4xkv - Revision history

OCA at 10:49, 10 January 2024

OCA — Wed, 10 Jan 2024 10:49:07 GMT

←Older revision		Revision as of 10:49, 10 January 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4xkv]] 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=4XKV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XKV FirstGlance]. <br>		<table><tr><td colspan='2'>[[4xkv]] 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=4XKV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XKV 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=4xkv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xkv OCA], [https://pdbe.org/4xkv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xkv RCSB], [https://www.ebi.ac.uk/pdbsum/4xkv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xkv 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=4xkv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xkv OCA], [https://pdbe.org/4xkv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xkv RCSB], [https://www.ebi.ac.uk/pdbsum/4xkv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xkv 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 17:41, 26 April 2023

OCA — Wed, 26 Apr 2023 17:41:34 GMT

←Older revision		Revision as of 17:41, 26 April 2023
Line 3:		Line 3:
	<StructureSection load='4xkv' size='340' side='right'caption='[[4xkv]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='4xkv' size='340' side='right'caption='[[4xkv]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4xkv]] 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=4XKV OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4XKV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4xkv]] 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=4XKV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XKV 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='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2vij\|2vij]], [[2vjj\|2vjj]], [[2x6w\|2x6w]], [[2x6x\|2x6x]], [[2x6y\|2x6y]], [[2x85\|2x85]], [[4avz\|4avz]], [[4pat\|4pat]]</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=4xkv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xkv OCA], [https://pdbe.org/4xkv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xkv RCSB], [https://www.ebi.ac.uk/pdbsum/4xkv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xkv 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=4xkv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xkv OCA], [~~http~~://pdbe.org/4xkv PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4xkv RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4xkv PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4xkv 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 4xkv" 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: Metal binding protein]]~~	+
-	~~[[Category: Pectin lyase fold]]~~	+
-	~~[[Category: Protein-carbohydrate complex]]~~	+
-	~~[[Category: Viral protein~~]]	+

OCA at 07:25, 29 May 2019

OCA — Wed, 29 May 2019 07:25:25 GMT

←Older revision		Revision as of 07:25, 29 May 2019
Line 1:		Line 1:
		+
	==Tailspike protein mutant D339N of E. coli bacteriophage HK620==		==Tailspike protein mutant D339N of E. coli bacteriophage HK620==
-	<StructureSection load='4xkv' size='340' side='right' caption='[[4xkv]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='4xkv' size='340' side='right'caption='[[4xkv]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4xkv]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XKV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XKV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4xkv]] 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=4XKV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XKV 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='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2vij\|2vij]], [[2vjj\|2vjj]], [[2x6w\|2x6w]], [[2x6x\|2x6x]], [[2x6y\|2x6y]], [[2x85\|2x85]], [[4avz\|4avz]], [[4pat\|4pat]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2vij\|2vij]], [[2vjj\|2vjj]], [[2x6w\|2x6w]], [[2x6x\|2x6x]], [[2x6y\|2x6y]], [[2x85\|2x85]], [[4avz\|4avz]], [[4pat\|4pat]]</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=4xkv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xkv OCA], [http://pdbe.org/4xkv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xkv RCSB], [http://www.ebi.ac.uk/pdbsum/4xkv 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=4xkv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xkv OCA], [http://pdbe.org/4xkv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xkv RCSB], [http://www.ebi.ac.uk/pdbsum/4xkv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4xkv ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 20:		Line 21:
	__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 17:01, 20 January 2016

OCA — Wed, 20 Jan 2016 17:01:56 GMT

←Older revision		Revision as of 17:01, 20 January 2016
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Tailspike protein mutant D339N of E. coli bacteriophage HK620==
		+	<StructureSection load='4xkv' size='340' side='right' caption='[[4xkv]], [[Resolution\|resolution]] 2.10Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4xkv]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XKV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XKV 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='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2vij\|2vij]], [[2vjj\|2vjj]], [[2x6w\|2x6w]], [[2x6x\|2x6x]], [[2x6y\|2x6y]], [[2x85\|2x85]], [[4avz\|4avz]], [[4pat\|4pat]]</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=4xkv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xkv OCA], [http://pdbe.org/4xkv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xkv RCSB], [http://www.ebi.ac.uk/pdbsum/4xkv 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 4xkv 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 mutant D339N of E. coli bacteriophage HK620~~	+	<div class="pdbe-citations 4xkv" 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: Metal binding protein]]
-	[[Category: ~~Barbirz, S~~]]	+	[[Category: Pectin lyase fold]]
		+	[[Category: Protein-carbohydrate complex]]
		+	[[Category: Viral protein]]

OCA at 23:13, 30 November 2015

OCA — Mon, 30 Nov 2015 23:13:21 GMT

←Older revision		Revision as of 23:13, 30 November 2015
Line 7:		Line 7:
	Description: Tailspike protein mutant D339N of E. coli bacteriophage HK620		Description: Tailspike protein mutant D339N 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 at 15:30, 28 January 2015

OCA — Wed, 28 Jan 2015 15:30:52 GMT

←Older revision		Revision as of 15:30, 28 January 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4xkv is ON HOLD	+	The entry 4xkv is ON HOLD until Paper Publication

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

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

OCA — Wed, 21 Jan 2015 15:58:16 GMT

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

←Older revision

Revision as of 15:58, 21 January 2015

OCA: New page: '''Unreleased structure''' The entry 4xkv is ON HOLD Authors: Gohlke, U., Broeker, N.K., Heinemann, U., Seckler, R., Barbirz, S. Description: Tailspike protein mutant D339N of E. coli ...

OCA — Wed, 21 Jan 2015 15:58:14 GMT

New page: '''Unreleased structure''' The entry 4xkv is ON HOLD Authors: Gohlke, U., Broeker, N.K., Heinemann, U., Seckler, R., Barbirz, S. Description: Tailspike protein mutant D339N of E. coli ...

New page

'''Unreleased structure'''

The entry 4xkv is ON HOLD

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

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