5xz2 - Revision history

OCA at 08:17, 22 November 2023

2023-11-22T08:17:52Z

←Older revision		Revision as of 08:17, 22 November 2023
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	==Crystal structure of adenylate kinase==		==Crystal structure of adenylate kinase==
-	<StructureSection load='5xz2' size='340' side='right' caption='[[5xz2]], [[Resolution\|resolution]] 1.75Å' scene=''>	+	<StructureSection load='5xz2' size='340' side='right'caption='[[5xz2]], [[Resolution\|resolution]] 1.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xz2]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Brachidanio_rerio Brachidanio~~ rerio]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XZ2 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5XZ2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xz2]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Danio_rerio Danio rerio]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XZ2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5XZ2 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='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.75Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~ak1, AK1, zgc~~:~~91930~~ (~~[http:~~/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=7955 Brachidanio rerio])~~</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~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5xz2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xz2 OCA], [~~http~~://pdbe.org/5xz2 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5xz2 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5xz2 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5xz2 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=5xz2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xz2 OCA], [https://pdbe.org/5xz2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5xz2 RCSB], [https://www.ebi.ac.uk/pdbsum/5xz2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5xz2 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/Q68EH2_DANRE Q68EH2_DANRE]] 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]	+	[https://www.uniprot.org/uniprot/Q68EH2_DANRE Q68EH2_DANRE] 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 19:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 5xz2" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5xz2" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Adenylate kinase 3D structures\|Adenylate kinase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Brachidanio~~ rerio]]	+	[[Category: Danio rerio]]
-	[[Category: ~~Bae, E~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Kim, J~~]]	+	[[Category: Bae E]]
-	[[Category: ~~Moon, S~~]]	+	[[Category: Kim J]]
-	[[Category: ~~Phosphorylation]]~~	+	[[Category: Moon S]]
-	~~[[Category: Transferase~~]]	+

OCA at 09:22, 30 January 2019

2019-01-30T09:22:49Z

←Older revision		Revision as of 09:22, 30 January 2019
Line 3:		Line 3:
	<StructureSection load='5xz2' size='340' side='right' caption='[[5xz2]], [[Resolution\|resolution]] 1.75Å' scene=''>		<StructureSection load='5xz2' size='340' side='right' caption='[[5xz2]], [[Resolution\|resolution]] 1.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xz2]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XZ2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XZ2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xz2]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Brachidanio_rerio Brachidanio rerio]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XZ2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XZ2 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='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ak1, AK1, zgc:91930 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7955 Brachidanio rerio])</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=5xz2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xz2 OCA], [http://pdbe.org/5xz2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xz2 RCSB], [http://www.ebi.ac.uk/pdbsum/5xz2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xz2 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=5xz2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xz2 OCA], [http://pdbe.org/5xz2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xz2 RCSB], [http://www.ebi.ac.uk/pdbsum/5xz2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xz2 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/Q68EH2_DANRE Q68EH2_DANRE]] 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]		[[http://www.uniprot.org/uniprot/Q68EH2_DANRE Q68EH2_DANRE]] 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;">
		+	== 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 5xz2" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Brachidanio rerio]]
	[[Category: Bae, E]]		[[Category: Bae, E]]
	[[Category: Kim, J]]		[[Category: Kim, J]]

OCA at 07:29, 18 July 2018

2018-07-18T07:29:03Z

←Older revision		Revision as of 07:29, 18 July 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5xz2 is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of adenylate kinase==
-		+	<StructureSection load='5xz2' size='340' side='right' caption='[[5xz2]], [[Resolution\|resolution]] 1.75Å' scene=''>
-	~~Authors~~: ~~Moon~~, S., ~~Bae~~, E., ~~Kim~~, J.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5xz2]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XZ2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XZ2 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='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=5xz2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xz2 OCA], [http://pdbe.org/5xz2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xz2 RCSB], [http://www.ebi.ac.uk/pdbsum/5xz2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xz2 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/Q68EH2_DANRE Q68EH2_DANRE]] 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]
		+	__TOC__
		+	</StructureSection>
	[[Category: Bae, E]]		[[Category: Bae, E]]
		+	[[Category: Kim, J]]
	[[Category: Moon, S]]		[[Category: Moon, S]]
-	[[Category: ~~Kim, J~~]]	+	[[Category: Phosphorylation]]
		+	[[Category: Transferase]]

OCA: Protected "5xz2" [edit=sysop:move=sysop]

2017-09-27T15:56:21Z

Protected "5xz2" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:56, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5xz2 is ON HOLD until Paper Publication Authors: Moon, S., Bae, E., Kim, J. Description: Crystal structure of adenylate kinase [[Category: Unreleas...

2017-09-27T15:56:20Z

New page: '''Unreleased structure''' The entry 5xz2 is ON HOLD until Paper Publication Authors: Moon, S., Bae, E., Kim, J. Description: Crystal structure of adenylate kinase [[Category: Unreleas...

New page

'''Unreleased structure'''

The entry 5xz2 is ON HOLD until Paper Publication

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

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