5z99 - Revision history

OCA at 08:50, 22 November 2023

2023-11-22T08:50:07Z

←Older revision		Revision as of 08:50, 22 November 2023
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	==Crystal structure of Sialic acid Binding protein from Haemophilus ducreyi with Neu5Ac==		==Crystal structure of Sialic acid Binding protein from Haemophilus ducreyi with Neu5Ac==
-	<StructureSection load='5z99' size='340' side='right' caption='[[5z99]], [[Resolution\|resolution]] 1.49Å' scene=''>	+	<StructureSection load='5z99' size='340' side='right'caption='[[5z99]], [[Resolution\|resolution]] 1.49Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5z99]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Haedu Haedu~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z99 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5Z99 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5z99]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Haemophilus_ducreyi_35000HP Haemophilus ducreyi 35000HP]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z99 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5Z99 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=SLB:5~~-~~N-ACETYL-BETA-D-NEURAMINIC+ACID'>SLB</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]] 1.494Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~HD_1669 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=5~~&id=233412 HAEDU])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SLB:5-N-ACETYL-BETA-D-NEURAMINIC+ACID'>SLB</scene></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=5z99 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z99 OCA], [~~http~~://pdbe.org/5z99 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5z99 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5z99 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5z99 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=5z99 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z99 OCA], [https://pdbe.org/5z99 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5z99 RCSB], [https://www.ebi.ac.uk/pdbsum/5z99 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5z99 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q7VL18_HAEDU Q7VL18_HAEDU]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Haedu~~]]	+	[[Category: Large Structures]]
-	[[Category: Setty~~, T G~~]]	+	[[Category: Setty TG]]
-	[[Category: Subramanian, R]]	+	[[Category: Subramanian R]]
-	~~[[Category: Adhesion]]~~	+
-	~~[[Category: Bacteria]]~~	+
-	~~[[Category: Cell signaling]]~~	+
-	~~[[Category: Molecular mimicry]]~~	+
-	~~[[Category: Nutrition]]~~	+
-	~~[[Category: Sialic acid neu5gc]]~~	+
-	~~[[Category: Sugar binding protein]]~~	+
-	~~[[Category: Three domain protein~~]]	+

OCA at 12:26, 16 January 2019

2019-01-16T12:26:37Z

←Older revision		Revision as of 12:26, 16 January 2019
Line 3:		Line 3:
	<StructureSection load='5z99' size='340' side='right' caption='[[5z99]], [[Resolution\|resolution]] 1.49Å' scene=''>		<StructureSection load='5z99' size='340' side='right' caption='[[5z99]], [[Resolution\|resolution]] 1.49Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5z99]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z99 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Z99 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5z99]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Haedu Haedu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z99 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Z99 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SLB:5-N-ACETYL-BETA-D-NEURAMINIC+ACID'>SLB</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SLB:5-N-ACETYL-BETA-D-NEURAMINIC+ACID'>SLB</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HD_1669 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=233412 HAEDU])</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=5z99 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z99 OCA], [http://pdbe.org/5z99 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5z99 RCSB], [http://www.ebi.ac.uk/pdbsum/5z99 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5z99 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=5z99 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z99 OCA], [http://pdbe.org/5z99 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5z99 RCSB], [http://www.ebi.ac.uk/pdbsum/5z99 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5z99 ProSAT]</span></td></tr>
	</table>		</table>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Haedu]]
	[[Category: Setty, T G]]		[[Category: Setty, T G]]
	[[Category: Subramanian, R]]		[[Category: Subramanian, R]]

OCA at 05:47, 24 October 2018

2018-10-24T05:47:03Z

←Older revision		Revision as of 05:47, 24 October 2018
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-	'''Unreleased structure'''

