1f7b - Revision history

OCA at 10:11, 20 March 2024

2024-03-20T10:11:22Z

←Older revision		Revision as of 10:11, 20 March 2024
Line 3:		Line 3:
	<StructureSection load='1f7b' size='340' side='right'caption='[[1f7b]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='1f7b' size='340' side='right'caption='[[1f7b]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1f7b]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacterium_influenzae"_lehmann_and_neumann_1896 "bacterium~~ influenzae~~" lehmann and neumann 1896~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F7B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1F7B FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1f7b]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Haemophilus_influenzae Haemophilus influenzae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F7B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1F7B FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NAU:4,4,6,7,8,9-HEXAHYDROXY-5-METHYLCARBOXAMIDONONANOIC+ACID'>NAU</scene>, <scene name='pdbligand=NAV:6,7,8,9-TETRAHYDROXY-5-METHYLCARBOXAMIDO-4-OXONONANOIC+ACID'>NAV</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]] 1.8Å</td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1nal\|1nal]], [[1fdy\|1fdy]], [[1fdz\|1fdz]], [[1f5z\|1f5z]], [[1f6k\|1f6k]], [[1f73\|1f73]]</div></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NAU:4,4,6,7,8,9-HEXAHYDROXY-5-METHYLCARBOXAMIDONONANOIC+ACID'>NAU</scene>, <scene name='pdbligand=NAV:6,7,8,9-TETRAHYDROXY-5-METHYLCARBOXAMIDO-4-OXONONANOIC+ACID'>NAV</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/N-acetylneuraminate_lyase N-acetylneuraminate lyase], with EC number [https://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=1f7b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f7b OCA], [https://pdbe.org/1f7b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1f7b RCSB], [https://www.ebi.ac.uk/pdbsum/1f7b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1f7b 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=1f7b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f7b OCA], [https://pdbe.org/1f7b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1f7b RCSB], [https://www.ebi.ac.uk/pdbsum/1f7b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1f7b ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/NANA_HAEIN NANA_HAEIN]] Catalyzes the cleavage of N-acetylneuraminic acid (sialic acid) to form pyruvate and N-acetylmannosamine via a Schiff base intermediate.	+	[https://www.uniprot.org/uniprot/NANA_HAEIN NANA_HAEIN] Catalyzes the cleavage of N-acetylneuraminic acid (sialic acid) to form pyruvate and N-acetylmannosamine via a Schiff base intermediate.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 21:		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=1f7b 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=1f7b ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The N-acetylneuraminate lyase (NAL) sub-family of (beta/alpha)(8) enzymes share a common catalytic step but catalyse reactions in different biological pathways. Known examples include NAL, dihydrodipicolinate synthetase (DHDPS), d-5-keto-4-deoxyglucarate dehydratase, 2-keto-3-deoxygluconate aldolase, trans-o-hydroxybenzylidenepyruvate hydrolase-aldolase and trans-2'-carboxybenzalpyruvate hydratase-aldolase. Little is known about the way in which the three-dimensional structure of the respective active sites are modulated across the sub-family to achieve cognate substrate recognition. We present here the structure of Haemophilus influenzae NAL determined by X-ray crystallography to a maximum resolution of 1.60 A, in native form and in complex with three substrate analogues (sialic acid alditol, 4-deoxy-sialic acid and 4-oxo-sialic acid). These structures reveal for the first time the mode of binding of the complete substrate in the NAL active site. On the basis of the above structures, that of substrate-complexed DHDPS and sequence comparison across the sub-family we are able to propose a unified model for active site modulation. The model is one of economy, allowing wherever appropriate the retention or relocation of residues associated with binding common substrate substituent groups. Our structures also suggest a role for the strictly conserved tyrosine residue found in all active sites of the sub-family, namely that it mediates proton abstraction by the alpha-keto acid carboxylate in a substrate-assisted catalytic reaction pathway.

