1m7h: Difference between revisions

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-[[Image:1m7h.jpg|left|200px]]<br /><applet load="1m7h" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1m7h, resolution 2.00&Aring;" />
-'''Crystal Structure of APS kinase from Penicillium Chrysogenum: Structure with APS soaked out of one dimer'''<br />
-==Overview==
+==Crystal Structure of APS kinase from Penicillium Chrysogenum: Structure with APS soaked out of one dimer==
-Adenosine 5'-phosphosulfate (APS) kinase catalyzes the second reaction in, the two-step, ATP-dependent conversion of inorganic sulfate to, 3'-phosphoadenosine 5'-phosphosulfate (PAPS). PAPS serves as the sulfuryl, donor for the biosynthesis of all sulfate esters and also as a precursor, of reduced sulfur biomolecules in many organisms. Previously, we, determined the crystal structure of ligand-free APS kinase from the, filamentous fungus, Penicillium chrysogenum [MacRae et al. (2000), Biochemistry 39, 1613-1621]. That structure contained a, protease-susceptible disordered region ("mobile lid"; residues 145-170)., Addition of MgADP and APS, which together promote the formation of a, nonproductive "dead-end" ternary complex, protected the lid from trypsin., This report presents the 1.43 A resolution crystal structure of APS kinase, with both ADP and APS bound at the active site and the 2.0 A resolution, structure of the enzyme with ADP alone bound. The mobile lid is ordered in, both complexes and is shown to provide part of the binding site for APS., That site is formed primarily by the highly conserved Arg 66, Arg 80, and, Phe 75 from the protein core and Phe 165 from the mobile lid. The two Phe, residues straddle the adenine ring of bound APS. Arg 148, a completely, conserved residue, is the only residue in the mobile lid that interacts, directly with bound ADP. Ser 34, located in the apex of the P-loop, hydrogen-bonds to the 3'-OH of APS, the phosphoryl transfer target. The, structure of the binary E.ADP complex revealed further changes in the, active site and N-terminal helix that occur upon the binding/release of, (P)APS.
+<StructureSection load='1m7h' size='340' side='right'caption='[[1m7h]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+== Structural highlights ==
-==About this Structure==
+<table><tr><td colspan='2'>[[1m7h]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Penicillium_chrysogenum Penicillium chrysogenum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M7H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1M7H FirstGlance]. <br>
-M7H is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Penicillium_chrysogenum Penicillium chrysogenum] with SO4, ADP and ADX as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Adenylyl-sulfate_kinase Adenylyl-sulfate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.25 2.7.1.25] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1M7H OCA].
+</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&#8491;</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=ADX:ADENOSINE-5-PHOSPHOSULFATE'>ADX</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-==Reference==
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1m7h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m7h OCA], [https://pdbe.org/1m7h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1m7h RCSB], [https://www.ebi.ac.uk/pdbsum/1m7h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1m7h ProSAT]</span></td></tr>
-Ligand-induced structural changes in adenosine 5'-phosphosulfate kinase from Penicillium chrysogenum., Lansdon EB, Segel IH, Fisher AJ, Biochemistry. 2002 Nov 19;41(46):13672-80. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12427029 12427029]
+</table>
-[[Category: Adenylyl-sulfate kinase]]
+== Function ==
+[https://www.uniprot.org/uniprot/KAPS_PENCH KAPS_PENCH] Catalyzes the synthesis of activated sulfate.
+== 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/m7/1m7h_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=1m7h ConSurf].
+<div style="clear:both"></div>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Penicillium chrysogenum]]
-[[Category: Single protein]]
+[[Category: Fisher AJ]]
-[[Category: Fisher, A.J.]]
+[[Category: Lansdon EB]]
-[[Category: Lansdon, E.B.]]
+[[Category: Sege IH]]
-[[Category: Sege, I.H.]]
-[[Category: ADP]]
-[[Category: ADX]]
-[[Category: SO4]]
-[[Category: adenylylsulfate kinase]]
-[[Category: aps kinase]]
-[[Category: nucleotide 2 kinase]]
-[[Category: sulfate metabolism]]
-[[Category: transferase]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 21:12:19 2007''