2dik: Difference between revisions

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-[[Image:2dik.jpg|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_2dik", creates the "Structure Box" on the page.
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-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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-{{STRUCTURE_2dik|  PDB=2dik  |  SCENE=  }}
-'''R337A MUTANT OF PYRUVATE PHOSPHATE DIKINASE'''
+==R337A MUTANT OF PYRUVATE PHOSPHATE DIKINASE==
+<StructureSection load='2dik' size='340' side='right'caption='[[2dik]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2dik]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Clostridium_symbiosum Clostridium symbiosum]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1buk 1buk]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DIK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DIK 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]] 2.5&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=2dik FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dik OCA], [https://pdbe.org/2dik PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dik RCSB], [https://www.ebi.ac.uk/pdbsum/2dik PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dik ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/PPDK_CLOSY PPDK_CLOSY] Catalyzes the reversible phosphorylation of pyruvate and phosphate. In E.histolytica and C.symbiosus, PPDK functions in the direction of ATP synthesis.
+== 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/di/2dik_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=2dik ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Pyruvate phosphate dikinase (PPDK) catalyzes the interconversion of ATP, Pi, and pyruvate with AMP, PPi, and PEP in three partial reactions: (1) E + ATP --&gt; E.ATP --&gt; E-PP.AMP, (2) E-PP.AMP + Pi --&gt; E-PP.AMP.Pi --&gt; E-P.AMP.PPi, and (3) E-P + pyruvate --&gt; E-P.pyruvate --&gt; E.PEP. The Clostridium symbiosum PPDK structure consists of N-terminal, central, and C-terminal domains. The N-terminal and central domains catalyze partial reactions 1 and 2 whereas the C-terminal and central domains catalyze partial reaction 3. The goal of the present work is to determine where on the N-terminal domain catalysis of partial reactions 1 and 2 occurs and, in particular, where the Pi binding site is located. Computer modeling studies implicated Arg337 as a key residue for Pi binding. This role was tested by site-directed mutagenesis. The R337A PPDK was shown to be impaired in catalysis of the forward (kcat 300-fold lower) and reverse (kcat 30-fold lower) full reactions. Time courses for the single turnover reactions were measured to show that catalysis of partial reaction 1 is 5-fold slower in the mutant, catalysis of the second partial reaction is 140-fold slower in the mutant, and catalysis of the third partial reaction is unaffected. With the exception of the mutation site, the crystal structure of the R337A PPDK closely resembles the structure of the wild-type protein. Thus, the altered kinetic properties observed for this mutant are attributed solely to the elimination of the interaction between substrate and the guanidinium group of the Arg337 side chain. On the basis of these findings we propose that the Pi binding site is located within the crevice of the PPDK N-terminal domain, at a site that is flanked by the ATP beta-P and the Mg2+ cofactor.
-==Overview==
+Location of the phosphate binding site within Clostridium symbiosum pyruvate phosphate dikinase.,McGuire M, Huang K, Kapadia G, Herzberg O, Dunaway-Mariano D Biochemistry. 1998 Sep 29;37(39):13463-74. PMID:9753432<ref>PMID:9753432</ref>
-Pyruvate phosphate dikinase (PPDK) catalyzes the interconversion of ATP, Pi, and pyruvate with AMP, PPi, and PEP in three partial reactions: (1) E + ATP --&gt; E.ATP --&gt; E-PP.AMP, (2) E-PP.AMP + Pi --&gt; E-PP.AMP.Pi --&gt; E-P.AMP.PPi, and (3) E-P + pyruvate --&gt; E-P.pyruvate --&gt; E.PEP. The Clostridium symbiosum PPDK structure consists of N-terminal, central, and C-terminal domains. The N-terminal and central domains catalyze partial reactions 1 and 2 whereas the C-terminal and central domains catalyze partial reaction 3. The goal of the present work is to determine where on the N-terminal domain catalysis of partial reactions 1 and 2 occurs and, in particular, where the Pi binding site is located. Computer modeling studies implicated Arg337 as a key residue for Pi binding. This role was tested by site-directed mutagenesis. The R337A PPDK was shown to be impaired in catalysis of the forward (kcat 300-fold lower) and reverse (kcat 30-fold lower) full reactions. Time courses for the single turnover reactions were measured to show that catalysis of partial reaction 1 is 5-fold slower in the mutant, catalysis of the second partial reaction is 140-fold slower in the mutant, and catalysis of the third partial reaction is unaffected. With the exception of the mutation site, the crystal structure of the R337A PPDK closely resembles the structure of the wild-type protein. Thus, the altered kinetic properties observed for this mutant are attributed solely to the elimination of the interaction between substrate and the guanidinium group of the Arg337 side chain. On the basis of these findings we propose that the Pi binding site is located within the crevice of the PPDK N-terminal domain, at a site that is flanked by the ATP beta-P and the Mg2+ cofactor.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-DIK is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Clostridium_symbiosum Clostridium symbiosum]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1buk 1buk]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DIK OCA].
+</div>
+<div class="pdbe-citations 2dik" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-Location of the phosphate binding site within Clostridium symbiosum pyruvate phosphate dikinase., McGuire M, Huang K, Kapadia G, Herzberg O, Dunaway-Mariano D, Biochemistry. 1998 Sep 29;37(39):13463-74. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9753432 9753432]
+*[[Pyruvate phosphate dikinase|Pyruvate phosphate dikinase]]
-[[Category: Clostridium symbiosum]]
+== References ==
-[[Category: Pyruvate, phosphate dikinase]]
+<references/>
-[[Category: Single protein]]
+__TOC__
-[[Category: Herzberg, O.]]
+</StructureSection>
-[[Category: Huang, K.]]
+[[Category: Large Structures]]
-[[Category: Kinase]]
+[[Category: Herzberg O]]
-[[Category: Phosphotransferase]]
+[[Category: Huang K]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 00:29:23 2008''