4xon - Revision history

OCA at 10:50, 10 January 2024

2024-01-10T10:50:05Z

←Older revision		Revision as of 10:50, 10 January 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4xon]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Enterobacteria_phage_HK620 Enterobacteria phage HK620]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XON OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XON FirstGlance]. <br>		<table><tr><td colspan='2'>[[4xon]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Enterobacteria_phage_HK620 Enterobacteria phage HK620]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XON OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XON FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.1Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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=4xon FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xon OCA], [https://pdbe.org/4xon PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xon RCSB], [https://www.ebi.ac.uk/pdbsum/4xon PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xon 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=4xon FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xon OCA], [https://pdbe.org/4xon PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xon RCSB], [https://www.ebi.ac.uk/pdbsum/4xon PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xon ProSAT]</span></td></tr>
	</table>		</table>
Line 11:		Line 12:

	==See Also==		==See Also==
-	*[[Tailspike protein\|Tailspike protein]]	+	*[[Tailspike protein 3D structures\|Tailspike protein 3D structures]]
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 17:45, 26 April 2023

2023-04-26T17:45:48Z

←Older revision		Revision as of 17:45, 26 April 2023
Line 3:		Line 3:
	<StructureSection load='4xon' size='340' side='right'caption='[[4xon]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='4xon' size='340' side='right'caption='[[4xon]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4xon]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Bphk6 Bphk6~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XON OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4XON FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4xon]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Enterobacteria_phage_HK620 Enterobacteria phage HK620]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XON OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XON FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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=4xon FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xon OCA], [~~http~~://pdbe.org/4xon PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4xon RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4xon PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4xon 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=4xon FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xon OCA], [https://pdbe.org/4xon PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xon RCSB], [https://www.ebi.ac.uk/pdbsum/4xon PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xon ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/Q9AYY6_BPHK6 Q9AYY6_BPHK6]
-	Bacteriophage HK620 recognizes and cleaves the Oantigen polysaccharide of E. coli serogroup O18A1 with its tailspike protein (TSP). HK620TSP binds hexasaccharide fragments with low affinity, but single amino acid exchanges generated a set of high-affinity mutants with submicromolar dissociation constants. Isothermal titration calorimetry showed that only small amounts of heat were released upon complex formation via a large number of direct and solvent mediated hydrogen bonds between carbohydrate and protein. At room temperature association was both enthalpy- and entropy-driven emphasizing major solvent rearrangements upon complex formation. Crystal structure analysis showed identical protein and sugar conformers in the TSP complexes regardless of their hexasaccharide affinity. Only in one case a TSP mutant bound a different hexasaccharide conformer. The extended sugar binding site could be dissected in two regions: Firstly, a hydrophobic pocket at the reducing end with minor affinity contributions. Access to this site could be blocked by a single aspartate to asparagine exchange without major loss in hexasaccharide affinity. Secondly, a region where specific exchange of glutamate for glutamine created a site for an additional water molecule. ~~Side chain rearrangements upon sugar binding led to desolvation and additional hydrogen bonding which define this region of the binding site as the high affinity scaffold~~.	+

-	Single amino acid exchange in bacteriophage HK620 tailspike protein results in thousand-fold increase of its oligosaccharide affinity.,Broeker NK, Gohlke U, Muller JJ, Uetrecht C, Heinemann U, Seckler R, Barbirz S Glycobiology. 2012 Aug 24. PMID:22923442<ref>PMID:22923442</ref>	+	==See Also==
-		+	*[[Tailspike protein\|Tailspike protein]]
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class~~=~~"pdbe-citations 4xon" style~~=~~"background-color:#fffaf0;"></div>~~	+
-	~~== References~~ ==	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bphk6~~]]	+	[[Category: Enterobacteria phage HK620]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Barbirz, S]]	+	[[Category: Barbirz S]]
-	[[Category: Broeker~~, N K~~]]	+	[[Category: Broeker NK]]
-	[[Category: Gohlke, U]]	+	[[Category: Gohlke U]]
-	[[Category: Heinemann, U]]	+	[[Category: Heinemann U]]
-	[[Category: Seckler, R]]	+	[[Category: Seckler R]]
-	~~[[Category: Beta helix]]~~	+
-	~~[[Category: Pectin lyase fold]]~~	+
-	~~[[Category: Protein-carbohydrate complex]]~~	+
-	~~[[Category: Viral protein~~]]	+

OCA at 00:17, 6 June 2019

2019-06-06T00:17:39Z

←Older revision		Revision as of 00:17, 6 June 2019
Line 1:		Line 1:
		+
	==Tailspike protein double mutant D339N/E372Q of E. coli bacteriophage HK620==		==Tailspike protein double mutant D339N/E372Q of E. coli bacteriophage HK620==
-	<StructureSection load='4xon' size='340' side='right' caption='[[4xon]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='4xon' size='340' side='right'caption='[[4xon]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4xon]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XON OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XON FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4xon]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bphk6 Bphk6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XON OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XON FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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=4xon FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xon OCA], [http://pdbe.org/4xon PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xon RCSB], [http://www.ebi.ac.uk/pdbsum/4xon 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=4xon FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xon OCA], [http://pdbe.org/4xon PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xon RCSB], [http://www.ebi.ac.uk/pdbsum/4xon PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4xon ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 19:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bphk6]]
		+	[[Category: Large Structures]]
	[[Category: Barbirz, S]]		[[Category: Barbirz, S]]
	[[Category: Broeker, N K]]		[[Category: Broeker, N K]]

