2fm4: Difference between revisions

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-[[Image:2fm4.png|left|200px]]
-{{STRUCTURE_2fm4|  PDB=2fm4  |  SCENE=  }}
+==NMR structure of the phosphoryl carrier domain of pyruvate phosphate dikinase==
+<StructureSection load='2fm4' size='340' side='right'caption='[[2fm4]]' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2fm4]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Clostridium_symbiosum Clostridium symbiosum]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FM4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2FM4 FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</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=2fm4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fm4 OCA], [https://pdbe.org/2fm4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2fm4 RCSB], [https://www.ebi.ac.uk/pdbsum/2fm4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2fm4 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/fm/2fm4_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=2fm4 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Pyruvate phosphate dikinase (PPDK) is a multidomain protein that catalyzes the interconversion of ATP, pyruvate, and phosphate with AMP, phosphoenolpyruvate (PEP), and pyrophosphate using its central domain to transport phosphoryl groups between two distant active sites. In this study, the mechanism by which the central domain moves between the two catalytic sites located on the N-terminal and C-terminal domains was probed by expressing this domain as an independent protein and measuring its structure, stability, and ability to catalyze the ATP/phosphate partial reaction in conjunction with the engineered N-terminal domain protein (residues 1-340 of the native PPDK). The encoding gene was engineered to express the central domain as residues 381-512 of the native PPDK. The central domain was purified and shown to be soluble, monomeric (13,438 Da), and stable (deltaG = 4.3 kcal/mol for unfolding in buffer at pH 7.0, 25 degrees C) and to possess native structure, as determined by multidimensional heteronuclear NMR analysis. The main chain structure of the central domain in solution aligns closely with that of the X-ray structure of native PPDK (the root-mean-square deviation is 2.2 A). Single turnover reactions of [14C]ATP and phosphate, carried out in the presence of equal concentrations of central domain and the N-terminal domain protein, did not produce the expected products, in contrast to efficient product formation observed for the N-terminal central domain construct (residues 1-553 of the native PPDK). These results are interpreted as evidence that the central domain, although solvent-compatible, must be tethered by the flexible linkers to the N-terminal domain for the productive domain-domain docking required for efficient catalysis.
-===NMR structure of the phosphoryl carrier domain of pyruvate phosphate dikinase===
+Examination of the structure, stability, and catalytic potential in the engineered phosphoryl carrier domain of pyruvate phosphate dikinase.,Lin Y, Lusin JD, Ye D, Dunaway-Mariano D, Ames JB Biochemistry. 2006 Feb 14;45(6):1702-11. PMID:16460017<ref>PMID:16460017</ref>
-{{ABSTRACT_PUBMED_16460017}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 2fm4" style="background-color:#fffaf0;"></div>
-[[2fm4]] is a 1 chain structure of [[Pyruvate phosphate dikinase]] with sequence from [http://en.wikipedia.org/wiki/Clostridium_symbiosum Clostridium symbiosum]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FM4 OCA].
 ==See Also==
 *[[Pyruvate phosphate dikinase|Pyruvate phosphate dikinase]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:016460017</ref><references group="xtra"/>
+__TOC__
-[[Category: Clostridium symbiosum]]
+</StructureSection>
-[[Category: Pyruvate, phosphate dikinase]]
+[[Category: Large Structures]]
-[[Category: Ames, J B.]]
+[[Category: Ames JB]]
-[[Category: Phosphohistidine carrier domain]]
-[[Category: Transferase]]