1dvr: Difference between revisions

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-[[Image:1dvr.jpg|left|200px]]<br /><applet load="1dvr" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1dvr, resolution 2.36&Aring;" />
-'''STRUCTURE OF A MUTANT ADENYLATE KINASE LIGATED WITH AN ATP-ANALOGUE SHOWING DOMAIN CLOSURE OVER ATP'''<br />
-==Overview==
+==STRUCTURE OF A MUTANT ADENYLATE KINASE LIGATED WITH AN ATP-ANALOGUE SHOWING DOMAIN CLOSURE OVER ATP==
-Structural studies on unligated and ligated adenylate kinases have shown, that two domains, LID and NMPbind, close over the bound substrates, ATP, and AMP, respectively. These motions can be, but need not be independent, from each other. Up to now, the known structures display only the states, "both domains open", "both closed" and "NMP bind closed". In spite of, numerous cocrystallization attempts with ATP, a crystalline state "LID, closed" has not yet been produced. These experiences suggested that LID, closure depends on a bound AMP molecule, in contrast to enzyme kinetic, studies indicating a random-bi-bi mechanism. Using an inactive mutant of, yeast adenylate kinase together with the ATP analogue AMPPCF2P, however, we have now crystallized an adenylate kinase in the LID closed state. The, structure was established at 2.36 A resolution; it indicates that the, domain motions occur largely independent from each other in agreement with, the kinetic studies. As a side-result, we report the protein environment, of the fluorine atoms of the bound ATP analogue.
+<StructureSection load='1dvr' size='340' side='right'caption='[[1dvr]], [[Resolution|resolution]] 2.36&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1dvr]] is a 2 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=1DVR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DVR FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.36&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATF:PHOSPHODIFLUOROMETHYLPHOSPHONIC+ACID-ADENYLATE+ESTER'>ATF</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=1dvr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dvr OCA], [https://pdbe.org/1dvr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dvr RCSB], [https://www.ebi.ac.uk/pdbsum/1dvr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dvr ProSAT]</span></td></tr>
+</table>
+== Function ==
+[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>
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dv/1dvr_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</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=1dvr ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-DVR 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 ATF as [http://en.wikipedia.org/wiki/ligand ligand]. 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=1DVR OCA].
+*[[Adenylate kinase 3D structures|Adenylate kinase 3D structures]]
+== References ==
-==Reference==
+<references/>
-Structure of a mutant adenylate kinase ligated with an ATP-analogue showing domain closure over ATP., Schlauderer GJ, Proba K, Schulz GE, J Mol Biol. 1996 Feb 23;256(2):223-7. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8594191 8594191]
+__TOC__
-[[Category: Adenylate kinase]]
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Saccharomyces cerevisiae]]
-[[Category: Single protein]]
+[[Category: Schlauderer GJ]]
-[[Category: Schlauderer, G.J.]]
+[[Category: Schulz GE]]
-[[Category: Schulz, G.E.]]
-[[Category: ATF]]
-[[Category: myokinase]]
-[[Category: nucleoside monophosphate kinase]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 13:37:39 2007''