OCA at 02:18, 28 January 2016

2016-01-28T02:18:16Z

←Older revision		Revision as of 02:18, 28 January 2016
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Tailspike protein double mutant D339N/E372Q of E. coli bacteriophage HK620==
		+	<StructureSection load='4xon' size='340' side='right' caption='[[4xon]], [[Resolution\|resolution]] 2.10Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4xon]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XON OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XON FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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=4xon FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xon OCA], [http://pdbe.org/4xon PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xon RCSB], [http://www.ebi.ac.uk/pdbsum/4xon PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Bacteriophage HK620 recognizes and cleaves the Oantigen polysaccharide of E. coli serogroup O18A1 with its tailspike protein (TSP). HK620TSP binds hexasaccharide fragments with low affinity, but single amino acid exchanges generated a set of high-affinity mutants with submicromolar dissociation constants. Isothermal titration calorimetry showed that only small amounts of heat were released upon complex formation via a large number of direct and solvent mediated hydrogen bonds between carbohydrate and protein. At room temperature association was both enthalpy- and entropy-driven emphasizing major solvent rearrangements upon complex formation. Crystal structure analysis showed identical protein and sugar conformers in the TSP complexes regardless of their hexasaccharide affinity. Only in one case a TSP mutant bound a different hexasaccharide conformer. The extended sugar binding site could be dissected in two regions: Firstly, a hydrophobic pocket at the reducing end with minor affinity contributions. Access to this site could be blocked by a single aspartate to asparagine exchange without major loss in hexasaccharide affinity. Secondly, a region where specific exchange of glutamate for glutamine created a site for an additional water molecule. Side chain rearrangements upon sugar binding led to desolvation and additional hydrogen bonding which define this region of the binding site as the high affinity scaffold.

-	~~The entry 4xon is ON HOLD until Paper Publication~~	+	Single amino acid exchange in bacteriophage HK620 tailspike protein results in thousand-fold increase of its oligosaccharide affinity.,Broeker NK, Gohlke U, Muller JJ, Uetrecht C, Heinemann U, Seckler R, Barbirz S Glycobiology. 2012 Aug 24. PMID:22923442<ref>PMID:22923442</ref>

-	~~Authors: Gohlke~~, U.~~, Broeker, N~~.K.~~, Heinemann, U., Seckler, R.,~~ Barbirz, S.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~: ~~Tailspike protein double mutant D339N/E372Q of E. coli bacteriophage HK620~~	+	<div class="pdbe-citations 4xon" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Unreleased Structures~~]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Barbirz, S]]
		+	[[Category: Broeker, N K]]
		+	[[Category: Gohlke, U]]
	[[Category: Heinemann, U]]		[[Category: Heinemann, U]]
	[[Category: Seckler, R]]		[[Category: Seckler, R]]
-	[[Category: ~~Broeker, N.K~~]]	+	[[Category: Beta helix]]
-	[[Category: ~~Gohlke, U~~]]	+	[[Category: Pectin lyase fold]]
-	[[Category: ~~Barbirz, S~~]]	+	[[Category: Protein-carbohydrate complex]]
		+	[[Category: Viral protein]]

OCA at 23:16, 30 November 2015

2015-11-30T23:16:09Z

←Older revision		Revision as of 23:16, 30 November 2015
Line 7:		Line 7:
	Description: Tailspike protein double mutant D339N/E372Q of E. coli bacteriophage HK620		Description: Tailspike protein double mutant D339N/E372Q of E. coli bacteriophage HK620
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Seckler, R]]
	[[Category: Heinemann, U]]		[[Category: Heinemann, U]]
		+	[[Category: Seckler, R]]
	[[Category: Broeker, N.K]]		[[Category: Broeker, N.K]]
	[[Category: Gohlke, U]]		[[Category: Gohlke, U]]
	[[Category: Barbirz, S]]		[[Category: Barbirz, S]]

OCA: Protected "4xon" [edit=sysop:move=sysop]

2015-01-28T15:37:13Z

Protected "4xon" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:37, 28 January 2015

OCA: New page: '''Unreleased structure''' The entry 4xon is ON HOLD until Paper Publication Authors: Gohlke, U., Broeker, N.K., Heinemann, U., Seckler, R., Barbirz, S. Description: Tailspike protein ...

2015-01-28T15:37:12Z

New page: '''Unreleased structure''' The entry 4xon is ON HOLD until Paper Publication Authors: Gohlke, U., Broeker, N.K., Heinemann, U., Seckler, R., Barbirz, S. Description: Tailspike protein ...

New page

'''Unreleased structure'''

The entry 4xon is ON HOLD until Paper Publication

Authors: Gohlke, U., Broeker, N.K., Heinemann, U., Seckler, R., Barbirz, S.

Description: Tailspike protein double mutant D339N/E372Q of E. coli bacteriophage HK620
[[Category: Unreleased Structures]]
[[Category: Seckler, R]]
[[Category: Heinemann, U]]
[[Category: Broeker, N.K]]
[[Category: Gohlke, U]]
[[Category: Barbirz, S]]