resolution\|resolution]] 1.40Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[3e2d]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Vibrio_sp._g15-21 Vibrio sp. g15-21]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E2D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3E2D FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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/Alkaline_phosphatase Alkaline phosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.1 3.1.3.1] </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=3e2d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e2d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3e2d RCSB], [http://www.ebi.ac.uk/pdbsum/3e2d 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/e2/3e2d_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 ==
			Alkaline phosphatase (AP) from the cold-adapted Vibrio strain G15-21 is among the AP variants with the highest known k(cat) value. Here the structure of the enzyme at 1.4 A resolution is reported and compared to APs from E. coli, human placenta, shrimp and the Antarctic bacterium strain TAB5. The Vibrio AP is a dimer although its monomers are without the long N-terminal helix that embraces the other subunit in many other APs. The long insertion loop, previously noted as a special feature of the Vibrio AP, serves a similar function. The surface does not have the high negative charge density as observed in shrimp AP, but a positively charged patch is observed around the active site that may be favourable for substrate binding. The dimer interface has a similar number of non-covalent interactions as other APs and the "crown"-domain is the largest observed in known APs. Part of it slopes over the catalytic site suggesting that the substrates may be small molecules. The catalytic serines are refined with multiple conformations in both monomers. One of the ligands to the catalytic zinc ion in binding site M1 is directly connected to the crown-domain and is closest to the dimer interface. Subtle movements in metal ligands may help in the release of the product and/or facilitate prior dephosphorylation of the covalent intermediate. Intersubunit interactions may be a major factor for promoting active site geometries that lead to the high catalytic activity of Vibrio AP at low temperatures.

	~~{{STRUCTURE_3e2d\| PDB=3e2d \| SCENE= }}~~		The 1.4 A crystal structure of the large and cold-active Vibrio sp. alkaline phosphatase.,Helland R, Larsen RL, Asgeirsson B Biochim Biophys Acta. 2009 Feb;1794(2):297-308. Epub 2008 Oct 15. PMID:18977465<ref>PMID:18977465</ref>

	~~===The 1.4 A crystal structure~~ of the ~~large and cold-active Vibrio sp~~. ~~alkaline phosphatase===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_18977465}}~~

	~~==About this Structure==~~
	~~[[3e2d]] is a 2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org~~/~~wiki/Vibrio_sp._g15-21 Vibrio sp. g15-21]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E2D OCA].~~

	==See Also==		==See Also==
	*[[Alkaline phosphatase\|Alkaline phosphatase]]		*[[Alkaline phosphatase\|Alkaline phosphatase]]
			== References ==
	==~~Reference~~==		<references/>
	<~~ref group="xtra">PMID:018977465<~~/~~ref~~><~~references group="xtra"~~/>		__TOC__
			</StructureSection>
	[[Category: Alkaline phosphatase]]		[[Category: Alkaline phosphatase]]
	[[Category: Vibrio sp. g15-21]]		[[Category: Vibrio sp. g15-21]]

OCA at 17:53, 20 October 2012

2012-10-20T17:53:44Z

← Older revision		Revision as of 17:53, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
	[[3e2d]] is a 2 chain structure ~~of [[Alkaline phosphatase]]~~ with sequence from [http://en.wikipedia.org/wiki/~~Bacteria Bacteria~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E2D OCA].		[[3e2d]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Vibrio_sp._g15-21 Vibrio sp. g15-21]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E2D OCA].

	==See Also==		==See Also==
Line 16:		Line 16:
	<ref group="xtra">PMID:018977465</ref><references group="xtra"/>		<ref group="xtra">PMID:018977465</ref><references group="xtra"/>
	[[Category: Alkaline phosphatase]]		[[Category: Alkaline phosphatase]]
	[[Category: ~~Bacteria~~]]		[[Category: Vibrio sp. g15-21]]
	[[Category: Asgeirsson, B.]]		[[Category: Asgeirsson, B.]]
	[[Category: Helland, R.]]		[[Category: Helland, R.]]

OCA: Protected "3e2d" [edit=sysop:move=sysop]

2012-07-27T02:20:22Z

Protected "3e2d" [edit=sysop:move=sysop]

← Older revision	Revision as of 02:20, 27 July 2012
(No difference)

OCA at 02:20, 27 July 2012

2012-07-27T02:20:21Z

← Older revision		Revision as of 02:20, 27 July 2012
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	~~{{Seed}}~~
	[[Image:3e2d.png\|left\|200px]]		[[Image:3e2d.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_3e2d", creates the "Structure Box" on the page.~~
	~~You may change the PDB parameter (which sets the PDB file loaded into the applet)~~
	~~or the SCENE parameter (which sets the initial scene displayed when the page is loaded),~~
	~~or leave the SCENE parameter empty for the default display.~~
	~~-->~~
	{{STRUCTURE_3e2d\| PDB=3e2d \| SCENE= }}		{{STRUCTURE_3e2d\| PDB=3e2d \| SCENE= }}

	===The 1.4 A crystal structure of the large and cold-active Vibrio sp. alkaline phosphatase===		===The 1.4 A crystal structure of the large and cold-active Vibrio sp. alkaline phosphatase===


	~~<!--~~
	~~The line below this paragraph, {{ABSTRACT_PUBMED_18977465}}, adds the Publication Abstract to the page~~
	~~(as it appears on PubMed at http://www.pubmed.gov), where 18977465 is the PubMed ID number.~~
	~~-->~~
	{{ABSTRACT_PUBMED_18977465}}		{{ABSTRACT_PUBMED_18977465}}

	==About this Structure==		==About this Structure==
	~~3E2D~~ is a 2 ~~chains~~ structure of ~~sequences~~ from [http://en.wikipedia.org/wiki/Bacteria Bacteria]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E2D OCA].		[[3e2d]] is a 2 chain structure of [[Alkaline phosphatase]] with sequence from [http://en.wikipedia.org/wiki/Bacteria Bacteria]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E2D OCA].

			==See Also==
			*[[Alkaline phosphatase\|Alkaline phosphatase]]

	==Reference==		==Reference==
	<ref group="xtra">PMID:~~18977465~~</ref><references group="xtra"/>		<ref group="xtra">PMID:018977465</ref><references group="xtra"/>
	[[Category: Alkaline phosphatase]]		[[Category: Alkaline phosphatase]]
	[[Category: Bacteria]]		[[Category: Bacteria]]
Line 30:		Line 21:
	[[Category: Larsen, R L.]]		[[Category: Larsen, R L.]]
	[[Category: Cold-adaptation]]		[[Category: Cold-adaptation]]
	~~[[Category: Crystallography]]~~
	[[Category: Dimer]]		[[Category: Dimer]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Metalloenzyme]]		[[Category: Metalloenzyme]]
	[[Category: Psychrophilic bacteria]]		[[Category: Psychrophilic bacteria]]

	~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Jun 25 08:31:59 2009''~~