5x6k - Revision history

OCA at 07:54, 22 November 2023

OCA — Wed, 22 Nov 2023 07:54:48 GMT

←Older revision		Revision as of 07:54, 22 November 2023
Line 3:		Line 3:
	<StructureSection load='5x6k' size='340' side='right'caption='[[5x6k]], [[Resolution\|resolution]] 1.99Å' scene=''>		<StructureSection load='5x6k' size='340' side='right'caption='[[5x6k]], [[Resolution\|resolution]] 1.99Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5x6k]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Notothenia_coriiceps Notothenia coriiceps]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X6K OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5X6K FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5x6k]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Notothenia_coriiceps Notothenia coriiceps]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X6K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5X6K FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=AP5:BIS(ADENOSINE)~~-~~5-PENTAPHOSPHATE'>AP5</scene>~~, ~~<scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.99Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[5x6l\|5x6l]]~~, ~~[[5x6j\|5x6j]], [[5x6i\|5x6i]]~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AP5:BIS(ADENOSINE)-5-PENTAPHOSPHATE'>AP5</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5x6k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x6k OCA], [~~http~~://pdbe.org/5x6k PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5x6k RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5x6k PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5x6k 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=5x6k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x6k OCA], [https://pdbe.org/5x6k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5x6k RCSB], [https://www.ebi.ac.uk/pdbsum/5x6k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5x6k ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A2R2JFU5_9TELE A0A2R2JFU5_9TELE] Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. Also displays broad nucleoside diphosphate kinase activity. Plays an important role in cellular energy homeostasis and in adenine nucleotide metabolism.[HAMAP-Rule:MF_03171]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 26:		Line 28:
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Notothenia coriiceps]]		[[Category: Notothenia coriiceps]]
-	[[Category: Bae, E]]	+	[[Category: Bae E]]
-	[[Category: Moon, S]]	+	[[Category: Moon S]]
-	~~[[Category: Phosphorylation]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 08:29, 4 November 2020

OCA — Wed, 04 Nov 2020 08:29:03 GMT

←Older revision		Revision as of 08:29, 4 November 2020
Line 1:		Line 1:

	==Crystal structure of adenylate kinase==		==Crystal structure of adenylate kinase==
-	<StructureSection load='5x6k' size='340' side='right' caption='[[5x6k]], [[Resolution\|resolution]] 1.99Å' scene=''>	+	<StructureSection load='5x6k' size='340' side='right'caption='[[5x6k]], [[Resolution\|resolution]] 1.99Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5x6k]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Notothenia_coriiceps Notothenia coriiceps]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X6K OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5X6K FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5x6k]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Notothenia_coriiceps Notothenia coriiceps]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X6K OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5X6K FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AP5:BIS(ADENOSINE)-5-PENTAPHOSPHATE'>AP5</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AP5:BIS(ADENOSINE)-5-PENTAPHOSPHATE'>AP5</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5x6l\|5x6l]], [[5x6j\|5x6j]], [[5x6i\|5x6i]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5x6l\|5x6l]], [[5x6j\|5x6j]], [[5x6i\|5x6i]]</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=5x6k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x6k OCA], [http://pdbe.org/5x6k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x6k RCSB], [http://www.ebi.ac.uk/pdbsum/5x6k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x6k ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5x6k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x6k OCA], [http://pdbe.org/5x6k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x6k RCSB], [http://www.ebi.ac.uk/pdbsum/5x6k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x6k ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 19:		Line 19:

	==See Also==		==See Also==
-	*[[Adenylate kinase\|Adenylate kinase]]	+	*[[Adenylate kinase 3D structures\|Adenylate kinase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Notothenia coriiceps]]		[[Category: Notothenia coriiceps]]
	[[Category: Bae, E]]		[[Category: Bae, E]]

