2bf6 - Revision history

OCA at 13:31, 13 December 2023

2023-12-13T13:31:55Z

← Older revision		Revision as of 13:31, 13 December 2023
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	==Atomic Resolution Structure of the bacterial sialidase NanI from Clostridium perfringens in complex with alpha-Sialic Acid (Neu5Ac).==		==Atomic Resolution Structure of the bacterial sialidase NanI from Clostridium perfringens in complex with alpha-Sialic Acid (Neu5Ac).==
	<StructureSection load='2bf6' size='340' side='right'caption='[[2bf6]]' scene=''>		<StructureSection load='2bf6' size='340' side='right'caption='[[2bf6]], [[Resolution\|resolution]] 0.97Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BF6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BF6 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2bf6]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Clostridium_perfringens Clostridium perfringens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BF6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BF6 FirstGlance]. <br>
	</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=2bf6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bf6 OCA], [https://pdbe.org/2bf6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2bf6 RCSB], [https://www.ebi.ac.uk/pdbsum/2bf6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2bf6 ProSAT]</span></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]] 0.97Å</td></tr>
			<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SIA:O-SIALIC+ACID'>SIA</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=2bf6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bf6 OCA], [https://pdbe.org/2bf6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2bf6 RCSB], [https://www.ebi.ac.uk/pdbsum/2bf6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2bf6 ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[https://www.uniprot.org/uniprot/Q59310_CLOPF Q59310_CLOPF]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 16:		Line 20:
	</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=2bf6 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=2bf6 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Clostridium perfringens is a Gram-positive bacterium responsible for bacteremia, gas gangrene, and occasionally food poisoning. Its genome encodes three sialidases, nanH, nanI, and nanJ, that are involved in the removal of sialic acids from a variety of glycoconjugates and that play a role in bacterial nutrition and pathogenesis. Recent studies on trypanosomal (trans-) sialidases have suggested that catalysis in all sialidases may proceed via a covalent intermediate similar to that of other retaining glycosidases. Here we provide further evidence to support this suggestion by reporting the 0.97A resolution atomic structure of the catalytic domain of the C. perfringens NanI sialidase, and complexes with its substrate sialic acid (N-acetylneuramic acid) also to 0.97A resolution, with a transition-state analogue (2-deoxy-2,3-dehydro-N-acetylneuraminic acid) to 1.5A resolution, and with a covalent intermediate formed using a fluorinated sialic acid analogue to 1.2A resolution. Together, these structures provide high resolution snapshots along the catalytic pathway. The crystal structures suggested that NanI is able to hydrate 2-deoxy-2,3-dehydro-N-acetylneuraminic acid to N-acetylneuramic acid. This was confirmed by NMR, and a mechanism for this activity is suggested.

			The structure of Clostridium perfringens NanI sialidase and its catalytic intermediates.,Newstead SL, Potter JA, Wilson JC, Xu G, Chien CH, Watts AG, Withers SG, Taylor GL J Biol Chem. 2008 Apr 4;283(14):9080-8. Epub 2008 Jan 24. PMID:18218621<ref>PMID:18218621</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 2bf6" style="background-color:#fffaf0;"></div>
			== References ==
			<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Clostridium perfringens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Newstead S]]		[[Category: Newstead S]]
	[[Category: Taylor GL]]		[[Category: Taylor GL]]

OCA at 15:25, 3 March 2021

2021-03-03T15:25:39Z

← Older revision		Revision as of 15:25, 3 March 2021
Line 1:		Line 1:

