1n1v - Revision history

OCA at 08:44, 10 April 2024

2024-04-10T08:44:49Z

←Older revision		Revision as of 08:44, 10 April 2024
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	<StructureSection load='1n1v' size='340' side='right'caption='[[1n1v]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='1n1v' size='340' side='right'caption='[[1n1v]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1n1v]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Tryra Tryra~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N1V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1N1V FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1n1v]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Trypanosoma_rangeli Trypanosoma rangeli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N1V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1N1V FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=DAN:2-DEOXY~~-2~~,3-DEHYDRO-N-ACETYL-NEURAMINIC+ACID'>DAN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.1Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height: 3em;~~'>~~[[1mz6\|1mz6]], [[1mz5\|1mz5]], [[1n1s\|1n1s]], [[1n1t\|1n1t]], [[1n1y\|1n1y]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DAN:2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC+ACID'>DAN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[https://en.wikipedia.org/wiki/Exo-alpha-sialidase Exo-alpha-sialidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.18 3.2.1.18]~~ </~~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=1n1v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n1v OCA], [https://pdbe.org/1n1v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1n1v RCSB], [https://www.ebi.ac.uk/pdbsum/1n1v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1n1v 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=1n1v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n1v OCA], [https://pdbe.org/1n1v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1n1v RCSB], [https://www.ebi.ac.uk/pdbsum/1n1v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1n1v ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/O44049_TRYRA O44049_TRYRA]
	== 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=1n1v 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=1n1v ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The structure of the recombinant Trypanosoma rangeli sialidase (TrSA) has been determined at 1.6A resolution, and the structures of its complexes with the transition state analog inhibitor 2-deoxy-2,3-dehydro-N-acetyl-neuraminic acid (DANA), Neu-5-Ac-thio-alpha(2,3)-galactoside (NATG) and N-acetylneuraminic acid (NANA) have been determined at 1.64A, 2.1A and 2.85A, respectively. The 3D structure of TrSA is essentially identical to that of the natural enzyme, except for the absence of covalently attached sugar at five distinct N-glycosylation sites. The protein exhibits a topologically rigid active site architecture that is unaffected by ligand binding. The overall binding of DANA to the active site cleft is similar to that observed for other viral and bacterial sialidases, dominated by the interactions of the inhibitor carboxylate with the conserved arginine triad. However, the interactions of the other pyranoside ring substituents (hydroxyl, N-acetyl and glycerol moieties) differ between trypanosomal, bacterial and viral sialidases, providing a structural basis for specific inhibitor design. Sialic acid is found to bind the enzyme with the sugar ring in a distorted (half-chair or boat) conformation and the 2-OH hydroxyl group at hydrogen bonding distance of the carboxylate of Asp60, substantiating a direct catalytic role for this residue. A detailed comparison of TrSA with the closely related structure of T.cruzi trans-sialidase (TcTS) reveals a highly conserved catalytic center, where subtle structural differences account for strikingly different enzymatic activities and inhibition properties. The structure of TrSA in complex with NATG shows the active site cleft occupied by a smaller compound which could be identified as DANA, probably the product of a hydrolytic side reaction. Indeed, TrSA (but not TcTS) was found to cleave O and S-linked sialylated substrates, further stressing the functional differences between trypanosomal sialidases and trans-sialidases.
-
-	The high resolution structures of free and inhibitor-bound Trypanosoma rangeli sialidase and its comparison with T. cruzi trans-sialidase.,Amaya MF, Buschiazzo A, Nguyen T, Alzari PM J Mol Biol. 2003 Jan 24;325(4):773-84. PMID:12507479<ref>PMID:12507479</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1n1v" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Exo-alpha-sialidase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Tryra~~]]	+	[[Category: Trypanosoma rangeli]]
-	[[Category: Alzari~~, P M~~]]	+	[[Category: Alzari PM]]
-	[[Category: Amaya~~, M F~~]]	+	[[Category: Amaya MF]]
-	[[Category: Buschiazzo, A]]	+	[[Category: Buschiazzo A]]
-	[[Category: Nguyen, T]]	+	[[Category: Nguyen T]]
-	~~[[Category: Beta propeller]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Lectin-like fold~~]]	+

