7apu - Revision history

OCA at 12:13, 1 February 2024

OCA — Thu, 01 Feb 2024 12:13:56 GMT

←Older revision		Revision as of 12:13, 1 February 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7apu]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7APU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7APU FirstGlance]. <br>		<table><tr><td colspan='2'>[[7apu]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7APU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7APU 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=NA:SODIUM+ION'>NA</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]] 1.36Å</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=NA:SODIUM+ION'>NA</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=7apu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7apu OCA], [https://pdbe.org/7apu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7apu RCSB], [https://www.ebi.ac.uk/pdbsum/7apu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7apu 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=7apu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7apu OCA], [https://pdbe.org/7apu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7apu RCSB], [https://www.ebi.ac.uk/pdbsum/7apu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7apu ProSAT]</span></td></tr>
	</table>		</table>

OCA at 10:05, 21 December 2022

OCA — Wed, 21 Dec 2022 10:05:47 GMT

←Older revision		Revision as of 10:05, 21 December 2022
Line 1:		Line 1:

	==Structure of Adenylate kinase from Escherichia coli in complex with two ADP molecules refined at 1.36 A resolution.==		==Structure of Adenylate kinase from Escherichia coli in complex with two ADP molecules refined at 1.36 A resolution.==
-	<StructureSection load='7apu' size='340' side='right'caption='[[7apu]]' scene=''>	+	<StructureSection load='7apu' size='340' side='right'caption='[[7apu]], [[Resolution\|resolution]] 1.36Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7APU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7APU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7apu]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7APU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7APU FirstGlance]. <br>
-	</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=7apu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7apu OCA], [https://pdbe.org/7apu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7apu RCSB], [https://www.ebi.ac.uk/pdbsum/7apu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7apu ProSAT]</span></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=NA:SODIUM+ION'>NA</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=7apu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7apu OCA], [https://pdbe.org/7apu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7apu RCSB], [https://www.ebi.ac.uk/pdbsum/7apu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7apu ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/KAD_ECOLI KAD_ECOLI] 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.[HAMAP-Rule:MF_00235]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Enzymes employ a wide range of protein motions to achieve efficient catalysis of chemical reactions. While the role of collective protein motions in substrate binding, product release, and regulation of enzymatic activity is generally understood, their roles in catalytic steps per se remain uncertain. Here, molecular dynamics simulations, enzyme kinetics, X-ray crystallography, and nuclear magnetic resonance spectroscopy are combined to elucidate the catalytic mechanism of adenylate kinase and to delineate the roles of catalytic residues in catalysis and the conformational change in the enzyme. This study reveals that the motions in the active site, which occur on a time scale of picoseconds to nanoseconds, link the catalytic reaction to the slow conformational dynamics of the enzyme by modulating the free energy landscapes of subdomain motions. In particular, substantial conformational rearrangement occurs in the active site following the catalytic reaction. This rearrangement not only affects the reaction barrier but also promotes a more open conformation of the enzyme after the reaction, which then results in an accelerated opening of the enzyme compared to that of the reactant state. The results illustrate a linkage between enzymatic catalysis and collective protein motions, whereby the disparate time scales between the two processes are bridged by a cascade of intermediate-scale motion of catalytic residues modulating the free energy landscapes of the catalytic and conformational change processes.
		+
		+	Dynamic Connection between Enzymatic Catalysis and Collective Protein Motions.,Ojeda-May P, Mushtaq AU, Rogne P, Verma A, Ovchinnikov V, Grundstrom C, Dulko-Smith B, Sauer UH, Wolf-Watz M, Nam K Biochemistry. 2021 Jul 20;60(28):2246-2258. doi: 10.1021/acs.biochem.1c00221. , Epub 2021 Jul 12. PMID:34250801<ref>PMID:34250801</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7apu" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Adenylate kinase 3D structures\|Adenylate kinase 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Escherichia coli K-12]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Grundstom C]]		[[Category: Grundstom C]]

OCA at 06:14, 2 March 2022

OCA — Wed, 02 Mar 2022 06:14:28 GMT

←Older revision		Revision as of 06:14, 2 March 2022
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-	'''Unreleased structure'''

-	~~The entry 7apu is ON HOLD~~	+	==Structure of Adenylate kinase from Escherichia coli in complex with two ADP molecules refined at 1.36 A resolution.==
-		+	<StructureSection load='7apu' size='340' side='right'caption='[[7apu]]' scene=''>
-	~~Authors: Grundstom, C., Wolf-Watz, M., Nam, K., Sauer, U.H.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7APU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7APU FirstGlance]. <br>
-	~~Description:~~ Structure of Adenylate kinase from Escherichia coli in complex with two ADP molecules refined at 1.36 A resolution.	+	</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=7apu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7apu OCA], [https://pdbe.org/7apu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7apu RCSB], [https://www.ebi.ac.uk/pdbsum/7apu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7apu ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: Grundstom, C]]	+	__TOC__
-	[[Category: Nam, K]]	+	</StructureSection>
-	[[Category: ~~Wolf-Watz, M~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Sauer, U.H~~]]	+	[[Category: Grundstom C]]
		+	[[Category: Nam K]]
		+	[[Category: Sauer UH]]
		+	[[Category: Wolf-Watz M]]

OCA: Protected "7apu" [edit=sysop:move=sysop]

OCA — Wed, 28 Oct 2020 18:56:55 GMT

Protected "7apu" [edit=sysop:move=sysop]

←Older revision

Revision as of 18:56, 28 October 2020

OCA: New page: '''Unreleased structure''' The entry 7apu is ON HOLD Authors: Grundstom, C., Wolf-Watz, M., Nam, K., Sauer, U.H. Description: Structure of Adenylate kinase from Escherichia coli in com...

OCA — Wed, 28 Oct 2020 18:56:53 GMT

New page: '''Unreleased structure''' The entry 7apu is ON HOLD Authors: Grundstom, C., Wolf-Watz, M., Nam, K., Sauer, U.H. Description: Structure of Adenylate kinase from Escherichia coli in com...

New page

'''Unreleased structure'''

The entry 7apu is ON HOLD

Authors: Grundstom, C., Wolf-Watz, M., Nam, K., Sauer, U.H.

Description: Structure of Adenylate kinase from Escherichia coli in complex with two ADP molecules refined at 1.36 A resolution.
[[Category: Unreleased Structures]]
[[Category: Grundstom, C]]
[[Category: Nam, K]]
[[Category: Wolf-Watz, M]]
[[Category: Sauer, U.H]]