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3sr0

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Current revision (09:54, 1 March 2024) (edit) (undo)
 
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<StructureSection load='3sr0' size='340' side='right'caption='[[3sr0]], [[Resolution|resolution]] 1.56&Aring;' scene=''>
<StructureSection load='3sr0' size='340' side='right'caption='[[3sr0]], [[Resolution|resolution]] 1.56&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3sr0]] is a 2 chain structure with sequence from [https://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=3SR0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3SR0 FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3sr0]] 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=3SR0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3SR0 FirstGlance]. <br>
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</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=ALF:TETRAFLUOROALUMINATE+ION'>ALF</scene>, <scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.565&#8491;</td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">adk, Aquifex, aq_078 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=63363 "Aquifex aeolicus" Huber and Stetter 2001])</td></tr>
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<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=ALF:TETRAFLUOROALUMINATE+ION'>ALF</scene>, <scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
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<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>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3sr0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3sr0 OCA], [https://pdbe.org/3sr0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3sr0 RCSB], [https://www.ebi.ac.uk/pdbsum/3sr0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3sr0 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=3sr0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3sr0 OCA], [https://pdbe.org/3sr0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3sr0 RCSB], [https://www.ebi.ac.uk/pdbsum/3sr0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3sr0 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
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[[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).
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[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).
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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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>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 3sr0" style="background-color:#fffaf0;"></div>
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==See Also==
==See Also==
*[[Adenylate kinase 3D structures|Adenylate kinase 3D structures]]
*[[Adenylate kinase 3D structures|Adenylate kinase 3D structures]]
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== References ==
 
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<references/>
 
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Aquifex aeolicus huber and stetter 2001]]
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[[Category: Aquifex aeolicus]]
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[[Category: Adenylate kinase]]
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[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Cho, Y J]]
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[[Category: Cho Y-J]]
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[[Category: Kern, D]]
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[[Category: Kern D]]
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[[Category: Alf4]]
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[[Category: Nucleotide-binding]]
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[[Category: Phosphoryl transfer]]
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[[Category: Phosphoryl transfer analogue]]
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[[Category: Phosphoryl transfer of nucleotide]]
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[[Category: Transferase]]
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Current revision

Crystal Structure of the Phosphoryl Transfer Transition State Mimic in the Adenylate Kinase: ADP/AlF4/AMP in the active site

PDB ID 3sr0

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