2aky

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(New page: 200px<br /><applet load="2aky" size="450" color="white" frame="true" align="right" spinBox="true" caption="2aky, resolution 1.96&Aring;" /> '''HIGH-RESOLUTION STRU...)
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[[Image:2aky.jpg|left|200px]]<br /><applet load="2aky" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="2aky, resolution 1.96&Aring;" />
 
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'''HIGH-RESOLUTION STRUCTURES OF ADENYLATE KINASE FROM YEAST LIGATED WITH INHIBITOR AP5A, SHOWING THE PATHWAY OF PHOSPHORYL TRANSFER'''<br />
 
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==Overview==
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==HIGH-RESOLUTION STRUCTURES OF ADENYLATE KINASE FROM YEAST LIGATED WITH INHIBITOR AP5A, SHOWING THE PATHWAY OF PHOSPHORYL TRANSFER==
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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.
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<StructureSection load='2aky' size='340' side='right'caption='[[2aky]], [[Resolution|resolution]] 1.96&Aring;' scene=''>
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== Structural highlights ==
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<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>
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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]] 1.96&#8491;</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=AP5:BIS(ADENOSINE)-5-PENTAPHOSPHATE'>AP5</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=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>
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</table>
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== Function ==
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[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>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ak/2aky_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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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].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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2AKY is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae] with MG and AP5 as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2AKY OCA].
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*[[Adenylate kinase 3D structures|Adenylate kinase 3D structures]]
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== References ==
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==Reference==
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<references/>
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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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=7670369 7670369]
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__TOC__
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[[Category: Adenylate kinase]]
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</StructureSection>
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[[Category: Large Structures]]
[[Category: Saccharomyces cerevisiae]]
[[Category: Saccharomyces cerevisiae]]
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[[Category: Single protein]]
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[[Category: Abele U]]
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[[Category: Abele, U.]]
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[[Category: Schulz GE]]
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[[Category: Schulz, G.E.]]
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[[Category: AP5]]
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[[Category: MG]]
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[[Category: atp:amp phosphotransferase]]
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[[Category: myokinase]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 08:11:43 2007''
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Current revision

HIGH-RESOLUTION STRUCTURES OF ADENYLATE KINASE FROM YEAST LIGATED WITH INHIBITOR AP5A, SHOWING THE PATHWAY OF PHOSPHORYL TRANSFER

PDB ID 2aky

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