1q97: Difference between revisions

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-[[Image:1q97.gif|left|200px]]
-<!--
+==The structure of the Saccharomyces cerevisiae SR protein kinase, Sky1p, with bound ATP==
-The line below this paragraph, containing "STRUCTURE_1q97", creates the "Structure Box" on the page.
+<StructureSection load='1q97' size='340' side='right'caption='[[1q97]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[1q97]] 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=1Q97 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Q97 FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADN:ADENOSINE'>ADN</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-{{STRUCTURE_1q97|  PDB=1q97  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1q97 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q97 OCA], [https://pdbe.org/1q97 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1q97 RCSB], [https://www.ebi.ac.uk/pdbsum/1q97 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1q97 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/SKY1_YEAST SKY1_YEAST] Constitutively active kinase, specifically and sequentially phosphorylates serine/arginine (SR)-type shuttling mRNA binding proteins in their RS dipeptide repeats.<ref>PMID:11175909</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/q9/1q97_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=1q97 ConSurf].
+<div style="clear:both"></div>
-'''The structure of the Saccharomyces cerevisiae SR protein kinase, Sky1p, with bound ATP'''
+==See Also==
+*[[Serine/threonine protein kinase 3D structures|Serine/threonine protein kinase 3D structures]]
+== References ==
-==Overview==
+<references/>
-Conformational changes are thought to play a key role in the function of active protein kinases, although little is known about how these changes relate to the mechanism of phosphorylation. Here we present four high-resolution structures of a single crystal form of Sky1p, a constitutively active serine kinase implicated in yeast RNA processing, each in a different state of nucleotide binding. By comparing the apoenzyme structure to the ADP- and ATP-bound Sky1p structures, we have revealed conformational changes caused by ATP binding or conversion from nucleotide reactant to product. Rotation of the small lobe of the kinase closes the cleft upon binding, allowing the nucleotide to interact with residues from both lobes of the kinase, although some interactions thought to be important for phosphotransfer are missing in the ATP-containing structure. In the apoenzyme, a kinase-conserved phosphate-anchoring loop is in a twisted conformation that is incompatible with ADP and ATP binding, providing a potential mechanism for facilitating ADP release in Sky1p. The nonhydrolyzable ATP analogue AMP-PNP binds in a unique mode that fails to induce lobe closure. This observation, along with comparisons between the two independent molecules in the asymmetric unit of each structure, has provided new molecular details about how the nucleotide binds and induces closure. Finally, we have used mutational analysis to establish the importance of a glycine within the linker that connects the two lobes of Sky1p.
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-Q97 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q97 OCA].
-==Reference==
-Nucleotide-induced conformational changes in the Saccharomyces cerevisiae SR protein kinase, Sky1p, revealed by X-ray crystallography., Nolen B, Ngo J, Chakrabarti S, Vu D, Adams JA, Ghosh G, Biochemistry. 2003 Aug 19;42(32):9575-85. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12911299 12911299]
 [[Category: Saccharomyces cerevisiae]]
-[[Category: Single protein]]
+[[Category: Adams JA]]
-[[Category: Adams, J A.]]
+[[Category: Chakrabarti S]]
-[[Category: Chakrabarti, S.]]
+[[Category: Ghosh G]]
-[[Category: Ghosh, G.]]
+[[Category: Ngo J]]
-[[Category: Ngo, J.]]
+[[Category: Nolen B]]
-[[Category: Nolen, B.]]
+[[Category: Vu D]]
-[[Category: Vu, D.]]
-[[Category: Protein kinase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 06:01:33 2008''