-	~~Active site modulation in the~~ N-acetylneuraminate lyase ~~sub~~-family as revealed by the structure of the inhibitor-complexed Haemophilus influenzae enzyme.,Barbosa JA, Smith BJ, DeGori R, Ooi HC, Marcuccio SM, Campi EM, Jackson WR, Brossmer R, Sommer M, Lawrence MC J Mol Biol. 2000 Oct 27;303(3):405-21. PMID:11031117<ref>PMID:11031117</ref>	+	==See Also==
-		+	*[[N-acetylneuraminate lyase 3D structures\|N-acetylneuraminate lyase 3D structures]]
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 1f7b" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacterium~~ influenzae ~~lehmann and neumann 1896~~]]	+	[[Category: Haemophilus influenzae]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: N-acetylneuraminate lyase]]~~	+	[[Category: Barbosa JARG]]
-	[[Category: Barbosa~~, J A.R G~~]]	+	[[Category: DeGori R]]
-	[[Category: DeGori, R]]	+	[[Category: Lawrence MC]]
-	[[Category: Lawrence~~, M C~~]]	+	[[Category: Smith BJ]]
-	[[Category: Smith~~, B J]]~~	+
-	~~[[Category: Beta barrel]]~~	+
-	~~[[Category: Lyase~~]]	+

OCA at 09:47, 21 July 2021

2021-07-21T09:47:09Z

←Older revision		Revision as of 09:47, 21 July 2021
Line 3:		Line 3:
	<StructureSection load='1f7b' size='340' side='right'caption='[[1f7b]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='1f7b' size='340' side='right'caption='[[1f7b]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1f7b]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacterium_influenzae"_lehmann_and_neumann_1896 "bacterium influenzae" lehmann and neumann 1896]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F7B OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1F7B FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1f7b]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacterium_influenzae"_lehmann_and_neumann_1896 "bacterium influenzae" lehmann and neumann 1896]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F7B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1F7B FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NAU:4,4,6,7,8,9-HEXAHYDROXY-5-METHYLCARBOXAMIDONONANOIC+ACID'>NAU</scene>, <scene name='pdbligand=NAV:6,7,8,9-TETRAHYDROXY-5-METHYLCARBOXAMIDO-4-OXONONANOIC+ACID'>NAV</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NAU:4,4,6,7,8,9-HEXAHYDROXY-5-METHYLCARBOXAMIDONONANOIC+ACID'>NAU</scene>, <scene name='pdbligand=NAV:6,7,8,9-TETRAHYDROXY-5-METHYLCARBOXAMIDO-4-OXONONANOIC+ACID'>NAV</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1nal\|1nal]], [[1fdy\|1fdy]], [[1fdz\|1fdz]], [[1f5z\|1f5z]], [[1f6k\|1f6k]], [[1f73\|1f73]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1nal\|1nal]], [[1fdy\|1fdy]], [[1fdz\|1fdz]], [[1f5z\|1f5z]], [[1f6k\|1f6k]], [[1f73\|1f73]]</div></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'>[https://en.wikipedia.org/wiki/N-acetylneuraminate_lyase N-acetylneuraminate lyase], with EC number [https://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=1f7b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f7b OCA], [~~http~~://pdbe.org/1f7b PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1f7b RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1f7b PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1f7b 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=1f7b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f7b OCA], [https://pdbe.org/1f7b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1f7b RCSB], [https://www.ebi.ac.uk/pdbsum/1f7b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1f7b ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/NANA_HAEIN NANA_HAEIN]] Catalyzes the cleavage of N-acetylneuraminic acid (sialic acid) to form pyruvate and N-acetylmannosamine via a Schiff base intermediate.	+	[[https://www.uniprot.org/uniprot/NANA_HAEIN NANA_HAEIN]] Catalyzes the cleavage of N-acetylneuraminic acid (sialic acid) to form pyruvate and N-acetylmannosamine via a Schiff base intermediate.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 13:56, 16 October 2019

2019-10-16T13:56:37Z

←Older revision		Revision as of 13:56, 16 October 2019
Line 1:		Line 1:

