1vjc: Difference between revisions

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-{{Seed}}
-[[Image:1vjc.png|left|200px]]
-<!--
+==Structure of pig muscle PGK complexed with MgATP==
-The line below this paragraph, containing "STRUCTURE_1vjc", creates the "Structure Box" on the page.
+<StructureSection load='1vjc' size='340' side='right'caption='[[1vjc]], [[Resolution|resolution]] 2.10&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'>[[1vjc]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Sus_scrofa Sus scrofa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VJC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VJC 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]] 2.1&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-{{STRUCTURE_1vjc|  PDB=1vjc  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1vjc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vjc OCA], [https://pdbe.org/1vjc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vjc RCSB], [https://www.ebi.ac.uk/pdbsum/1vjc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vjc ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/PGK1_PIG PGK1_PIG]
+== 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/vj/1vjc_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=1vjc ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The complexes of pig muscle 3-phosphoglycerate kinase with the substrate MgATP and with the nonsubstrate Mg(2+)-free ATP have been characterized by binding, kinetic, and crystallographic studies. Comparative experiments with ADP and MgADP have also been carried out. In contrast to the less specific and largely ionic binding of Mg(2+)-free ATP and ADP, specific occupation of the adenosine binding pocket by MgATP and MgADP has been revealed by displacement experiments with adenosine and anions, as well as supported by isothermal calorimetric titrations. The Mg(2+)-free nucleotides similarly stabilize the overall protein structure and restrict the conformational flexibility around the reactive thiol groups of helix 13, as observed by differential scanning microcalorimetry and thiol reactivity studies, respectively. The metal complexes, however, behave differently. MgADP, but not MgATP, further increases the conformational stability with respect to its Mg(2+)-free form, which indicates their different modes of binding to the enzyme. Crystal structures of the binary complexes of the enzyme with MgATP and with ATP (2.1 and 1.9 A resolution, respectively) have shown that the orientation and interaction of phosphates of MgATP largely differ not only from those of ATP but also from the previously determined ones of either MgADP [Davies, G. J., Gamblin, S. J., Littlechild, J. A., Dauter, Z., Wilson, K. S., and Watson, H. C. (1994) Acta Crystallogr. D50, 202-209] or the metal complexes of AMP-PNP [May, A., Vas, M., Harlos, K., and Blake, C. C. F. (1996) Proteins 24, 292-303; Auerbach, G., Huber, R., Grattinger, M., Zaiss, K., Schurig, H., Jaenicke, R., and Jacob, U. (1997) Structure 5, 1475-1483] and are more similar to the interactions formed with MgAMP-PCP [Kovari, Z., Flachner, B., Naray-Szabo, G., and Vas, M. (2002) Biochemistry 41, 8796-8806]. Mg(2+) is liganded to both beta- and gamma-phosphates of ATP, while beta-phosphate is linked to the conserved Asp218, i.e., to the N-terminus of helix 8, through a water molecule; the known interactions of either MgADP or the metal complexes of AMP-PNP with the N-terminus of helix 13 and with Asn336 of beta-strand J are absent in the case of MgATP. Fluctuation of MgATP phosphates between two alternative sites has been proposed to facilitate the correct positioning of the mobile side chain of Lys215, and the catalytically competent active site is thereby completed.
-===Structure of pig muscle PGK complexed with MgATP===
+Role of phosphate chain mobility of MgATP in completing the 3-phosphoglycerate kinase catalytic site: binding, kinetic, and crystallographic studies with ATP and MgATP.,Flachner B, Kovari Z, Varga A, Gugolya Z, Vonderviszt F, Naray-Szabo G, Vas M Biochemistry. 2004 Mar 30;43(12):3436-49. PMID:15035615<ref>PMID:15035615</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1vjc" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_15035615}}, adds the Publication Abstract to the page
+*[[Phosphoglycerate kinase 3D structures|Phosphoglycerate kinase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 15035615 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_15035615}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-VJC is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Sus_scrofa Sus scrofa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VJC OCA].
-==Reference==
-<ref group="xtra">PMID:15035615</ref><references group="xtra"/>
-[[Category: Phosphoglycerate kinase]]
 [[Category: Sus scrofa]]
-[[Category: Flachner, B.]]
+[[Category: Flachner B]]
-[[Category: Gugolya, Z.]]
+[[Category: Gugolya Z]]
-[[Category: Kovari, Z.]]
+[[Category: Kovari Z]]
-[[Category: Naray-Szabo, G.]]
+[[Category: Naray-Szabo G]]
-[[Category: Varga, A.]]
+[[Category: Varga A]]
-[[Category: Vas, M.]]
+[[Category: Vas M]]
-[[Category: Vonderviszt, F.]]
+[[Category: Vonderviszt F]]
-[[Category: Atp]]
-[[Category: Mg]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 14:59:15 2009''