5afd - Revision history

OCA at 11:08, 10 January 2024

OCA — Wed, 10 Jan 2024 11:08:44 GMT

←Older revision		Revision as of 11:08, 10 January 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5afd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aliivibrio_salmonicida_LFI1238 Aliivibrio salmonicida LFI1238]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AFD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5AFD FirstGlance]. <br>		<table><tr><td colspan='2'>[[5afd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aliivibrio_salmonicida_LFI1238 Aliivibrio salmonicida LFI1238]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AFD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5AFD 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=GOL:GLYCEROL'>GOL</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]] 1.65Å</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=GOL:GLYCEROL'>GOL</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=5afd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5afd OCA], [https://pdbe.org/5afd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5afd RCSB], [https://www.ebi.ac.uk/pdbsum/5afd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5afd 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=5afd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5afd OCA], [https://pdbe.org/5afd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5afd RCSB], [https://www.ebi.ac.uk/pdbsum/5afd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5afd ProSAT]</span></td></tr>
	</table>		</table>

OCA at 04:55, 25 May 2023

OCA — Thu, 25 May 2023 04:55:24 GMT

←Older revision		Revision as of 04:55, 25 May 2023
Line 3:		Line 3:
	<StructureSection load='5afd' size='340' side='right'caption='[[5afd]], [[Resolution\|resolution]] 1.65Å' scene=''>		<StructureSection load='5afd' size='340' side='right'caption='[[5afd]], [[Resolution\|resolution]] 1.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5afd]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Alisl Alisl~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AFD OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5AFD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5afd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aliivibrio_salmonicida_LFI1238 Aliivibrio salmonicida LFI1238]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AFD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5AFD 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=GOL:GLYCEROL'>GOL</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=GOL:GLYCEROL'>GOL</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/N-acetylneuraminate_lyase N-acetylneuraminate lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.3.3 4.1.3.3] </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=5afd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5afd OCA], [https://pdbe.org/5afd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5afd RCSB], [https://www.ebi.ac.uk/pdbsum/5afd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5afd ProSAT]</span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5afd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5afd OCA], [~~http~~://pdbe.org/5afd PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5afd RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5afd PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5afd ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/B6EI04_ALISL B6EI04_ALISL]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 17:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 5afd" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5afd" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[N-acetylneuraminate lyase 3D structures\|N-acetylneuraminate lyase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Alisl~~]]	+	[[Category: Aliivibrio salmonicida LFI1238]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: N-acetylneuraminate lyase]]~~	+	[[Category: Altermark B]]
-	[[Category: Altermark, B]]	+	[[Category: Gurung MK]]
-	[[Category: Gurung~~, M K~~]]	+	[[Category: Helland R]]
-	[[Category: Helland, R]]	+	[[Category: Rader ILU]]
-	[[Category: Rader~~, I L.U~~]]	+	[[Category: Smalas AO]]
-	[[Category: Smalas~~, A O]]~~	+
-	~~[[Category: Alkaline]]~~	+
-	~~[[Category: Cold active]]~~	+
-	~~[[Category: Lyase]]~~	+
-	~~[[Category: Psychrophile]]~~	+
-	~~[[Category: Sialic acid aldolase~~]]	+

OCA at 07:18, 26 June 2019

OCA — Wed, 26 Jun 2019 07:18:09 GMT

←Older revision		Revision as of 07:18, 26 June 2019
Line 1:		Line 1:

	==Native structure of N-acetylneuramininate lyase (sialic acid aldolase) from Aliivibrio salmonicida==		==Native structure of N-acetylneuramininate lyase (sialic acid aldolase) from Aliivibrio salmonicida==
-	<StructureSection load='5afd' size='340' side='right' caption='[[5afd]], [[Resolution\|resolution]] 1.65Å' scene=''>	+	<StructureSection load='5afd' size='340' side='right'caption='[[5afd]], [[Resolution\|resolution]] 1.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5afd]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AFD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5AFD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5afd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Alisl Alisl]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AFD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5AFD 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=GOL:GLYCEROL'>GOL</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=GOL:GLYCEROL'>GOL</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/N-acetylneuraminate_lyase N-acetylneuraminate lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.3.3 4.1.3.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/N-acetylneuraminate_lyase N-acetylneuraminate lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.3.3 4.1.3.3] </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=5afd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5afd OCA], [http://pdbe.org/5afd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5afd RCSB], [http://www.ebi.ac.uk/pdbsum/5afd 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=5afd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5afd OCA], [http://pdbe.org/5afd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5afd RCSB], [http://www.ebi.ac.uk/pdbsum/5afd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5afd ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	N-acetylneuraminate lyases (NALs) are enzymes that catalyze the reversible cleavage and synthesis of sialic acids. They are therefore commonly used for the production of these high-value sugars. This study presents the recombinant production, together with biochemical and structural data, of the NAL from the psychrophilic bacterium Aliivibrio salmonicida LFI1238 (AsNAL). Our characterization shows that AsNAL possesses high activity and stability at alkaline pH. We confirm that these properties allow for the use in a one-pot reaction at alkaline pH for the synthesis of N-acetylneuraminic acid (Neu5Ac, the most common sialic acid) from the inexpensive precursor N-acetylglucosamine. We also show that the enzyme has a cold active nature with an optimum temperature for Neu5Ac synthesis at 20 degrees C. The equilibrium constant for the reaction was calculated at different temperatures, and the formation of Neu5Ac acid is favored at low temperatures, making the cold active enzyme a well-suited candidate for use in such exothermic reactions. The specific activity is high compared to the homologue from Escherichia coli at three tested temperatures, and the enzyme shows a higher catalytic efficiency and turnover number for cleavage at 37 degrees C. Mutational studies reveal that amino acid residue Asn 168 is important for the high kcat. The crystal structure of AsNAL was solved to 1.65 A resolution and reveals a compact, tetrameric protein similar to other NAL structures. The data presented provides a framework to guide further optimization of its application in sialic acid production and opens the possibility for further design of the enzyme.
		+
		+	Features and structure of a cold active N-acetylneuraminate lyase.,Gurung MK, Altermark B, Helland R, Smalas AO, Raeder ILU PLoS One. 2019 Jun 11;14(6):e0217713. doi: 10.1371/journal.pone.0217713., eCollection 2019. PMID:31185017<ref>PMID:31185017</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5afd" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Alisl]]
		+	[[Category: Large Structures]]
	[[Category: N-acetylneuraminate lyase]]		[[Category: N-acetylneuraminate lyase]]
	[[Category: Altermark, B]]		[[Category: Altermark, B]]