	==CRYSTAL STRUCTURE ANALYSIS OF N-ACETYLNEURAMINATE LYASE FROM HAEMOPHILUS INFLUENZAE: CRYSTAL FORM II IN COMPLEX WITH 4-OXO-SIALIC ACID==		==CRYSTAL STRUCTURE ANALYSIS OF N-ACETYLNEURAMINATE LYASE FROM HAEMOPHILUS INFLUENZAE: CRYSTAL FORM II IN COMPLEX WITH 4-OXO-SIALIC ACID==
-	<StructureSection load='1f7b' size='340' side='right' caption='[[1f7b]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='1f7b' size='340' side='right'caption='[[1f7b]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1f7b]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacterium_influenzae"_lehmann_and_neumann_1896 "bacterium influenzae" lehmann and neumann 1896]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F7B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1F7B FirstGlance]. <br>		<table><tr><td colspan='2'>[[1f7b]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacterium_influenzae"_lehmann_and_neumann_1896 "bacterium influenzae" lehmann and neumann 1896]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F7B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1F7B FirstGlance]. <br>
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	</StructureSection>		</StructureSection>
	[[Category: Bacterium influenzae lehmann and neumann 1896]]		[[Category: Bacterium influenzae lehmann and neumann 1896]]
		+	[[Category: Large Structures]]
	[[Category: N-acetylneuraminate lyase]]		[[Category: N-acetylneuraminate lyase]]
	[[Category: Barbosa, J A.R G]]		[[Category: Barbosa, J A.R G]]

OCA at 09:27, 27 December 2017

2017-12-27T09:27:07Z

←Older revision		Revision as of 09:27, 27 December 2017
Line 1:		Line 1:
		+
	==CRYSTAL STRUCTURE ANALYSIS OF N-ACETYLNEURAMINATE LYASE FROM HAEMOPHILUS INFLUENZAE: CRYSTAL FORM II IN COMPLEX WITH 4-OXO-SIALIC ACID==		==CRYSTAL STRUCTURE ANALYSIS OF N-ACETYLNEURAMINATE LYASE FROM HAEMOPHILUS INFLUENZAE: CRYSTAL FORM II IN COMPLEX WITH 4-OXO-SIALIC ACID==
	<StructureSection load='1f7b' size='340' side='right' caption='[[1f7b]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='1f7b' size='340' side='right' caption='[[1f7b]], [[Resolution\|resolution]] 1.80Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1nal\|1nal]], [[1fdy\|1fdy]], [[1fdz\|1fdz]], [[1f5z\|1f5z]], [[1f6k\|1f6k]], [[1f73\|1f73]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1nal\|1nal]], [[1fdy\|1fdy]], [[1fdz\|1fdz]], [[1f5z\|1f5z]], [[1f6k\|1f6k]], [[1f73\|1f73]]</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=1f7b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f7b OCA], [http://pdbe.org/1f7b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1f7b RCSB], [http://www.ebi.ac.uk/pdbsum/1f7b 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=1f7b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f7b OCA], [http://pdbe.org/1f7b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1f7b RCSB], [http://www.ebi.ac.uk/pdbsum/1f7b PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1f7b ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 14:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/f7/1f7b_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/f7/1f7b_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 11:57, 8 February 2016

2016-02-08T11:57:05Z

←Older revision		Revision as of 11:57, 8 February 2016
Line 18:		Line 18:
	<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=1f7b ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 11:20, 10 September 2015

2015-09-10T11:20:34Z

←Older revision		Revision as of 11:20, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1f7b' size='340' side='right' caption='[[1f7b]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='1f7b' size='340' side='right' caption='[[1f7b]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1f7b]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Haemophilus_influenzae Haemophilus~~ influenzae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F7B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1F7B FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1f7b]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacterium_influenzae"_lehmann_and_neumann_1896 "bacterium influenzae" lehmann and neumann 1896]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F7B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1F7B FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NAU:4,4,6,7,8,9-HEXAHYDROXY-5-METHYLCARBOXAMIDONONANOIC+ACID'>NAU</scene>, <scene name='pdbligand=NAV:6,7,8,9-TETRAHYDROXY-5-METHYLCARBOXAMIDO-4-OXONONANOIC+ACID'>NAV</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NAU:4,4,6,7,8,9-HEXAHYDROXY-5-METHYLCARBOXAMIDONONANOIC+ACID'>NAU</scene>, <scene name='pdbligand=NAV:6,7,8,9-TETRAHYDROXY-5-METHYLCARBOXAMIDO-4-OXONONANOIC+ACID'>NAV</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1nal\|1nal]], [[1fdy\|1fdy]], [[1fdz\|1fdz]], [[1f5z\|1f5z]], [[1f6k\|1f6k]], [[1f73\|1f73]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1nal\|1nal]], [[1fdy\|1fdy]], [[1fdz\|1fdz]], [[1f5z\|1f5z]], [[1f6k\|1f6k]], [[1f73\|1f73]]</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=1f7b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f7b OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1f7b RCSB], [http://www.ebi.ac.uk/pdbsum/1f7b 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=1f7b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f7b OCA], [http://pdbe.org/1f7b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1f7b RCSB], [http://www.ebi.ac.uk/pdbsum/1f7b PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 28:		Line 28:
	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 1f7b" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Haemophilus~~ influenzae]]	+	[[Category: Bacterium influenzae lehmann and neumann 1896]]
	[[Category: N-acetylneuraminate lyase]]		[[Category: N-acetylneuraminate lyase]]
	[[Category: Barbosa, J A.R G]]		[[Category: Barbosa, J A.R G]]

