2aky - Revision history

OCA at 09:13, 14 February 2024

2024-02-14T09:13:18Z

← Older revision		Revision as of 09:13, 14 February 2024
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	<StructureSection load='2aky' size='340' side='right'caption='[[2aky]], [[Resolution\|resolution]] 1.96Å' scene=''>		<StructureSection load='2aky' size='340' side='right'caption='[[2aky]], [[Resolution\|resolution]] 1.96Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2aky]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Atcc_18824 Atcc 18824~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AKY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2AKY FirstGlance]. <br>		<table><tr><td colspan='2'>[[2aky]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AKY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2AKY 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=MG:MAGNESIUM+ION'>MG</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]] 1.96Å</td></tr>
	<tr id='~~activity~~'><td class="sblockLbl"><b>~~Activity~~:</b></td><td class="sblockDat"><~~span class~~='~~plainlinks~~'>~~[https:~~/~~/en.wikipedia.org/wiki/Adenylate_kinase Adenylate kinase]~~, ~~with EC number [https~~:~~//www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.3 2.7.4.3]~~ </~~span~~></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=MG:MAGNESIUM+ION'>MG</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=2aky FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2aky OCA], [https://pdbe.org/2aky PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2aky RCSB], [https://www.ebi.ac.uk/pdbsum/2aky PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2aky 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=2aky FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2aky OCA], [https://pdbe.org/2aky PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2aky RCSB], [https://www.ebi.ac.uk/pdbsum/2aky PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2aky ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/KAD2_YEAST KAD2_YEAST]] Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. Plays an important role in cellular energy homeostasis and in adenine nucleotide metabolism. Adenylate kinase activity is critical for regulation of the phosphate utilization and the AMP de novo biosynthesis pathways.[HAMAP-Rule:MF_03168]<ref>PMID:18433446</ref> <ref>PMID:2848829</ref> <ref>PMID:2850178</ref>		[https://www.uniprot.org/uniprot/KAD2_YEAST KAD2_YEAST] Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. Plays an important role in cellular energy homeostasis and in adenine nucleotide metabolism. Adenylate kinase activity is critical for regulation of the phosphate utilization and the AMP de novo biosynthesis pathways.[HAMAP-Rule:MF_03168]<ref>PMID:18433446</ref> <ref>PMID:2848829</ref> <ref>PMID:2850178</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2aky ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2aky ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	The structure of adenylate kinase from yeast ligated with the two-substrate-mimicking inhibitor Ap5A and Mg2+ has been refined to 1.96 A resolution. In addition, the refined structure of the same complex with a bound imidazole molecule replacing Mg2+ has been determined at 1.63 A. These structures indicate that replacing Mg2+ by imidazole disturbs the water structure and thus the complex. A comparison with the G-proteins shows that Mg2+ is exactly at the same position with respect to the phosphates. However, although the Mg2+ ligand sphere of the G-proteins is a regular octahedron containing peptide ligands, the reported adenylate kinase has no such ligands and an open octahedron leaving space for the Mg2+ to accompany the transferred phosphoryl group. A superposition of the known crystalline and therefore perturbed phosphoryl transfer geometries in the adenylate kinases demonstrates that all of them are close to the start of the forward reaction with bound ATP and AMP. Averaging all observed perturbed structures gives rise to a close approximation of the transition state, indicating in general how to establish an elusive transition state geometry. The average shows that the in-line phosphoryl transfer is associative, because there is no space for a dissociative metaphosphate intermediate. As a side result, the secondary dipole interaction in the alpha-helices of both protein structures has been quantified.

	High-resolution structures of adenylate kinase from yeast ligated with inhibitor Ap5A, showing the pathway of phosphoryl transfer.,Abele U, Schulz GE Protein Sci. 1995 Jul;4(7):1262-71. PMID:7670369<ref>PMID:7670369</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 2aky" style="background-color:#fffaf0;"></div>~~

	==See Also==		==See Also==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	~~[[Category: Adenylate kinase]]~~
	~~[[Category: Atcc 18824]]~~
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: ~~Abele, U~~]]		[[Category: Saccharomyces cerevisiae]]
	[[Category: ~~Schulz, G E~~]]		[[Category: Abele U]]
	[[Category: ~~Atp:amp phosphotransferase]]~~		[[Category: Schulz GE]]
	~~[[Category: Myokinase~~]]