OCA at 15:20, 2 March 2016

OCA — Wed, 02 Mar 2016 15:20:32 GMT

←Older revision		Revision as of 15:20, 2 March 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5afd ~~is ON HOLD until Jan 21 2017~~	+	==Native structure of N-acetylneuramininate lyase (sialic acid aldolase) from Aliivibrio salmonicida==
-		+	<StructureSection load='5afd' size='340' side='right' caption='[[5afd]], [[Resolution\|resolution]] 1.65Å' scene=''>
-	~~Authors~~: ~~Gurung, M~~.K., ~~Altermark~~, B., ~~Rader~~, I.L.U., ~~Helland~~, R., ~~Smalas, A~~.O.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5afd]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AFD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5AFD FirstGlance]. <br>
-	~~Description: Native structure of N-acetylneuramininate lyase (sialic acid aldolase) from Aliivibrio salmonicida~~	+	</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=GOL:GLYCEROL'>GOL</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/N-acetylneuraminate_lyase N-acetylneuraminate lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.3.3 4.1.3.3] </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=5afd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5afd OCA], [http://pdbe.org/5afd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5afd RCSB], [http://www.ebi.ac.uk/pdbsum/5afd PDBsum]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: N-acetylneuraminate lyase]]
	[[Category: Altermark, B]]		[[Category: Altermark, B]]
-	~~[[Category: Rader, I.L.U]]~~	+	[[Category: Gurung, M K]]
-	[[Category: Gurung, M.K]]	+
-	~~[[Category: Smalas, A.O~~]]	+
	[[Category: Helland, R]]		[[Category: Helland, R]]
		+	[[Category: Rader, I L.U]]
		+	[[Category: Smalas, A O]]
		+	[[Category: Alkaline]]
		+	[[Category: Cold active]]
		+	[[Category: Lyase]]
		+	[[Category: Psychrophile]]
		+	[[Category: Sialic acid aldolase]]

OCA at 10:29, 30 April 2015

OCA — Thu, 30 Apr 2015 10:29:01 GMT

←Older revision		Revision as of 10:29, 30 April 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5afd is ON HOLD	+	The entry 5afd is ON HOLD until Jan 21 2017

	Authors: Gurung, M.K., Altermark, B., Rader, I.L.U., Helland, R., Smalas, A.O.		Authors: Gurung, M.K., Altermark, B., Rader, I.L.U., Helland, R., Smalas, A.O.

OCA: Protected "5afd" [edit=sysop:move=sysop]

OCA — Wed, 28 Jan 2015 15:52:44 GMT

Protected "5afd" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:52, 28 January 2015

OCA: New page: '''Unreleased structure''' The entry 5afd is ON HOLD Authors: Gurung, M.K., Altermark, B., Rader, I.L.U., Helland, R., Smalas, A.O. Description: Native structure of N-acetylneuraminina...

OCA — Wed, 28 Jan 2015 15:52:43 GMT

New page: '''Unreleased structure''' The entry 5afd is ON HOLD Authors: Gurung, M.K., Altermark, B., Rader, I.L.U., Helland, R., Smalas, A.O. Description: Native structure of N-acetylneuraminina...

New page

'''Unreleased structure'''

The entry 5afd is ON HOLD

Authors: Gurung, M.K., Altermark, B., Rader, I.L.U., Helland, R., Smalas, A.O.

Description: Native structure of N-acetylneuramininate lyase (sialic acid aldolase) from Aliivibrio salmonicida
[[Category: Unreleased Structures]]
[[Category: Altermark, B]]
[[Category: Rader, I.L.U]]
[[Category: Gurung, M.K]]
[[Category: Smalas, A.O]]
[[Category: Helland, R]]