	==Atomic Resolution Structure of the bacterial sialidase NanI from Clostridium perfringens in complex with alpha-Sialic Acid (Neu5Ac).==		==Atomic Resolution Structure of the bacterial sialidase NanI from Clostridium perfringens in complex with alpha-Sialic Acid (Neu5Ac).==
	<StructureSection load='2bf6' size='340' side='right'caption='[[2bf6]]~~, [[Resolution\|resolution]] 0.97Å~~' scene=''>		<StructureSection load='2bf6' size='340' side='right'caption='[[2bf6]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>~~[[2bf6]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_perfringens"_veillon_and_zuber_1898 "bacillus perfringens" veillon and zuber 1898].~~ Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BF6 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2BF6 FirstGlance]. <br>		<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BF6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BF6 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SIA:O-SIALIC+ACID'>SIA</scene></td></tr>		</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=2bf6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bf6 OCA], [https://pdbe.org/2bf6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2bf6 RCSB], [https://www.ebi.ac.uk/pdbsum/2bf6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2bf6 ProSAT]</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=2bf6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bf6 OCA], [~~http~~://pdbe.org/2bf6 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2bf6 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2bf6 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2bf6 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 18:		Line 16:
	</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=2bf6 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=2bf6 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	Clostridium perfringens is a Gram-positive bacterium responsible for bacteremia, gas gangrene, and occasionally food poisoning. Its genome encodes three sialidases, nanH, nanI, and nanJ, that are involved in the removal of sialic acids from a variety of glycoconjugates and that play a role in bacterial nutrition and pathogenesis. Recent studies on trypanosomal (trans-) sialidases have suggested that catalysis in all sialidases may proceed via a covalent intermediate similar to that of other retaining glycosidases. Here we provide further evidence to support this suggestion by reporting the 0.97A resolution atomic structure of the catalytic domain of the C. perfringens NanI sialidase, and complexes with its substrate sialic acid (N-acetylneuramic acid) also to 0.97A resolution, with a transition-state analogue (2-deoxy-2,3-dehydro-N-acetylneuraminic acid) to 1.5A resolution, and with a covalent intermediate formed using a fluorinated sialic acid analogue to 1.2A resolution. Together, these structures provide high resolution snapshots along the catalytic pathway. The crystal structures suggested that NanI is able to hydrate 2-deoxy-2,3-dehydro-N-acetylneuraminic acid to N-acetylneuramic acid. This was confirmed by NMR, and a mechanism for this activity is suggested.

	The structure of Clostridium perfringens NanI sialidase and its catalytic intermediates.,Newstead SL, Potter JA, Wilson JC, Xu G, Chien CH, Watts AG, Withers SG, Taylor GL J Biol Chem. 2008 Apr 4;283(14):9080-8. Epub 2008 Jan 24. PMID:18218621<ref>PMID:18218621</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 2bf6" style="background-color:#fffaf0;"></div>~~

	~~==See Also==~~
	*[[Sialidase\|Sialidase]]
	~~== References ==~~
	~~<references/>~~
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	~~[[Category: Bacillus perfringens veillon and zuber 1898]]~~
	~~[[Category: Exo-alpha-sialidase]]~~
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Newstead, S]]		[[Category: Newstead S]]
	[[Category: Taylor~~, G L]]~~		[[Category: Taylor GL]]
	~~[[Category: Clostridium perfringen]]~~
	~~[[Category: Hydrolase]]~~
	~~[[Category: Sialic acid]]~~
	~~[[Category: Sialidase~~]]

OCA at 07:09, 23 May 2019

2019-05-23T07:09:21Z

← Older revision		Revision as of 07:09, 23 May 2019
Line 1:		Line 1:

	==Atomic Resolution Structure of the bacterial sialidase NanI from Clostridium perfringens in complex with alpha-Sialic Acid (Neu5Ac).==		==Atomic Resolution Structure of the bacterial sialidase NanI from Clostridium perfringens in complex with alpha-Sialic Acid (Neu5Ac).==
	<StructureSection load='2bf6' size='340' side='right' caption='[[2bf6]], [[Resolution\|resolution]] 0.97Å' scene=''>		<StructureSection load='2bf6' size='340' side='right'caption='[[2bf6]], [[Resolution\|resolution]] 0.97Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2bf6]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_perfringens"_veillon_and_zuber_1898 "bacillus perfringens" veillon and zuber 1898]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BF6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2BF6 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2bf6]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_perfringens"_veillon_and_zuber_1898 "bacillus perfringens" veillon and zuber 1898]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BF6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2BF6 FirstGlance]. <br>
Line 27:		Line 27:
	</div>		</div>
	<div class="pdbe-citations 2bf6" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2bf6" style="background-color:#fffaf0;"></div>