OCA at 14:42, 17 November 2021

2021-11-17T14:42:28Z

← Older revision		Revision as of 14:42, 17 November 2021
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	<StructureSection load='2aky' size='340' side='right'caption='[[2aky]], [[Resolution\|resolution]] 1.96Å' scene=''>		<StructureSection load='2aky' size='340' side='right'caption='[[2aky]], [[Resolution\|resolution]] 1.96Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2aky]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AKY OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2AKY FirstGlance]. <br>		<table><tr><td colspan='2'>[[2aky]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AKY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2AKY 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=MG:MAGNESIUM+ION'>MG</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=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Adenylate_kinase Adenylate kinase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.3 2.7.4.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Adenylate_kinase Adenylate kinase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.3 2.7.4.3] </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=2aky FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2aky OCA], [~~http~~://pdbe.org/2aky PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2aky RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2aky PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2aky 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=2aky FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2aky OCA], [https://pdbe.org/2aky PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2aky RCSB], [https://www.ebi.ac.uk/pdbsum/2aky PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2aky ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[~~http~~://www.uniprot.org/uniprot/KAD2_YEAST KAD2_YEAST]] Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. Plays an important role in cellular energy homeostasis and in adenine nucleotide metabolism. Adenylate kinase activity is critical for regulation of the phosphate utilization and the AMP de novo biosynthesis pathways.[HAMAP-Rule:MF_03168]<ref>PMID:18433446</ref> <ref>PMID:2848829</ref> <ref>PMID:2850178</ref>		[[https://www.uniprot.org/uniprot/KAD2_YEAST KAD2_YEAST]] Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. Plays an important role in cellular energy homeostasis and in adenine nucleotide metabolism. Adenylate kinase activity is critical for regulation of the phosphate utilization and the AMP de novo biosynthesis pathways.[HAMAP-Rule:MF_03168]<ref>PMID:18433446</ref> <ref>PMID:2848829</ref> <ref>PMID:2850178</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 05:09, 13 February 2020

2020-02-13T05:09:22Z

← Older revision		Revision as of 05:09, 13 February 2020
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	==HIGH-RESOLUTION STRUCTURES OF ADENYLATE KINASE FROM YEAST LIGATED WITH INHIBITOR AP5A, SHOWING THE PATHWAY OF PHOSPHORYL TRANSFER==		==HIGH-RESOLUTION STRUCTURES OF ADENYLATE KINASE FROM YEAST LIGATED WITH INHIBITOR AP5A, SHOWING THE PATHWAY OF PHOSPHORYL TRANSFER==
	<StructureSection load='2aky' size='340' side='right' caption='[[2aky]], [[Resolution\|resolution]] 1.96Å' scene=''>		<StructureSection load='2aky' size='340' side='right'caption='[[2aky]], [[Resolution\|resolution]] 1.96Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2aky]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AKY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2AKY FirstGlance]. <br>		<table><tr><td colspan='2'>[[2aky]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AKY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2AKY FirstGlance]. <br>
Line 31:		Line 31:

	==See Also==		==See Also==
	*[[Adenylate kinase\|Adenylate kinase]]		*[[Adenylate kinase 3D structures\|Adenylate kinase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	[[Category: Adenylate kinase]]		[[Category: Adenylate kinase]]
	[[Category: Atcc 18824]]		[[Category: Atcc 18824]]
			[[Category: Large Structures]]
	[[Category: Abele, U]]		[[Category: Abele, U]]
	[[Category: Schulz, G E]]		[[Category: Schulz, G E]]
	[[Category: Atp:amp phosphotransferase]]		[[Category: Atp:amp phosphotransferase]]
	[[Category: Myokinase]]		[[Category: Myokinase]]

OCA at 06:59, 9 May 2018

2018-05-09T06:59:30Z

← Older revision		Revision as of 06:59, 9 May 2018
Line 1:		Line 1:

	==HIGH-RESOLUTION STRUCTURES OF ADENYLATE KINASE FROM YEAST LIGATED WITH INHIBITOR AP5A, SHOWING THE PATHWAY OF PHOSPHORYL TRANSFER==		==HIGH-RESOLUTION STRUCTURES OF ADENYLATE KINASE FROM YEAST LIGATED WITH INHIBITOR AP5A, SHOWING THE PATHWAY OF PHOSPHORYL TRANSFER==
	<StructureSection load='2aky' size='340' side='right' caption='[[2aky]], [[Resolution\|resolution]] 1.96Å' scene=''>		<StructureSection load='2aky' size='340' side='right' caption='[[2aky]], [[Resolution\|resolution]] 1.96Å' scene=''>
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	</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=MG:MAGNESIUM+ION'>MG</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=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Adenylate_kinase Adenylate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.3 2.7.4.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Adenylate_kinase Adenylate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.3 2.7.4.3] </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=2aky FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2aky OCA], [http://pdbe.org/2aky PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2aky RCSB], [http://www.ebi.ac.uk/pdbsum/2aky 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=2aky FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2aky OCA], [http://pdbe.org/2aky PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2aky RCSB], [http://www.ebi.ac.uk/pdbsum/2aky PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2aky ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ak/2aky_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ak/2aky_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 14:54, 9 February 2016

