4cf7 - Revision history

OCA at 12:09, 20 December 2023

OCA — Wed, 20 Dec 2023 12:09:11 GMT

←Older revision		Revision as of 12:09, 20 December 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4cf7]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4CF7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4CF7 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4cf7]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4CF7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4CF7 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</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]] 1.594Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</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=4cf7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4cf7 OCA], [https://pdbe.org/4cf7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4cf7 RCSB], [https://www.ebi.ac.uk/pdbsum/4cf7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4cf7 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=4cf7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4cf7 OCA], [https://pdbe.org/4cf7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4cf7 RCSB], [https://www.ebi.ac.uk/pdbsum/4cf7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4cf7 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/KAD_AQUAE KAD_AQUAE]] Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. This small ubiquitous enzyme involved in the energy metabolism and nucleotide synthesis, is essential for maintenance and cell growth (By similarity).	+	[https://www.uniprot.org/uniprot/KAD_AQUAE KAD_AQUAE] Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. This small ubiquitous enzyme involved in the energy metabolism and nucleotide synthesis, is essential for maintenance and cell growth (By similarity).
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Kinases perform phosphoryl-transfer reactions in milliseconds; without enzymes, these reactions would take about 8,000 years under physiological conditions. Despite extensive studies, a comprehensive understanding of kinase energy landscapes, including both chemical and conformational steps, is lacking. Here we scrutinize the microscopic steps in the catalytic cycle of adenylate kinase, through a combination of NMR measurements during catalysis, pre-steady-state kinetics, molecular-dynamics simulations and crystallography of active complexes. We find that the Mg2+ cofactor activates two distinct molecular events: phosphoryl transfer (>105-fold) and lid opening (103-fold). In contrast, mutation of an essential active site arginine decelerates phosphoryl transfer 103-fold without substantially affecting lid opening. Our results highlight the importance of the entire energy landscape in catalysis and suggest that adenylate kinases have evolved to activate key processes simultaneously by precise placement of a single, charged and very abundant cofactor in a preorganized active site.
		+
		+	The energy landscape of adenylate kinase during catalysis.,Kerns SJ, Agafonov RV, Cho YJ, Pontiggia F, Otten R, Pachov DV, Kutter S, Phung LA, Murphy PN, Thai V, Alber T, Hagan MF, Kern D Nat Struct Mol Biol. 2015 Jan 12. doi: 10.1038/nsmb.2941. PMID:25580578<ref>PMID:25580578</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 4cf7" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Adenylate kinase 3D structures\|Adenylate kinase 3D structures]]		*[[Adenylate kinase 3D structures\|Adenylate kinase 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 17:42, 7 September 2022

OCA — Wed, 07 Sep 2022 17:42:41 GMT

←Older revision		Revision as of 17:42, 7 September 2022
Line 3:		Line 3:
	<StructureSection load='4cf7' size='340' side='right'caption='[[4cf7]], [[Resolution\|resolution]] 1.59Å' scene=''>		<StructureSection load='4cf7' size='340' side='right'caption='[[4cf7]], [[Resolution\|resolution]] 1.59Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4cf7]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"aquifex_aeolicus"_huber_and_stetter_2001 "aquifex~~ aeolicus~~" huber and stetter 2001~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4CF7 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4CF7 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4cf7]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4CF7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4CF7 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</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=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4cf7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4cf7 OCA], [https://pdbe.org/4cf7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4cf7 RCSB], [https://www.ebi.ac.uk/pdbsum/4cf7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4cf7 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=4cf7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4cf7 OCA], [~~http~~://pdbe.org/4cf7 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4cf7 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4cf7 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4cf7 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/KAD_AQUAE KAD_AQUAE]] Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. This small ubiquitous enzyme involved in the energy metabolism and nucleotide synthesis, is essential for maintenance and cell growth (By similarity).	+	[[https://www.uniprot.org/uniprot/KAD_AQUAE KAD_AQUAE]] Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. This small ubiquitous enzyme involved in the energy metabolism and nucleotide synthesis, is essential for maintenance and cell growth (By similarity).
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Kinases perform phosphoryl-transfer reactions in milliseconds; without enzymes, these reactions would take about 8,000 years under physiological conditions. Despite extensive studies, a comprehensive understanding of kinase energy landscapes, including both chemical and conformational steps, is lacking. Here we scrutinize the microscopic steps in the catalytic cycle of adenylate kinase, through a combination of NMR measurements during catalysis, pre-steady-state kinetics, molecular-dynamics simulations and crystallography of active complexes. We find that the Mg2+ cofactor activates two distinct molecular events: phosphoryl transfer (>105-fold) and lid opening (103-fold). In contrast, mutation of an essential active site arginine decelerates phosphoryl transfer 103-fold without substantially affecting lid opening. Our results highlight the importance of the entire energy landscape in catalysis and suggest that adenylate kinases have evolved to activate key processes simultaneously by precise placement of a single, charged and very abundant cofactor in a preorganized active site.	+
-		+
-	The energy landscape of adenylate kinase during catalysis.,Kerns SJ, Agafonov RV, Cho YJ, Pontiggia F, Otten R, Pachov DV, Kutter S, Phung LA, Murphy PN, Thai V, Alber T, Hagan MF, Kern D Nat Struct Mol Biol. 2015 Jan 12. doi: 10.1038/nsmb.2941. PMID:25580578<ref>PMID:25580578</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 4cf7" style="background-color:#fffaf0;"></div>~~	+