			==See Also==
			*[[Sialidase\|Sialidase]]
	== References ==		== References ==
	<references/>		<references/>
Line 33:		Line 36:
	[[Category: Bacillus perfringens veillon and zuber 1898]]		[[Category: Bacillus perfringens veillon and zuber 1898]]
	[[Category: Exo-alpha-sialidase]]		[[Category: Exo-alpha-sialidase]]
			[[Category: Large Structures]]
	[[Category: Newstead, S]]		[[Category: Newstead, S]]
	[[Category: Taylor, G L]]		[[Category: Taylor, G L]]

OCA at 05:32, 8 March 2018

2018-03-08T05:32:14Z

← Older revision		Revision as of 05:32, 8 March 2018
Line 1:		Line 1:
	==~~ATOMIC RESOLUTION STRUCTURE OF THE BACTERIAL SIALIDASE NANI FROM CLOSTRIDIUM PERFRINGENS IN COMPLEX WITH ALPHA~~-~~SIALIC ACID~~ (~~NEU5AC~~).==
			==Atomic Resolution Structure of the bacterial sialidase NanI from Clostridium perfringens in complex with alpha-Sialic Acid (Neu5Ac).==
	<StructureSection load='2bf6' size='340' side='right' caption='[[2bf6]], [[Resolution\|resolution]] 0.97Å' scene=''>		<StructureSection load='2bf6' size='340' side='right' caption='[[2bf6]], [[Resolution\|resolution]] 0.97Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SIA:O-SIALIC+ACID'>SIA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SIA:O-SIALIC+ACID'>SIA</scene></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=2bf6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bf6 OCA], [http://pdbe.org/2bf6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2bf6 RCSB], [http://www.ebi.ac.uk/pdbsum/2bf6 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=2bf6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bf6 OCA], [http://pdbe.org/2bf6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2bf6 RCSB], [http://www.ebi.ac.uk/pdbsum/2bf6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2bf6 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/bf/2bf6_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bf/2bf6_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>
	</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=2bf6 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 08:41, 11 September 2015

2015-09-11T08:41:30Z

← Older revision		Revision as of 08:41, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='2bf6' size='340' side='right' caption='[[2bf6]], [[Resolution\|resolution]] 0.97Å' scene=''>		<StructureSection load='2bf6' size='340' side='right' caption='[[2bf6]], [[Resolution\|resolution]] 0.97Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2bf6]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Clostridium_perfringens Clostridium~~ perfringens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BF6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2BF6 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2bf6]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_perfringens"_veillon_and_zuber_1898 "bacillus perfringens" veillon and zuber 1898]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BF6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2BF6 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SIA:O-SIALIC+ACID'>SIA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SIA:O-SIALIC+ACID'>SIA</scene></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=2bf6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bf6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2bf6 RCSB], [http://www.ebi.ac.uk/pdbsum/2bf6 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=2bf6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bf6 OCA], [http://pdbe.org/2bf6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2bf6 RCSB], [http://www.ebi.ac.uk/pdbsum/2bf6 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 2bf6" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Clostridium~~ perfringens]]		[[Category: Bacillus perfringens veillon and zuber 1898]]
	[[Category: Exo-alpha-sialidase]]		[[Category: Exo-alpha-sialidase]]
	[[Category: Newstead, S]]		[[Category: Newstead, S]]

OCA at 10:30, 8 January 2015

2015-01-08T10:30:24Z

← Older revision		Revision as of 10:30, 8 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2bf6]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Clostridium_perfringens Clostridium perfringens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BF6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2BF6 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2bf6]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Clostridium_perfringens Clostridium perfringens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BF6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2BF6 FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SIA:O-SIALIC+ACID'>SIA</scene><br>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SIA:O-SIALIC+ACID'>SIA</scene></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=2bf6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bf6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2bf6 RCSB], [http://www.ebi.ac.uk/pdbsum/2bf6 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=2bf6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bf6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2bf6 RCSB], [http://www.ebi.ac.uk/pdbsum/2bf6 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 31:		Line 31:
	[[Category: Clostridium perfringens]]		[[Category: Clostridium perfringens]]
	[[Category: Exo-alpha-sialidase]]		[[Category: Exo-alpha-sialidase]]
	[[Category: Newstead, S.]]		[[Category: Newstead, S]]
	[[Category: Taylor, G L.]]		[[Category: Taylor, G L]]
	[[Category: Clostridium perfringen]]		[[Category: Clostridium perfringen]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Sialic acid]]		[[Category: Sialic acid]]
	[[Category: Sialidase]]		[[Category: Sialidase]]