OCA at 06:58, 25 August 2021

2021-08-25T06:58:01Z

←Older revision		Revision as of 06:58, 25 August 2021
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	<StructureSection load='1n1v' size='340' side='right'caption='[[1n1v]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='1n1v' size='340' side='right'caption='[[1n1v]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1n1v]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Tryra Tryra]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N1V OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1N1V FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1n1v]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Tryra Tryra]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N1V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1N1V FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DAN:2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC+ACID'>DAN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DAN:2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC+ACID'>DAN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1mz6\|1mz6]], [[1mz5\|1mz5]], [[1n1s\|1n1s]], [[1n1t\|1n1t]], [[1n1y\|1n1y]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1mz6\|1mz6]], [[1mz5\|1mz5]], [[1n1s\|1n1s]], [[1n1t\|1n1t]], [[1n1y\|1n1y]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Exo-alpha-sialidase Exo-alpha-sialidase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.18 3.2.1.18] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Exo-alpha-sialidase Exo-alpha-sialidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.18 3.2.1.18] </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=1n1v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n1v OCA], [~~http~~://pdbe.org/1n1v PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1n1v RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1n1v PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1n1v 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=1n1v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n1v OCA], [https://pdbe.org/1n1v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1n1v RCSB], [https://www.ebi.ac.uk/pdbsum/1n1v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1n1v ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	</div>		</div>
	<div class="pdbe-citations 1n1v" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1n1v" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Sialidase\|Sialidase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 18:49, 20 November 2019

2019-11-20T18:49:20Z

←Older revision		Revision as of 18:49, 20 November 2019
Line 1:		Line 1:

	==Trypanosoma rangeli sialidase in complex with DANA==		==Trypanosoma rangeli sialidase in complex with DANA==
-	<StructureSection load='1n1v' size='340' side='right' caption='[[1n1v]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='1n1v' size='340' side='right'caption='[[1n1v]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1n1v]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Tryra Tryra]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N1V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1N1V FirstGlance]. <br>		<table><tr><td colspan='2'>[[1n1v]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Tryra Tryra]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N1V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1N1V FirstGlance]. <br>
Line 28:		Line 28:
	</div>		</div>
	<div class="pdbe-citations 1n1v" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1n1v" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Sialidase\|Sialidase]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Exo-alpha-sialidase]]		[[Category: Exo-alpha-sialidase]]
		+	[[Category: Large Structures]]
	[[Category: Tryra]]		[[Category: Tryra]]
	[[Category: Alzari, P M]]		[[Category: Alzari, P M]]

OCA at 08:12, 31 January 2018

2018-01-31T08:12:13Z

←Older revision		Revision as of 08:12, 31 January 2018
Line 1:		Line 1:
		+
	==Trypanosoma rangeli sialidase in complex with DANA==		==Trypanosoma rangeli sialidase in complex with DANA==
	<StructureSection load='1n1v' size='340' side='right' caption='[[1n1v]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='1n1v' size='340' side='right' caption='[[1n1v]], [[Resolution\|resolution]] 2.10Å' scene=''>
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	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1mz6\|1mz6]], [[1mz5\|1mz5]], [[1n1s\|1n1s]], [[1n1t\|1n1t]], [[1n1y\|1n1y]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1mz6\|1mz6]], [[1mz5\|1mz5]], [[1n1s\|1n1s]], [[1n1t\|1n1t]], [[1n1y\|1n1y]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Exo-alpha-sialidase Exo-alpha-sialidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.18 3.2.1.18] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Exo-alpha-sialidase Exo-alpha-sialidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.18 3.2.1.18] </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=1n1v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n1v OCA], [http://pdbe.org/1n1v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1n1v RCSB], [http://www.ebi.ac.uk/pdbsum/1n1v 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=1n1v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n1v OCA], [http://pdbe.org/1n1v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1n1v RCSB], [http://www.ebi.ac.uk/pdbsum/1n1v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1n1v ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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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/n1/1n1v_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/n1/1n1v_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>

OCA at 08:34, 8 February 2016

2016-02-08T08:34:40Z

←Older revision		Revision as of 08:34, 8 February 2016
Line 16:		Line 16:
	<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=1n1v ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 09:46, 10 September 2015