2016-02-09T14:54:00Z

← Older revision		Revision as of 14:54, 9 February 2016
Line 17:		Line 17:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2aky ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 23:20, 10 September 2015

2015-09-10T23:20:12Z

← Older revision		Revision as of 23:20, 10 September 2015
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	<StructureSection load='2aky' size='340' side='right' caption='[[2aky]], [[Resolution\|resolution]] 1.96Å' scene=''>		<StructureSection load='2aky' size='340' side='right' caption='[[2aky]], [[Resolution\|resolution]] 1.96Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2aky]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Saccharomyces_cerevisiae Saccharomyces cerevisiae~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AKY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2AKY FirstGlance]. <br>		<table><tr><td colspan='2'>[[2aky]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AKY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2AKY 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=MG:MAGNESIUM+ION'>MG</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=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Adenylate_kinase Adenylate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.3 2.7.4.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Adenylate_kinase Adenylate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.3 2.7.4.3] </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=2aky FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2aky OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2aky RCSB], [http://www.ebi.ac.uk/pdbsum/2aky 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=2aky FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2aky OCA], [http://pdbe.org/2aky PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2aky RCSB], [http://www.ebi.ac.uk/pdbsum/2aky PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/~~KAD1_YEAST KAD1_YEAST~~]] Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. Plays an important role in cellular energy homeostasis and in adenine nucleotide metabolism. Adenylate kinase activity is critical for regulation of the phosphate utilization and the AMP de novo biosynthesis pathways.		[[http://www.uniprot.org/uniprot/KAD2_YEAST KAD2_YEAST]] Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. Plays an important role in cellular energy homeostasis and in adenine nucleotide metabolism. Adenylate kinase activity is critical for regulation of the phosphate utilization and the AMP de novo biosynthesis pathways.[HAMAP-Rule:MF_03168]<ref>PMID:18433446</ref> <ref>PMID:2848829</ref> <ref>PMID:2850178</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
			<div class="pdbe-citations 2aky" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 35:		Line 36:
	</StructureSection>		</StructureSection>
	[[Category: Adenylate kinase]]		[[Category: Adenylate kinase]]
	[[Category: ~~Saccharomyces cerevisiae~~]]		[[Category: Atcc 18824]]
	[[Category: Abele, U]]		[[Category: Abele, U]]
	[[Category: Schulz, G E]]		[[Category: Schulz, G E]]
	[[Category: Atp:amp phosphotransferase]]		[[Category: Atp:amp phosphotransferase]]
	[[Category: Myokinase]]		[[Category: Myokinase]]

OCA at 07:31, 25 December 2014

2014-12-25T07:31:25Z

← Older revision		Revision as of 07:31, 25 December 2014
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2aky]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AKY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2AKY FirstGlance]. <br>		<table><tr><td colspan='2'>[[2aky]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AKY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2AKY FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AP5:BIS(ADENOSINE)-5-PENTAPHOSPHATE'>AP5</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><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=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Adenylate_kinase Adenylate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.3 2.7.4.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Adenylate_kinase Adenylate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.3 2.7.4.3] </span></td></tr>
	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2aky FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2aky OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2aky RCSB], [http://www.ebi.ac.uk/pdbsum/2aky 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=2aky FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2aky OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2aky RCSB], [http://www.ebi.ac.uk/pdbsum/2aky PDBsum]</span></td></tr>
	<table>		</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/KAD1_YEAST KAD1_YEAST]] Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. Plays an important role in cellular energy homeostasis and in adenine nucleotide metabolism. Adenylate kinase activity is critical for regulation of the phosphate utilization and the AMP de novo biosynthesis pathways.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	[[Category: Adenylate kinase]]		[[Category: Adenylate kinase]]
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
	[[Category: Abele, U.]]		[[Category: Abele, U]]
	[[Category: Schulz, G E~~.]]~~		[[Category: Schulz, G E]]
	~~[[Category: Adenylate kinase~~]]
	[[Category: Atp:amp phosphotransferase]]		[[Category: Atp:amp phosphotransferase]]
	[[Category: Myokinase]]		[[Category: Myokinase]]