OCA at 01:14, 30 September 2014

2014-09-30T01:14:31Z

← Older revision		Revision as of 01:14, 30 September 2014
Line 1:		Line 1:
	[[Image:~~2bf6~~.~~png~~\|~~left~~\|~~200px~~]]		==ATOMIC RESOLUTION STRUCTURE OF THE BACTERIAL SIALIDASE NANI FROM CLOSTRIDIUM PERFRINGENS IN COMPLEX WITH ALPHA-SIALIC ACID (NEU5AC).==
			<StructureSection load='2bf6' size='340' side='right' caption='[[2bf6]], [[Resolution\|resolution]] 0.97Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[2bf6]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Clostridium_perfringens Clostridium perfringens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BF6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2BF6 FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SIA:O-SIALIC+ACID'>SIA</scene><br>
			<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=2bf6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bf6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2bf6 RCSB], [http://www.ebi.ac.uk/pdbsum/2bf6 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/bf/2bf6_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 ==
			Clostridium perfringens is a Gram-positive bacterium responsible for bacteremia, gas gangrene, and occasionally food poisoning. Its genome encodes three sialidases, nanH, nanI, and nanJ, that are involved in the removal of sialic acids from a variety of glycoconjugates and that play a role in bacterial nutrition and pathogenesis. Recent studies on trypanosomal (trans-) sialidases have suggested that catalysis in all sialidases may proceed via a covalent intermediate similar to that of other retaining glycosidases. Here we provide further evidence to support this suggestion by reporting the 0.97A resolution atomic structure of the catalytic domain of the C. perfringens NanI sialidase, and complexes with its substrate sialic acid (N-acetylneuramic acid) also to 0.97A resolution, with a transition-state analogue (2-deoxy-2,3-dehydro-N-acetylneuraminic acid) to 1.5A resolution, and with a covalent intermediate formed using a fluorinated sialic acid analogue to 1.2A resolution. Together, these structures provide high resolution snapshots along the catalytic pathway. The crystal structures suggested that NanI is able to hydrate 2-deoxy-2,3-dehydro-N-acetylneuraminic acid to N-acetylneuramic acid. This was confirmed by NMR, and a mechanism for this activity is suggested.

	~~{{STRUCTURE_2bf6\| PDB=2bf6 \| SCENE= }}~~		The structure of Clostridium perfringens NanI sialidase and its catalytic intermediates.,Newstead SL, Potter JA, Wilson JC, Xu G, Chien CH, Watts AG, Withers SG, Taylor GL J Biol Chem. 2008 Apr 4;283(14):9080-8. Epub 2008 Jan 24. PMID:18218621<ref>PMID:18218621</ref>

	~~===ATOMIC RESOLUTION STRUCTURE OF THE BACTERIAL SIALIDASE NANI FROM CLOSTRIDIUM PERFRINGENS IN COMPLEX WITH ALPHA-SIALIC ACID (NEU5AC).===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_18218621}}~~		== References ==
			<references/>
	~~==About this Structure==~~		__TOC__
	~~[[2bf6]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Clostridium_perfringens Clostridium perfringens]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2BF6 OCA].~~		</StructureSection>

	==~~Reference~~==
	<~~ref group="xtra">PMID:018218621<~~/~~ref~~><~~references group="xtra"~~/>
	[[Category: Clostridium perfringens]]		[[Category: Clostridium perfringens]]
	[[Category: Exo-alpha-sialidase]]		[[Category: Exo-alpha-sialidase]]