	==See Also==		==See Also==
	*[[Adenylate kinase 3D structures\|Adenylate kinase 3D structures]]		*[[Adenylate kinase 3D structures\|Adenylate kinase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Aquifex aeolicus ~~huber and stetter 2001]]~~	+	[[Category: Aquifex aeolicus]]
-	~~[[Category: Adenylate kinase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Agafonov~~, R V~~]]	+	[[Category: Agafonov RV]]
-	[[Category: Cho, Y J]]	+	[[Category: Cho Y-J]]
-	[[Category: Hagan~~, M F~~]]	+	[[Category: Hagan MF]]
-	[[Category: Kern, D]]	+	[[Category: Kern D]]
-	[[Category: Kerns~~, S J~~]]	+	[[Category: Kerns SJ]]
-	[[Category: Kutter, S]]	+	[[Category: Kutter S]]
-	[[Category: Murphy~~, P N~~]]	+	[[Category: Murphy PN]]
-	[[Category: Otten, R]]	+	[[Category: Otten R]]
-	[[Category: Pachov~~, D V~~]]	+	[[Category: Pachov DV]]
-	[[Category: Phung~~, L A~~]]	+	[[Category: Phung LA]]
-	[[Category: Pontiggia, F]]	+	[[Category: Pontiggia F]]
-	[[Category: Thai, V]]	+	[[Category: Thai V]]
-	~~[[Category: Nucleotide-binding]]~~	+
-	~~[[Category: Phosphoryl transfer]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 07:20, 23 May 2019

OCA — Thu, 23 May 2019 07:20:30 GMT

←Older revision		Revision as of 07:20, 23 May 2019
Line 1:		Line 1:

	==Crystal structure of adenylate kinase from Aquifex aeolicus with MgADP bound==		==Crystal structure of adenylate kinase from Aquifex aeolicus with MgADP bound==
-	<StructureSection load='4cf7' size='340' side='right' caption='[[4cf7]], [[Resolution\|resolution]] 1.59Å' scene=''>	+	<StructureSection load='4cf7' size='340' side='right'caption='[[4cf7]], [[Resolution\|resolution]] 1.59Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4cf7]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"aquifex_aeolicus"_huber_and_stetter_2001 "aquifex aeolicus" huber and stetter 2001]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4CF7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4CF7 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4cf7]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"aquifex_aeolicus"_huber_and_stetter_2001 "aquifex aeolicus" huber and stetter 2001]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4CF7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4CF7 FirstGlance]. <br>
Line 21:		Line 21:

