5ax2 - Revision history

OCA at 06:29, 31 May 2023

2023-05-31T06:29:17Z

←Older revision		Revision as of 06:29, 31 May 2023
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	==Crystal structure of S.cerevisiae Kti11p==		==Crystal structure of S.cerevisiae Kti11p==
-	<StructureSection load='5ax2' size='340' side='right' caption='[[5ax2]], [[Resolution\|resolution]] 2.40Å' scene=''>	+	<StructureSection load='5ax2' size='340' side='right'caption='[[5ax2]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ax2]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Baker's_yeast Baker's yeast~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AX2 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5AX2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ax2]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AX2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5AX2 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">KTI11, DPH3, YBL071W-A ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</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=5ax2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ax2 OCA], [https://pdbe.org/5ax2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ax2 RCSB], [https://www.ebi.ac.uk/pdbsum/5ax2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ax2 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=5ax2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ax2 OCA], [~~http~~://pdbe.org/5ax2 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ax2 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ax2 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ax2 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/DPH3_YEAST DPH3_YEAST]] Required for the first step of diphthamide biosynthesis, the transfer of 3-amino-3-carboxypropyl from S-adenosyl-L-methionine to a histidine residue. Diphthamide is a post-translational modification of histidine which occurs in elongation factor 2. Required for conferring sensitivity to K.lactis zymocin.<ref>PMID:15485916</ref>	+	[https://www.uniprot.org/uniprot/DPH3_YEAST DPH3_YEAST] Required for the first step of diphthamide biosynthesis, the transfer of 3-amino-3-carboxypropyl from S-adenosyl-L-methionine to a histidine residue. Diphthamide is a post-translational modification of histidine which occurs in elongation factor 2. Required for conferring sensitivity to K.lactis zymocin.<ref>PMID:15485916</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Baker's yeast~~]]	+	[[Category: Large Structures]]
-	[[Category: Balbach, J]]	+	[[Category: Saccharomyces cerevisiae S288C]]
-	[[Category: Kumar, A]]	+	[[Category: Balbach J]]
-	[[Category: Nagarathinam, K]]	+	[[Category: Kumar A]]
-	[[Category: Tanabe, M]]	+	[[Category: Nagarathinam K]]
-	~~[[Category: Cytoplasm]]~~	+	[[Category: Tanabe M]]
-	~~[[Category: High-pressure nmr]]~~	+
-	~~[[Category: Metal binding]]~~	+
-	~~[[Category: Metal binding protein]]~~	+
-	~~[[Category: Mr-sad]]~~	+
-	~~[[Category: Protein folding~~]]	+

OCA at 07:06, 21 February 2019

2019-02-21T07:06:41Z

←Older revision		Revision as of 07:06, 21 February 2019
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	<StructureSection load='5ax2' size='340' side='right' caption='[[5ax2]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='5ax2' size='340' side='right' caption='[[5ax2]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ax2]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AX2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5AX2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ax2]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AX2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5AX2 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">KTI11, DPH3, YBL071W-A ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</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=5ax2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ax2 OCA], [http://pdbe.org/5ax2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ax2 RCSB], [http://www.ebi.ac.uk/pdbsum/5ax2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ax2 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=5ax2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ax2 OCA], [http://pdbe.org/5ax2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ax2 RCSB], [http://www.ebi.ac.uk/pdbsum/5ax2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ax2 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/DPH3_YEAST DPH3_YEAST]] Required for the first step of diphthamide biosynthesis, the transfer of 3-amino-3-carboxypropyl from S-adenosyl-L-methionine to a histidine residue. Diphthamide is a post-translational modification of histidine which occurs in elongation factor 2. Required for conferring sensitivity to K.lactis zymocin.<ref>PMID:15485916</ref>		[[http://www.uniprot.org/uniprot/DPH3_YEAST DPH3_YEAST]] Required for the first step of diphthamide biosynthesis, the transfer of 3-amino-3-carboxypropyl from S-adenosyl-L-methionine to a histidine residue. Diphthamide is a post-translational modification of histidine which occurs in elongation factor 2. Required for conferring sensitivity to K.lactis zymocin.<ref>PMID:15485916</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	For a comprehensive understanding of the thermodynamic state functions describing the stability of a protein, the influence of the intensive properties of temperature and pressure has to be known. With the zinc-finger-containing Kti11, we found a suitable protein for this purpose because folding and unfolding transitions occur at an experimentally accessible temperature (280-330 degrees K) and pressure (0.1-240 MPa) range. We solved the crystal structure of the apo form of Kti11 to reveal two disulfide bonds at the metal-binding site, which seals off a cavity in the beta-barrel part of the protein. From a generally applicable proton NMR approach, we could determine the populations of folded and unfolded chains under all conditions, leading to a hyperbolic pressure-temperature phase diagram rarely observed for proteins. A global fit of a two-state model to all derived populations disclosed reliable values for the change in Gibbs free energy, volume, entropy, heat capacity, compressibility, and thermal expansion upon unfolding. The unfolded state of apoKti11 has a lower compressibility compared to the native state and a smaller volume at ambient pressure. Therefore, a pressure increase up to 200 MPa reduces the population of the native state, and above this value, the native population increases again. Pressure-induced chemical-shift changes in two-dimensional (1)H-(15)N NMR spectra could be employed for a molecular interpretation of the thermodynamic properties of apoKti11.
		+
		+	Hyperbolic Pressure-Temperature Phase Diagram of the Zinc-Finger Protein apoKti11 Detected by NMR Spectroscopy.,Klamt A, Nagarathinam K, Tanabe M, Kumar A, Balbach J J Phys Chem B. 2019 Jan 31;123(4):792-801. doi: 10.1021/acs.jpcb.8b11019. Epub, 2019 Jan 16. PMID:30608169<ref>PMID:30608169</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5ax2" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Baker's yeast]]
	[[Category: Balbach, J]]		[[Category: Balbach, J]]
	[[Category: Kumar, A]]		[[Category: Kumar, A]]