OCA: Protected "2bf6" [edit=sysop:move=sysop]

2013-01-06T10:29:44Z

Protected "2bf6" [edit=sysop:move=sysop]

← Older revision	Revision as of 10:29, 6 January 2013
(No difference)

OCA at 10:29, 6 January 2013

2013-01-06T10:29:41Z

← Older revision		Revision as of 10:29, 6 January 2013
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	~~{{Seed}}~~
	[[Image:2bf6.png\|left\|200px]]		[[Image:2bf6.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_2bf6", 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_2bf6\| PDB=2bf6 \| SCENE= }}		{{STRUCTURE_2bf6\| PDB=2bf6 \| SCENE= }}

	===ATOMIC RESOLUTION STRUCTURE OF THE BACTERIAL SIALIDASE NANI FROM CLOSTRIDIUM PERFRINGENS IN COMPLEX WITH ALPHA-SIALIC ACID (NEU5AC).===		===ATOMIC RESOLUTION STRUCTURE OF THE BACTERIAL SIALIDASE NANI FROM CLOSTRIDIUM PERFRINGENS IN COMPLEX WITH ALPHA-SIALIC ACID (NEU5AC).===


	~~<!--~~
	~~The line below this paragraph, {{ABSTRACT_PUBMED_18218621}}, adds the Publication Abstract to the page~~
	~~(as it appears on PubMed at http://www.pubmed.gov), where 18218621 is the PubMed ID number.~~
	~~-->~~
	{{ABSTRACT_PUBMED_18218621}}		{{ABSTRACT_PUBMED_18218621}}

	==About this Structure==		==About this Structure==
	~~2BF6~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Clostridium_perfringens Clostridium perfringens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BF6 OCA].		[[2bf6]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Clostridium_perfringens Clostridium perfringens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BF6 OCA].

	==Reference==		==Reference==
	<ref group="xtra">PMID:~~18218621~~</ref><references group="xtra"/>		<ref group="xtra">PMID:018218621</ref><references group="xtra"/>
	[[Category: Clostridium perfringens]]		[[Category: Clostridium perfringens]]
	[[Category: Exo-alpha-sialidase]]		[[Category: Exo-alpha-sialidase]]
Line 32:		Line 20:
	[[Category: Sialic acid]]		[[Category: Sialic acid]]
	[[Category: Sialidase]]		[[Category: Sialidase]]

	~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 22 11:20:30 2009''~~

OCA at 09:20, 22 March 2009

2009-03-22T09:20:30Z

← Older revision		Revision as of 09:20, 22 March 2009
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	===ATOMIC RESOLUTION STRUCTURE OF THE BACTERIAL SIALIDASE NANI FROM CLOSTRIDIUM PERFRINGENS IN COMPLEX WITH ALPHA-SIALIC ACID (NEU5AC).===		===ATOMIC RESOLUTION STRUCTURE OF THE BACTERIAL SIALIDASE NANI FROM CLOSTRIDIUM PERFRINGENS IN COMPLEX WITH ALPHA-SIALIC ACID (NEU5AC).===


			<!--
			The line below this paragraph, {{ABSTRACT_PUBMED_18218621}}, adds the Publication Abstract to the page
			(as it appears on PubMed at http://www.pubmed.gov), where 18218621 is the PubMed ID number.
			-->
			{{ABSTRACT_PUBMED_18218621}}

	==About this Structure==		==About this Structure==
	2BF6 is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Clostridium_perfringens Clostridium perfringens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BF6 OCA].		2BF6 is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Clostridium_perfringens Clostridium perfringens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BF6 OCA].

			==Reference==
			<ref group="xtra">PMID:18218621</ref><references group="xtra"/>
	[[Category: Clostridium perfringens]]		[[Category: Clostridium perfringens]]
	[[Category: Exo-alpha-sialidase]]		[[Category: Exo-alpha-sialidase]]
Line 24:		Line 33:
	[[Category: Sialidase]]		[[Category: Sialidase]]

	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Tue Feb 17 18~~:06:35 2009''		''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 22 11:20:30 2009''