OCA at 23:08, 24 December 2014

2014-12-24T23:08:31Z

←Older revision		Revision as of 23:08, 24 December 2014
Line 8:		Line 8:
	<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=1f7b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f7b OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1f7b RCSB], [http://www.ebi.ac.uk/pdbsum/1f7b 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=1f7b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f7b OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1f7b RCSB], [http://www.ebi.ac.uk/pdbsum/1f7b PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/NANA_HAEIN NANA_HAEIN]] Catalyzes the cleavage of N-acetylneuraminic acid (sialic acid) to form pyruvate and N-acetylmannosamine via a Schiff base intermediate.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 19:47, 22 December 2014

2014-12-22T19:47:16Z

←Older revision		Revision as of 19:47, 22 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1f7b]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Haemophilus_influenzae Haemophilus influenzae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F7B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1F7B FirstGlance]. <br>		<table><tr><td colspan='2'>[[1f7b]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Haemophilus_influenzae Haemophilus influenzae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F7B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1F7B FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NAU:4,4,6,7,8,9-HEXAHYDROXY-5-METHYLCARBOXAMIDONONANOIC+ACID'>NAU</scene>, <scene name='pdbligand=NAV:6,7,8,9-TETRAHYDROXY-5-METHYLCARBOXAMIDO-4-OXONONANOIC+ACID'>NAV</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NAU:4,4,6,7,8,9-HEXAHYDROXY-5-METHYLCARBOXAMIDONONANOIC+ACID'>NAU</scene>, <scene name='pdbligand=NAV:6,7,8,9-TETRAHYDROXY-5-METHYLCARBOXAMIDO-4-OXONONANOIC+ACID'>NAV</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1nal\|1nal]], [[1fdy\|1fdy]], [[1fdz\|1fdz]], [[1f5z\|1f5z]], [[1f6k\|1f6k]], [[1f73\|1f73]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1nal\|1nal]], [[1fdy\|1fdy]], [[1fdz\|1fdz]], [[1f5z\|1f5z]], [[1f6k\|1f6k]], [[1f73\|1f73]]</td></tr>
-	<tr><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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1f7b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f7b OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1f7b RCSB], [http://www.ebi.ac.uk/pdbsum/1f7b 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=1f7b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f7b OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1f7b RCSB], [http://www.ebi.ac.uk/pdbsum/1f7b 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: Haemophilus influenzae]]		[[Category: Haemophilus influenzae]]
	[[Category: N-acetylneuraminate lyase]]		[[Category: N-acetylneuraminate lyase]]
-	[[Category: Barbosa, J A.R G.]]	+	[[Category: Barbosa, J A.R G]]
-	[[Category: DeGori, R.]]	+	[[Category: DeGori, R]]
-	[[Category: Lawrence, M C.]]	+	[[Category: Lawrence, M C]]
-	[[Category: Smith, B J.]]	+	[[Category: Smith, B J]]
	[[Category: Beta barrel]]		[[Category: Beta barrel]]
	[[Category: Lyase]]		[[Category: Lyase]]