OCA at 09:22, 30 January 2019

OCA — Wed, 30 Jan 2019 09:22:36 GMT

←Older revision		Revision as of 09:22, 30 January 2019
Line 3:		Line 3:
	<StructureSection load='5x6k' size='340' side='right' caption='[[5x6k]], [[Resolution\|resolution]] 1.99Å' scene=''>		<StructureSection load='5x6k' size='340' side='right' caption='[[5x6k]], [[Resolution\|resolution]] 1.99Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5x6k]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X6K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5X6K FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5x6k]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Notothenia_coriiceps Notothenia coriiceps]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X6K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5X6K FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AP5:BIS(ADENOSINE)-5-PENTAPHOSPHATE'>AP5</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AP5:BIS(ADENOSINE)-5-PENTAPHOSPHATE'>AP5</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5x6l\|5x6l]], [[5x6j\|5x6j]], [[5x6i\|5x6i]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5x6l\|5x6l]], [[5x6j\|5x6j]], [[5x6i\|5x6i]]</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=5x6k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x6k OCA], [http://pdbe.org/5x6k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x6k RCSB], [http://www.ebi.ac.uk/pdbsum/5x6k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x6k 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=5x6k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x6k OCA], [http://pdbe.org/5x6k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x6k RCSB], [http://www.ebi.ac.uk/pdbsum/5x6k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x6k ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Psychrophiles are extremophilic organisms capable of thriving in cold environments. Proteins from these cold-adapted organisms can remain physiologically functional at low temperatures, but are structurally unstable even at moderate temperatures. Here, we report the crystal structure of adenylate kinase (AK) from the Antarctic fish Notothenia coriiceps, and identify the structural basis of cold adaptation by comparison with homologues from tropical fishes including Danio rerio. The structure of N. coriiceps AK (AKNc) revealed suboptimal hydrophobic packing around three Val residues in its central CORE domain, which are replaced with Ile residues in D. rerio AK (AKDr). The Val-to-Ile mutations that improve hydrophobic CORE packing in AKNc increased stability at high temperatures but decreased activity at low temperatures, suggesting that the suboptimal hydrophobic CORE packing is important for cold adaptation. Such linkage between stability and activity was also observed in AKDr. Ile-to-Val mutations that destabilized the tropical AK resulted in increased activity at low temperatures. Our results provide the structural basis of cold adaptation of a psychrophilic enzyme from a multicellular, eukaryotic organism, and highlight the similarities and differences in the structural adjustment of vertebrate and bacterial psychrophilic AKs during cold adaptation.
		+
		+	Structural analyses of adenylate kinases from Antarctic and tropical fishes for understanding cold adaptation of enzymes.,Moon S, Kim J, Bae E Sci Rep. 2017 Nov 22;7(1):16027. doi: 10.1038/s41598-017-16266-9. PMID:29167503<ref>PMID:29167503</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5x6k" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Adenylate kinase\|Adenylate kinase]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Notothenia coriiceps]]
	[[Category: Bae, E]]		[[Category: Bae, E]]
	[[Category: Moon, S]]		[[Category: Moon, S]]
	[[Category: Phosphorylation]]		[[Category: Phosphorylation]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 06:26, 28 February 2018

OCA — Wed, 28 Feb 2018 06:26:39 GMT

←Older revision		Revision as of 06:26, 28 February 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5x6k ~~is ON HOLD until Paper Publication~~	+	==Crystal structure of adenylate kinase==
-		+	<StructureSection load='5x6k' size='340' side='right' caption='[[5x6k]], [[Resolution\|resolution]] 1.99Å' scene=''>
-	~~Authors~~: ~~Moon, S~~.~~, Bae, E~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5x6k]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X6K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5X6K FirstGlance]. <br>
-	~~Description~~: ~~Crystal structure of adenylate kinase~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AP5:BIS(ADENOSINE)-5-PENTAPHOSPHATE'>AP5</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5x6l\|5x6l]], [[5x6j\|5x6j]], [[5x6i\|5x6i]]</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=5x6k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x6k OCA], [http://pdbe.org/5x6k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x6k RCSB], [http://www.ebi.ac.uk/pdbsum/5x6k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x6k ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
	[[Category: Bae, E]]		[[Category: Bae, E]]
	[[Category: Moon, S]]		[[Category: Moon, S]]
		+	[[Category: Phosphorylation]]
		+	[[Category: Transferase]]

OCA at 12:18, 5 April 2017

OCA — Wed, 05 Apr 2017 12:18:20 GMT

←Older revision		Revision as of 12:18, 5 April 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5x6k is ON HOLD	+	The entry 5x6k is ON HOLD until Paper Publication

	Authors: Moon, S., Bae, E.		Authors: Moon, S., Bae, E.

OCA: Protected "5x6k" [edit=sysop:move=sysop]

OCA — Thu, 09 Mar 2017 15:49:15 GMT

Protected "5x6k" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:49, 9 March 2017

OCA: New page: '''Unreleased structure''' The entry 5x6k is ON HOLD Authors: Moon, S., Bae, E. Description: Crystal structure of adenylate kinase Category: Unreleased Structures [[Category: Bae, ...

OCA — Thu, 09 Mar 2017 15:49:14 GMT

New page: '''Unreleased structure''' The entry 5x6k is ON HOLD Authors: Moon, S., Bae, E. Description: Crystal structure of adenylate kinase Category: Unreleased Structures [[Category: Bae, ...

New page

'''Unreleased structure'''

The entry 5x6k is ON HOLD

Authors: Moon, S., Bae, E.

Description: Crystal structure of adenylate kinase
[[Category: Unreleased Structures]]
[[Category: Bae, E]]
[[Category: Moon, S]]