OCA at 02:55, 29 September 2014

2014-09-29T02:55:51Z

← Older revision		Revision as of 02:55, 29 September 2014
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	[[Image:~~2aky~~.~~png~~\|~~left~~\|~~200px~~]]		==HIGH-RESOLUTION STRUCTURES OF ADENYLATE KINASE FROM YEAST LIGATED WITH INHIBITOR AP5A, SHOWING THE PATHWAY OF PHOSPHORYL TRANSFER==
			<StructureSection load='2aky' size='340' side='right' caption='[[2aky]], [[Resolution\|resolution]] 1.96Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[2aky]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AKY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2AKY FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AP5:BIS(ADENOSINE)-5-PENTAPHOSPHATE'>AP5</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>
			<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Adenylate_kinase Adenylate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.3 2.7.4.3] </span></td></tr>
			<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2aky FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2aky OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2aky RCSB], [http://www.ebi.ac.uk/pdbsum/2aky PDBsum]</span></td></tr>
			<table>
			== Evolutionary Conservation ==
			[[Image:Consurf_key_small.gif\|200px\|right]]
			Check<jmol>
			<jmolCheckbox>
			<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ak/2aky_consurf.spt"</scriptWhenChecked>
			<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
			<text>to colour the structure by Evolutionary Conservation</text>
			</jmolCheckbox>
			</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
			<div style="clear:both"></div>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			The structure of adenylate kinase from yeast ligated with the two-substrate-mimicking inhibitor Ap5A and Mg2+ has been refined to 1.96 A resolution. In addition, the refined structure of the same complex with a bound imidazole molecule replacing Mg2+ has been determined at 1.63 A. These structures indicate that replacing Mg2+ by imidazole disturbs the water structure and thus the complex. A comparison with the G-proteins shows that Mg2+ is exactly at the same position with respect to the phosphates. However, although the Mg2+ ligand sphere of the G-proteins is a regular octahedron containing peptide ligands, the reported adenylate kinase has no such ligands and an open octahedron leaving space for the Mg2+ to accompany the transferred phosphoryl group. A superposition of the known crystalline and therefore perturbed phosphoryl transfer geometries in the adenylate kinases demonstrates that all of them are close to the start of the forward reaction with bound ATP and AMP. Averaging all observed perturbed structures gives rise to a close approximation of the transition state, indicating in general how to establish an elusive transition state geometry. The average shows that the in-line phosphoryl transfer is associative, because there is no space for a dissociative metaphosphate intermediate. As a side result, the secondary dipole interaction in the alpha-helices of both protein structures has been quantified.

	~~{{STRUCTURE_2aky\| PDB=2aky \| SCENE= }}~~		High-resolution structures of adenylate kinase from yeast ligated with inhibitor Ap5A, showing the pathway of phosphoryl transfer.,Abele U, Schulz GE Protein Sci. 1995 Jul;4(7):1262-71. PMID:7670369<ref>PMID:7670369</ref>

	~~===HIGH-RESOLUTION STRUCTURES OF ADENYLATE KINASE FROM YEAST LIGATED WITH INHIBITOR AP5A~~, ~~SHOWING THE PATHWAY OF PHOSPHORYL TRANSFER===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_7670369}}~~

	~~==About this Structure==~~
	~~[[2aky]] is~~ a ~~1 chain structure with sequence from [http://en.wikipedia~~.~~org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]~~. ~~Full crystallographic information is available from [http://oca~~.~~weizmann.ac.il/oca-bin~~/~~ocashort?id=2AKY OCA].~~

	==See Also==		==See Also==
	*[[Adenylate kinase\|Adenylate kinase]]		*[[Adenylate kinase\|Adenylate kinase]]
			== References ==
	==~~Reference~~==		<references/>
	<~~ref group="xtra">PMID:007670369<~~/~~ref~~><~~references group="xtra"~~/>		__TOC__
			</StructureSection>
	[[Category: Adenylate kinase]]		[[Category: Adenylate kinase]]
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]

OCA at 14:13, 20 October 2012

2012-10-20T14:13:08Z

← Older revision		Revision as of 14:13, 20 October 2012
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	==About this Structure==		==About this Structure==
	[[2aky]] is a 1 chain structure ~~of [[Adenylate kinase]]~~ with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AKY OCA].		[[2aky]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AKY OCA].

	==See Also==		==See Also==

OCA: Protected "2aky" [edit=sysop:move=sysop]

2012-07-26T14:26:41Z

Protected "2aky" [edit=sysop:move=sysop]

← Older revision	Revision as of 14:26, 26 July 2012
(No difference)