OCA at 15:25, 26 July 2016

2016-07-26T15:25:16Z

←Older revision		Revision as of 15:25, 26 July 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5ax2 is ~~ON HOLD~~ ~~until Paper Publication~~	+	==Crystal structure of S.cerevisiae Kti11p==
-		+	<StructureSection load='5ax2' size='340' side='right' caption='[[5ax2]], [[Resolution\|resolution]] 2.40Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5ax2]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AX2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5AX2 FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<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=5ax2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ax2 OCA], [http://pdbe.org/5ax2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ax2 RCSB], [http://www.ebi.ac.uk/pdbsum/5ax2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ax2 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DPH3_YEAST DPH3_YEAST]] Required for the first step of diphthamide biosynthesis, the transfer of 3-amino-3-carboxypropyl from S-adenosyl-L-methionine to a histidine residue. Diphthamide is a post-translational modification of histidine which occurs in elongation factor 2. Required for conferring sensitivity to K.lactis zymocin.<ref>PMID:15485916</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Balbach, J]]
		+	[[Category: Kumar, A]]
		+	[[Category: Nagarathinam, K]]
		+	[[Category: Tanabe, M]]
		+	[[Category: Cytoplasm]]
		+	[[Category: High-pressure nmr]]
		+	[[Category: Metal binding]]
		+	[[Category: Metal binding protein]]
		+	[[Category: Mr-sad]]
		+	[[Category: Protein folding]]

OCA at 10:59, 15 May 2016

2016-05-15T10:59:03Z

←Older revision		Revision as of 10:59, 15 May 2016
Line 3:		Line 3:
	The entry 5ax2 is ON HOLD until Paper Publication		The entry 5ax2 is ON HOLD until Paper Publication

-	Authors: ~~Kumar, A., Nagarathinam, K., Tanabe, M., Balbach, J.~~	+	Authors:

	Description:		Description:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Tanabe, M]]
-	[[Category: Balbach, J]]
-	[[Category: Nagarathinam, K]]
-	[[Category: Kumar, A]]

OCA at 09:58, 16 December 2015

2015-12-16T09:58:13Z

←Older revision		Revision as of 09:58, 16 December 2015
Line 7:		Line 7:
	Description:		Description:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
		+	[[Category: Tanabe, M]]
	[[Category: Balbach, J]]		[[Category: Balbach, J]]
	[[Category: Nagarathinam, K]]		[[Category: Nagarathinam, K]]
	[[Category: Kumar, A]]		[[Category: Kumar, A]]
-	[[Category: Tanabe, M]]

OCA at 12:37, 29 July 2015

2015-07-29T12:37:30Z

←Older revision		Revision as of 12:37, 29 July 2015
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5ax2 is ON HOLD	+	The entry 5ax2 is ON HOLD until Paper Publication

	Authors: Kumar, A., Nagarathinam, K., Tanabe, M., Balbach, J.		Authors: Kumar, A., Nagarathinam, K., Tanabe, M., Balbach, J.

OCA: Protected "5ax2" [edit=sysop:move=sysop]

2015-07-22T12:20:24Z

Protected "5ax2" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:20, 22 July 2015

OCA: New page: '''Unreleased structure''' The entry 5ax2 is ON HOLD Authors: Kumar, A., Nagarathinam, K., Tanabe, M., Balbach, J. Description: Category: Unreleased Structures [[Category: Balbach...

2015-07-22T12:20:23Z

New page: '''Unreleased structure''' The entry 5ax2 is ON HOLD Authors: Kumar, A., Nagarathinam, K., Tanabe, M., Balbach, J. Description: Category: Unreleased Structures [[Category: Balbach...

New page

'''Unreleased structure'''

The entry 5ax2 is ON HOLD

Authors: Kumar, A., Nagarathinam, K., Tanabe, M., Balbach, J.

Description:
[[Category: Unreleased Structures]]
[[Category: Balbach, J]]
[[Category: Nagarathinam, K]]
[[Category: Kumar, A]]
[[Category: Tanabe, M]]