4jky: Difference between revisions

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<StructureSection load='4jky' size='340' side='right'caption='[[4jky]], [[Resolution|resolution]] 2.37&Aring;' scene=''>
<StructureSection load='4jky' size='340' side='right'caption='[[4jky]], [[Resolution|resolution]] 2.37&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[4jky]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Aquae Aquae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JKY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4JKY FirstGlance]. <br>
<table><tr><td colspan='2'>[[4jky]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Aquifex_aeolicus_VF5 Aquifex aeolicus VF5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JKY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4JKY 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=CO:COBALT+(II)+ION'>CO</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]] 2.373&#8491;</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">adk, aq_078 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224324 AQUAE])</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=CO:COBALT+(II)+ION'>CO</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=4jky FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jky OCA], [https://pdbe.org/4jky PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4jky RCSB], [https://www.ebi.ac.uk/pdbsum/4jky PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4jky 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=4jky FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jky OCA], [http://pdbe.org/4jky PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4jky RCSB], [http://www.ebi.ac.uk/pdbsum/4jky PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4jky 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 (&gt;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&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 4jky" 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: Adenylate kinase]]
[[Category: Aquifex aeolicus VF5]]
[[Category: Aquae]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Cho, Y J]]
[[Category: Cho Y-J]]
[[Category: Kern, D]]
[[Category: Kern D]]
[[Category: Cobalt binding]]
[[Category: Phosphoryl transfer reaction]]
[[Category: Transferase]]

Latest revision as of 15:04, 1 March 2024

Cobalt between two ADP's in the active site of adenylate kinaseCobalt between two ADP's in the active site of adenylate kinase

Structural highlights

4jky is a 2 chain structure with sequence from Aquifex aeolicus VF5. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.373Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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).

See Also

4jky, resolution 2.37Å

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OCA
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