2015-09-10T09:46:02Z

←Older revision		Revision as of 09:46, 10 September 2015
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	<StructureSection load='1n1v' size='340' side='right' caption='[[1n1v]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='1n1v' size='340' side='right' caption='[[1n1v]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1n1v]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Trypanosoma_rangeli Trypanosoma rangeli~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N1V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1N1V FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1n1v]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Tryra Tryra]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N1V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1N1V FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DAN:2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC+ACID'>DAN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DAN:2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC+ACID'>DAN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1mz6\|1mz6]], [[1mz5\|1mz5]], [[1n1s\|1n1s]], [[1n1t\|1n1t]], [[1n1y\|1n1y]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1mz6\|1mz6]], [[1mz5\|1mz5]], [[1n1s\|1n1s]], [[1n1t\|1n1t]], [[1n1y\|1n1y]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Exo-alpha-sialidase Exo-alpha-sialidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.18 3.2.1.18] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Exo-alpha-sialidase Exo-alpha-sialidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.18 3.2.1.18] </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=1n1v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n1v OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1n1v RCSB], [http://www.ebi.ac.uk/pdbsum/1n1v 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=1n1v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n1v OCA], [http://pdbe.org/1n1v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1n1v RCSB], [http://www.ebi.ac.uk/pdbsum/1n1v PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 26:		Line 26:
	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 1n1v" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
Line 31:		Line 32:
	</StructureSection>		</StructureSection>
	[[Category: Exo-alpha-sialidase]]		[[Category: Exo-alpha-sialidase]]
-	[[Category: ~~Trypanosoma rangeli~~]]	+	[[Category: Tryra]]
	[[Category: Alzari, P M]]		[[Category: Alzari, P M]]
	[[Category: Amaya, M F]]		[[Category: Amaya, M F]]

OCA at 17:07, 5 January 2015

2015-01-05T17:07:04Z

←Older revision		Revision as of 17:07, 5 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1n1v]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Trypanosoma_rangeli Trypanosoma rangeli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N1V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1N1V FirstGlance]. <br>		<table><tr><td colspan='2'>[[1n1v]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Trypanosoma_rangeli Trypanosoma rangeli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N1V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1N1V FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DAN:2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC+ACID'>DAN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DAN:2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC+ACID'>DAN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1mz6\|1mz6]], [[1mz5\|1mz5]], [[1n1s\|1n1s]], [[1n1t\|1n1t]], [[1n1y\|1n1y]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1mz6\|1mz6]], [[1mz5\|1mz5]], [[1n1s\|1n1s]], [[1n1t\|1n1t]], [[1n1y\|1n1y]]</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Exo-alpha-sialidase Exo-alpha-sialidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.18 3.2.1.18] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Exo-alpha-sialidase Exo-alpha-sialidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.18 3.2.1.18] </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=1n1v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n1v OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1n1v RCSB], [http://www.ebi.ac.uk/pdbsum/1n1v 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=1n1v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n1v OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1n1v RCSB], [http://www.ebi.ac.uk/pdbsum/1n1v 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 32:		Line 32:
	[[Category: Exo-alpha-sialidase]]		[[Category: Exo-alpha-sialidase]]
	[[Category: Trypanosoma rangeli]]		[[Category: Trypanosoma rangeli]]
-	[[Category: Alzari, P M.]]	+	[[Category: Alzari, P M]]
-	[[Category: Amaya, M F.]]	+	[[Category: Amaya, M F]]
-	[[Category: Buschiazzo, A.]]	+	[[Category: Buschiazzo, A]]
-	[[Category: Nguyen, T.]]	+	[[Category: Nguyen, T]]
	[[Category: Beta propeller]]		[[Category: Beta propeller]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Lectin-like fold]]		[[Category: Lectin-like fold]]

