1gqt: Difference between revisions

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-[[Image:1gqt.jpg|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_1gqt", creates the "Structure Box" on the page.
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-or leave the SCENE parameter empty for the default display.
--->
-{{STRUCTURE_1gqt|  PDB=1gqt  |  SCENE=  }}
-'''ACTIVATION OF RIBOKINASE BY MONOVALENT CATIONS'''
+==Activation of Ribokinase by Monovalent Cations==
+<StructureSection load='1gqt' size='340' side='right'caption='[[1gqt]], [[Resolution|resolution]] 2.34&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1gqt]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GQT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1GQT 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]] 2.34&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACP:PHOSPHOMETHYLPHOSPHONIC+ACID+ADENYLATE+ESTER'>ACP</scene>, <scene name='pdbligand=CS:CESIUM+ION'>CS</scene>, <scene name='pdbligand=RIB:RIBOSE'>RIB</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=1gqt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gqt OCA], [https://pdbe.org/1gqt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1gqt RCSB], [https://www.ebi.ac.uk/pdbsum/1gqt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1gqt ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RBSK_ECOLI RBSK_ECOLI]
+== 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/gq/1gqt_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=1gqt ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Carbohydrate kinases frequently require a monovalent cation for their activity. The physical basis of this phenomenon is, however, usually unclear. We report here that Escherichia coli ribokinase is activated by potassium with an apparent K(d) of 5 mM; the enzyme should therefore be fully activated under physiological conditions. Cesium can be used as an alternative ion, with an apparent K(d) of 17 mM. An X-ray structure of ribokinase in the presence of cesium was solved and refined at 2.34 A resolution. The cesium ion was bound between two loops immediately adjacent to the anion hole of the active site. The buried location of the site suggests that conformational changes will accompany ion binding, thus providing a direct mechanism for activation. Comparison with structures of a related enzyme, the adenosine kinase of Toxoplasma gondii, support this proposal. This is apparently the first instance in which conformational activation of a carbohydrate kinase by a monovalent cation has been assigned a clear structural basis. The mechanism is probably general to ribokinases, to some adenosine kinases, and to other members of the larger family. A careful re-evaluation of the biochemical and structural data is suggested for other enzyme systems.
-==Overview==
+Activation of ribokinase by monovalent cations.,Andersson CE, Mowbray SL J Mol Biol. 2002 Jan 18;315(3):409-19. PMID:11786021<ref>PMID:11786021</ref>
-Carbohydrate kinases frequently require a monovalent cation for their activity. The physical basis of this phenomenon is, however, usually unclear. We report here that Escherichia coli ribokinase is activated by potassium with an apparent K(d) of 5 mM; the enzyme should therefore be fully activated under physiological conditions. Cesium can be used as an alternative ion, with an apparent K(d) of 17 mM. An X-ray structure of ribokinase in the presence of cesium was solved and refined at 2.34 A resolution. The cesium ion was bound between two loops immediately adjacent to the anion hole of the active site. The buried location of the site suggests that conformational changes will accompany ion binding, thus providing a direct mechanism for activation. Comparison with structures of a related enzyme, the adenosine kinase of Toxoplasma gondii, support this proposal. This is apparently the first instance in which conformational activation of a carbohydrate kinase by a monovalent cation has been assigned a clear structural basis. The mechanism is probably general to ribokinases, to some adenosine kinases, and to other members of the larger family. A careful re-evaluation of the biochemical and structural data is suggested for other enzyme systems.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-GQT is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GQT OCA].
+</div>
+<div class="pdbe-citations 1gqt" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-Activation of ribokinase by monovalent cations., Andersson CE, Mowbray SL, J Mol Biol. 2002 Jan 18;315(3):409-19. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11786021 11786021]
+*[[Ribokinase 3D structures|Ribokinase 3D structures]]
-[[Category: Escherichia coli]]
+== References ==
-[[Category: Ribokinase]]
+<references/>
-[[Category: Single protein]]
+__TOC__
-[[Category: Andersson, C E.]]
+</StructureSection>
-[[Category: Mowbray, S L.]]
+[[Category: Escherichia coli K-12]]
-[[Category: Activation by monovalent cation]]
+[[Category: Large Structures]]
-[[Category: Binding of monovalent cation]]
+[[Category: Andersson CE]]
-[[Category: Carbohydrate kinase]]
+[[Category: Mowbray SL]]
-[[Category: Induced fit]]
-[[Category: Ribose]]
-[[Category: Transferase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 17:54:24 2008''