OCA at 09:04, 3 October 2014

2014-10-03T09:04:15Z

←Older revision		Revision as of 09:04, 3 October 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_1f7b\| PDB=1f7b \| SCENE= }}~~	+	==CRYSTAL STRUCTURE ANALYSIS OF N-ACETYLNEURAMINATE LYASE FROM HAEMOPHILUS INFLUENZAE: CRYSTAL FORM II IN COMPLEX WITH 4-OXO-SIALIC ACID==
-	===CRYSTAL STRUCTURE ANALYSIS OF N-ACETYLNEURAMINATE LYASE FROM HAEMOPHILUS INFLUENZAE: CRYSTAL FORM II IN COMPLEX WITH 4-OXO-SIALIC ACID===	+	<StructureSection load='1f7b' size='340' side='right' caption='[[1f7b]], [[Resolution\|resolution]] 1.80Å' scene=''>
-	~~{{ABSTRACT_PUBMED_11031117}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1f7b]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Haemophilus_influenzae Haemophilus influenzae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F7B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1F7B FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NAU:4,4,6,7,8,9-HEXAHYDROXY-5-METHYLCARBOXAMIDONONANOIC+ACID'>NAU</scene>, <scene name='pdbligand=NAV:6,7,8,9-TETRAHYDROXY-5-METHYLCARBOXAMIDO-4-OXONONANOIC+ACID'>NAV</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1nal\|1nal]], [[1fdy\|1fdy]], [[1fdz\|1fdz]], [[1f5z\|1f5z]], [[1f6k\|1f6k]], [[1f73\|1f73]]</td></tr>
		+	<tr><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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1f7b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f7b OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1f7b RCSB], [http://www.ebi.ac.uk/pdbsum/1f7b 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/f7/1f7b_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 N-acetylneuraminate lyase (NAL) sub-family of (beta/alpha)(8) enzymes share a common catalytic step but catalyse reactions in different biological pathways. Known examples include NAL, dihydrodipicolinate synthetase (DHDPS), d-5-keto-4-deoxyglucarate dehydratase, 2-keto-3-deoxygluconate aldolase, trans-o-hydroxybenzylidenepyruvate hydrolase-aldolase and trans-2'-carboxybenzalpyruvate hydratase-aldolase. Little is known about the way in which the three-dimensional structure of the respective active sites are modulated across the sub-family to achieve cognate substrate recognition. We present here the structure of Haemophilus influenzae NAL determined by X-ray crystallography to a maximum resolution of 1.60 A, in native form and in complex with three substrate analogues (sialic acid alditol, 4-deoxy-sialic acid and 4-oxo-sialic acid). These structures reveal for the first time the mode of binding of the complete substrate in the NAL active site. On the basis of the above structures, that of substrate-complexed DHDPS and sequence comparison across the sub-family we are able to propose a unified model for active site modulation. The model is one of economy, allowing wherever appropriate the retention or relocation of residues associated with binding common substrate substituent groups. Our structures also suggest a role for the strictly conserved tyrosine residue found in all active sites of the sub-family, namely that it mediates proton abstraction by the alpha-keto acid carboxylate in a substrate-assisted catalytic reaction pathway.

-	~~==Function==~~	+	Active site modulation in the N-acetylneuraminate lyase sub-family as revealed by the structure of the inhibitor-complexed Haemophilus influenzae enzyme.,Barbosa JA, Smith BJ, DeGori R, Ooi HC, Marcuccio SM, Campi EM, Jackson WR, Brossmer R, Sommer M, Lawrence MC J Mol Biol. 2000 Oct 27;303(3):405-21. PMID:11031117<ref>PMID:11031117</ref>
-	~~[[http://www.uniprot.org/uniprot/NANA_HAEIN NANA_HAEIN]] Catalyzes~~ the ~~cleavage of~~ N-~~acetylneuraminic acid~~ (~~sialic acid~~) ~~to form pyruvate and N~~-~~acetylmannosamine via a Schiff base intermediate~~.	+

-	~~==About this Structure==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[1f7b]] is~~ a ~~2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Haemophilus_influenzae Haemophilus influenzae]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1F7B OCA].~~	+	</div>
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:011031117</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Haemophilus influenzae]]		[[Category: Haemophilus influenzae]]
	[[Category: N-acetylneuraminate lyase]]		[[Category: N-acetylneuraminate lyase]]

OCA: Protected "1f7b" [edit=sysop:move=sysop]

2014-04-16T10:47:52Z

Protected "1f7b" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:47, 16 April 2014