OCA at 11:52, 3 October 2014

2014-10-03T11:52:03Z

←Older revision		Revision as of 11:52, 3 October 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_1n1v\| PDB~~=1n1v \| ~~SCENE~~= }}	+	==Trypanosoma rangeli sialidase in complex with DANA==
-	===Trypanosoma rangeli sialidase ~~in complex~~ with ~~DANA~~===	+	<StructureSection load='1n1v' size='340' side='right' caption='[[1n1v]], [[Resolution\|resolution]] 2.10Å' scene=''>
-	~~{{ABSTRACT_PUBMED_12507479}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1n1v]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Trypanosoma_rangeli Trypanosoma rangeli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N1V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1N1V FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DAN:2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC+ACID'>DAN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1mz6\|1mz6]], [[1mz5\|1mz5]], [[1n1s\|1n1s]], [[1n1t\|1n1t]], [[1n1y\|1n1y]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Exo-alpha-sialidase Exo-alpha-sialidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.18 3.2.1.18] </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=1n1v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n1v OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1n1v RCSB], [http://www.ebi.ac.uk/pdbsum/1n1v 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/n1/1n1v_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 structure of the recombinant Trypanosoma rangeli sialidase (TrSA) has been determined at 1.6A resolution, and the structures of its complexes with the transition state analog inhibitor 2-deoxy-2,3-dehydro-N-acetyl-neuraminic acid (DANA), Neu-5-Ac-thio-alpha(2,3)-galactoside (NATG) and N-acetylneuraminic acid (NANA) have been determined at 1.64A, 2.1A and 2.85A, respectively. The 3D structure of TrSA is essentially identical to that of the natural enzyme, except for the absence of covalently attached sugar at five distinct N-glycosylation sites. The protein exhibits a topologically rigid active site architecture that is unaffected by ligand binding. The overall binding of DANA to the active site cleft is similar to that observed for other viral and bacterial sialidases, dominated by the interactions of the inhibitor carboxylate with the conserved arginine triad. However, the interactions of the other pyranoside ring substituents (hydroxyl, N-acetyl and glycerol moieties) differ between trypanosomal, bacterial and viral sialidases, providing a structural basis for specific inhibitor design. Sialic acid is found to bind the enzyme with the sugar ring in a distorted (half-chair or boat) conformation and the 2-OH hydroxyl group at hydrogen bonding distance of the carboxylate of Asp60, substantiating a direct catalytic role for this residue. A detailed comparison of TrSA with the closely related structure of T.cruzi trans-sialidase (TcTS) reveals a highly conserved catalytic center, where subtle structural differences account for strikingly different enzymatic activities and inhibition properties. The structure of TrSA in complex with NATG shows the active site cleft occupied by a smaller compound which could be identified as DANA, probably the product of a hydrolytic side reaction. Indeed, TrSA (but not TcTS) was found to cleave O and S-linked sialylated substrates, further stressing the functional differences between trypanosomal sialidases and trans-sialidases.

-	~~==About this Structure==~~	+	The high resolution structures of free and inhibitor-bound Trypanosoma rangeli sialidase and its comparison with T. cruzi trans-sialidase.,Amaya MF, Buschiazzo A, Nguyen T, Alzari PM J Mol Biol. 2003 Jan 24;325(4):773-84. PMID:12507479<ref>PMID:12507479</ref>
-	~~[[1n1v]] is a 1 chain structure~~ with ~~sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Trypanosoma_rangeli Trypanosoma rangeli]~~. ~~Full crystallographic information is available from [http~~:~~//oca~~.~~weizmann.ac.il~~/~~oca-bin/ocashort?id=1N1V OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:012507479</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Exo-alpha-sialidase]]		[[Category: Exo-alpha-sialidase]]
	[[Category: Trypanosoma rangeli]]		[[Category: Trypanosoma rangeli]]

OCA at 10:59, 16 April 2014

2014-04-16T10:59:49Z

←Older revision		Revision as of 10:59, 16 April 2014
Line 1:		Line 1:
-	[[Image:1n1v.png\|left\|200px]]
-
-	<!--
-	The line below this paragraph, containing "STRUCTURE_1n1v", 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_1n1v\| PDB=1n1v \| SCENE= }}		{{STRUCTURE_1n1v\| PDB=1n1v \| SCENE= }}
-
	===Trypanosoma rangeli sialidase in complex with DANA===		===Trypanosoma rangeli sialidase in complex with DANA===
-
-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_12507479}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 12507479 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_12507479}}		{{ABSTRACT_PUBMED_12507479}}

Line 22:		Line 7:

	==Reference==		==Reference==
-	<ref group="xtra">PMID:012507479</ref><references group="xtra"/>	+	<ref group="xtra">PMID:012507479</ref><references group="xtra"/><references/>
	[[Category: Exo-alpha-sialidase]]		[[Category: Exo-alpha-sialidase]]
	[[Category: Trypanosoma rangeli]]		[[Category: Trypanosoma rangeli]]

OCA: Protected "1n1v" [edit=sysop:move=sysop]

2012-06-02T09:49:28Z

Protected "1n1v" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:49, 2 June 2012