-	~~The entry~~ 5z99 is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of Sialic acid Binding protein from Haemophilus ducreyi with Neu5Ac==
		+	<StructureSection load='5z99' size='340' side='right' caption='[[5z99]], [[Resolution\|resolution]] 1.49Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5z99]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z99 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Z99 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SLB:5-N-ACETYL-BETA-D-NEURAMINIC+ACID'>SLB</scene></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=5z99 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z99 OCA], [http://pdbe.org/5z99 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5z99 RCSB], [http://www.ebi.ac.uk/pdbsum/5z99 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5z99 ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The primary role of bacterial periplasmic binding proteins is sequestration of essential metabolites present at a low concentration in the periplasm and making them available for active transporters that transfer these ligands into the bacterial cell. The periplasmic binding proteins(SiaP) from the tripartite ATP-independent periplasmic (TRAP) transport system that transports mammalian host-derived sialic acids, have been well studied from different pathogenic bacteria, including Haemophilus influenzae, Fusobacterium nucleatum, Pasteurella multocida, and Vibrio cholerae SiaPs bind the sialic acid N-acetylneuraminic acid (Neu5Ac) with nanomolar affinity by forming electrostatic and hydrogen bonding interactions. Here, we report the crystal structure of a periplasmic binding protein (SatA) of the ATP-binding cassette (ABC) transport system from the pathogenic bacterium Haemophilus ducreyi The structure of Hd-SatA in the native form and sialic acid-bound forms (with Neu5Ac and N-glycolylneuraminic acid [Neu5Gc]), determined to 2.2, 1.5 and 2.5 A resolutions respectively, revealed a ligand-binding site that is very different from those of the SiaPs of the TRAP transport system. A structural comparison along with thermodynamic studies suggested that similar affinities are achieved in the two classes of proteins through distinct mechanisms, one enthalpically driven and the other entropically driven. In summary, our structural and thermodynamic characterization of Hd-SatA reveal that it binds sialic acids with nanomolar affinity and this binding is an entropically driven process. This information is important for future structure-based drug design against this pathogen and related bacteria.

-	~~Authors: Ramaswamy~~, S., ~~Thanuja~~, G.	+	Molecular characterization of the interaction of sialic acid with the periplasmic binding protein from Haemophilus ducreyi.,Setty TG, Mowers JC, Hobbs AG, Maiya SP, Syed S, Munson RS Jr, Apicella MA, Subramanian R J Biol Chem. 2018 Oct 12. pii: RA118.005151. doi: 10.1074/jbc.RA118.005151. PMID:30315109<ref>PMID:30315109</ref>

-	~~Description: Crystal structure~~ of ~~Sialic acid Binding protein from Haemophilus ducreyi with Neu5Ac~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: ~~Ramaswamy~~, S]]	+	<div class="pdbe-citations 5z99" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Thanuja, G~~]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Setty, T G]]
		+	[[Category: Subramanian, R]]
		+	[[Category: Adhesion]]
		+	[[Category: Bacteria]]
		+	[[Category: Cell signaling]]
		+	[[Category: Molecular mimicry]]
		+	[[Category: Nutrition]]
		+	[[Category: Sialic acid neu5gc]]
		+	[[Category: Sugar binding protein]]
		+	[[Category: Three domain protein]]

OCA at 05:45, 23 May 2018

2018-05-23T05:45:23Z

←Older revision		Revision as of 05:45, 23 May 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5z99 is ON HOLD	+	The entry 5z99 is ON HOLD until Paper Publication

	Authors: Ramaswamy, S., Thanuja, G.		Authors: Ramaswamy, S., Thanuja, G.

OCA at 04:01, 18 April 2018

2018-04-18T04:01:38Z

←Older revision		Revision as of 04:01, 18 April 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5z99 is ON HOLD ~~until Paper Publication~~	+	The entry 5z99 is ON HOLD

	Authors: Ramaswamy, S., Thanuja, G.		Authors: Ramaswamy, S., Thanuja, G.

OCA at 12:15, 11 April 2018

2018-04-11T12:15:05Z

←Older revision		Revision as of 12:15, 11 April 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5z99 is ON HOLD	+	The entry 5z99 is ON HOLD until Paper Publication

	Authors: Ramaswamy, S., Thanuja, G.		Authors: Ramaswamy, S., Thanuja, G.

OCA: Protected "5z99" [edit=sysop:move=sysop]

2018-02-07T05:05:11Z

Protected "5z99" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:05, 7 February 2018

OCA: New page: '''Unreleased structure''' The entry 5z99 is ON HOLD Authors: Ramaswamy, S., Thanuja, G. Description: Crystal structure of Sialic acid Binding protein from Haemophilus ducreyi with Neu...

2018-02-07T05:05:10Z

New page: '''Unreleased structure''' The entry 5z99 is ON HOLD Authors: Ramaswamy, S., Thanuja, G. Description: Crystal structure of Sialic acid Binding protein from Haemophilus ducreyi with Neu...

New page

'''Unreleased structure'''

The entry 5z99 is ON HOLD

Authors: Ramaswamy, S., Thanuja, G.

Description: Crystal structure of Sialic acid Binding protein from Haemophilus ducreyi with Neu5Ac
[[Category: Unreleased Structures]]
[[Category: Ramaswamy, S]]
[[Category: Thanuja, G]]