	==See Also==		==See Also==
-	*[[Adenylate kinase\|Adenylate kinase]]	+	*[[Adenylate kinase 3D structures\|Adenylate kinase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 28:		Line 28:
	[[Category: Aquifex aeolicus huber and stetter 2001]]		[[Category: Aquifex aeolicus huber and stetter 2001]]
	[[Category: Adenylate kinase]]		[[Category: Adenylate kinase]]
		+	[[Category: Large Structures]]
	[[Category: Agafonov, R V]]		[[Category: Agafonov, R V]]
	[[Category: Cho, Y J]]		[[Category: Cho, Y J]]

OCA at 09:10, 30 January 2019

OCA — Wed, 30 Jan 2019 09:10:37 GMT

←Older revision		Revision as of 09:10, 30 January 2019
Line 3:		Line 3:
	<StructureSection load='4cf7' size='340' side='right' caption='[[4cf7]], [[Resolution\|resolution]] 1.59Å' scene=''>		<StructureSection load='4cf7' size='340' side='right' caption='[[4cf7]], [[Resolution\|resolution]] 1.59Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4cf7]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4CF7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4CF7 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4cf7]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"aquifex_aeolicus"_huber_and_stetter_2001 "aquifex aeolicus" huber and stetter 2001]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4CF7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4CF7 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</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=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</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>
Line 26:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Aquifex aeolicus huber and stetter 2001]]
	[[Category: Adenylate kinase]]		[[Category: Adenylate kinase]]
	[[Category: Agafonov, R V]]		[[Category: Agafonov, R V]]

OCA at 06:57, 29 March 2017

OCA — Wed, 29 Mar 2017 06:57:02 GMT

←Older revision		Revision as of 06:57, 29 March 2017
Line 19:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 4cf7" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4cf7" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Adenylate kinase\|Adenylate kinase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 02:41, 11 December 2016

OCA — Sun, 11 Dec 2016 02:41:11 GMT

←Older revision		Revision as of 02:41, 11 December 2016
Line 1:		Line 1:
		+
	==Crystal structure of adenylate kinase from Aquifex aeolicus with MgADP bound==		==Crystal structure of adenylate kinase from Aquifex aeolicus with MgADP bound==
	<StructureSection load='4cf7' size='340' side='right' caption='[[4cf7]], [[Resolution\|resolution]] 1.59Å' scene=''>		<StructureSection load='4cf7' size='340' side='right' caption='[[4cf7]], [[Resolution\|resolution]] 1.59Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</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=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</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=4cf7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4cf7 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4cf7 RCSB], [http://www.ebi.ac.uk/pdbsum/4cf7 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=4cf7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4cf7 OCA], [http://pdbe.org/4cf7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4cf7 RCSB], [http://www.ebi.ac.uk/pdbsum/4cf7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4cf7 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 17:		Line 18:
	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 4cf7" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 11:18, 21 January 2015

OCA — Wed, 21 Jan 2015 11:18:55 GMT

←Older revision		Revision as of 11:18, 21 January 2015
Line 9:		Line 9:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/KAD_AQUAE KAD_AQUAE]] Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. This small ubiquitous enzyme involved in the energy metabolism and nucleotide synthesis, is essential for maintenance and cell growth (By similarity).		[[http://www.uniprot.org/uniprot/KAD_AQUAE KAD_AQUAE]] Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. This small ubiquitous enzyme involved in the energy metabolism and nucleotide synthesis, is essential for maintenance and cell growth (By similarity).
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Kinases perform phosphoryl-transfer reactions in milliseconds; without enzymes, these reactions would take about 8,000 years under physiological conditions. Despite extensive studies, a comprehensive understanding of kinase energy landscapes, including both chemical and conformational steps, is lacking. Here we scrutinize the microscopic steps in the catalytic cycle of adenylate kinase, through a combination of NMR measurements during catalysis, pre-steady-state kinetics, molecular-dynamics simulations and crystallography of active complexes. We find that the Mg2+ cofactor activates two distinct molecular events: phosphoryl transfer (>105-fold) and lid opening (103-fold). In contrast, mutation of an essential active site arginine decelerates phosphoryl transfer 103-fold without substantially affecting lid opening. Our results highlight the importance of the entire energy landscape in catalysis and suggest that adenylate kinases have evolved to activate key processes simultaneously by precise placement of a single, charged and very abundant cofactor in a preorganized active site.
		+
		+	The energy landscape of adenylate kinase during catalysis.,Kerns SJ, Agafonov RV, Cho YJ, Pontiggia F, Otten R, Pachov DV, Kutter S, Phung LA, Murphy PN, Thai V, Alber T, Hagan MF, Kern D Nat Struct Mol Biol. 2015 Jan 12. doi: 10.1038/nsmb.2941. PMID:25580578<ref>PMID:25580578</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 11:58, 25 December 2014

OCA — Thu, 25 Dec 2014 11:58:53 GMT

←Older revision		Revision as of 11:58, 25 December 2014
Line 7:		Line 7:
	<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=4cf7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4cf7 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4cf7 RCSB], [http://www.ebi.ac.uk/pdbsum/4cf7 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=4cf7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4cf7 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4cf7 RCSB], [http://www.ebi.ac.uk/pdbsum/4cf7 PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/KAD_AQUAE KAD_AQUAE]] Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. This small ubiquitous enzyme involved in the energy metabolism and nucleotide synthesis, is essential for maintenance and cell growth (By similarity).
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 09:38, 3 December 2014

OCA — Wed, 03 Dec 2014 09:38:20 GMT

←Older revision		Revision as of 09:38, 3 December 2014
Line 1:		Line 1:
-	'''~~Unreleased structure~~'''	+	==Crystal structure of adenylate kinase from Aquifex aeolicus with MgADP bound==
-		+	<StructureSection load='4cf7' size='340' side='right' caption='[[4cf7]], [[Resolution\|resolution]] 1.59Å' scene=''>
-	~~The entry~~ 4cf7 is ~~ON HOLD until Paper Publication~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4cf7]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4CF7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4CF7 FirstGlance]. <br>
-	~~Authors~~: ~~Kerns, S~~.J., ~~Agafonov~~, R.V., ~~Cho, Y~~.-J., ~~Pontiggia~~, F., ~~Otten~~, R., ~~Pachov~~, D~~.V.~~, Kutter, S~~., Phung, L.A.,~~ Murphy, P.N., ~~Thai~~, V., ~~Hagan~~, M.F., ~~Kern, D.~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</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>
-	~~Description~~: ~~Crystal structure of adenylate kinase from Aquifex aeolicus with MgADP bound~~	+	<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=4cf7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4cf7 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4cf7 RCSB], [http://www.ebi.ac.uk/pdbsum/4cf7 PDBsum]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Adenylate kinase]]
		+	[[Category: Agafonov, R V]]
		+	[[Category: Cho, Y J]]
		+	[[Category: Hagan, M F]]
		+	[[Category: Kern, D]]
		+	[[Category: Kerns, S J]]
		+	[[Category: Kutter, S]]
		+	[[Category: Murphy, P N]]
		+	[[Category: Otten, R]]
		+	[[Category: Pachov, D V]]
		+	[[Category: Phung, L A]]
		+	[[Category: Pontiggia, F]]
		+	[[Category: Thai, V]]
		+	[[Category: Nucleotide-binding]]
		+	[[Category: Phosphoryl transfer]]
		+	[[Category: Transferase]]

OCA at 06:31, 4 December 2013

OCA — Wed, 04 Dec 2013 06:31:14 GMT

←Older revision		Revision as of 06:31, 4 December 2013
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4cf7 is ON HOLD	+	The entry 4cf7 is ON HOLD until Paper Publication

	Authors: Kerns, S.J., Agafonov, R.V., Cho, Y.-J., Pontiggia, F., Otten, R., Pachov, D.V., Kutter, S., Phung, L.A., Murphy, P.N., Thai, V., Hagan, M.F., Kern, D.		Authors: Kerns, S.J., Agafonov, R.V., Cho, Y.-J., Pontiggia, F., Otten, R., Pachov, D.V., Kutter, S., Phung, L.A., Murphy, P.N., Thai, V., Hagan, M.F., Kern, D.

-	Description: Crystal structure of ~~Aquifex~~ adenylate kinase with MgADP bound	+	Description: Crystal structure of adenylate kinase from Aquifex aeolicus with MgADP bound