2dft: Difference between revisions

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-{{Seed}}
-[[Image:2dft.png|left|200px]]
-<!--
+==Structure of shikimate kinase from Mycobacterium tuberculosis complexed with ADP and Mg at 2.8 angstrons of resolution==
-The line below this paragraph, containing "STRUCTURE_2dft", creates the "Structure Box" on the page.
+<StructureSection load='2dft' size='340' side='right'caption='[[2dft]], [[Resolution|resolution]] 2.80&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'>[[2dft]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DFT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DFT 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]] 2.8&#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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-{{STRUCTURE_2dft|  PDB=2dft  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2dft FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dft OCA], [https://pdbe.org/2dft PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dft RCSB], [https://www.ebi.ac.uk/pdbsum/2dft PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dft ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/AROK_MYCTU AROK_MYCTU] Catalyzes the specific phosphorylation of the 3-hydroxyl group of shikimic acid using ATP as a cosubstrate.<ref>PMID:11483005</ref> <ref>PMID:17020768</ref>
+== 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/df/2dft_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=2dft ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Bacteria, fungi and plants can convert carbohydrate and phosphoenolpyruvate into chorismate, which is the precursor of various aromatic compounds. The seven enzymes of the shikimate pathway are responsible for this conversion. Shikimate kinase (SK) is the fifth enzyme in this pathway and converts shikimate to shikimate-3-phosphate. In this work, the conformational changes that occur on binding of shikimate, magnesium and chloride ions to SK from Mycobacterium tuberculosis (MtSK) are described. It was observed that both ions and shikimate influence the conformation of residues of the active site of MtSK. Magnesium influences the conformation of the shikimate hydroxyl groups and the position of the side chains of some of the residues of the active site. Chloride seems to influence the affinity of ADP and its position in the active site and the opening length of the LID domain. Shikimate binding causes a closing of the LID domain and also seems to influence the crystallographic packing of SK. The results shown here could be useful for understanding the catalytic mechanism of SK and the role of ions in the activity of this protein.
-===Structure of shikimate kinase from Mycobacterium tuberculosis complexed with ADP and Mg at 2.8 angstrons of resolution===
+Effects of the magnesium and chloride ions and shikimate on the structure of shikimate kinase from Mycobacterium tuberculosis.,Dias MV, Faim LM, Vasconcelos IB, de Oliveira JS, Basso LA, Santos DS, de Azevedo WF Jr Acta Crystallogr Sect F Struct Biol Cryst Commun. 2007 Jan 1;63(Pt 1):1-6., Epub 2006 Dec 16. PMID:17183161<ref>PMID:17183161</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2dft" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_17183161}}, adds the Publication Abstract to the page
+*[[Shikimate kinase 3D structures|Shikimate kinase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 17183161 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_17183161}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-DFT is a 4 chains structure of sequences from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DFT OCA].
-==Reference==
-<ref group="xtra">PMID:17183161</ref><references group="xtra"/>
 [[Category: Mycobacterium tuberculosis]]
-[[Category: Shikimate kinase]]
+[[Category: Basso LA]]
-[[Category: Azevedo, W F.de.]]
+[[Category: Dias MV]]
-[[Category: Basso, L A.]]
+[[Category: Faim LM]]
-[[Category: Dias, M V.]]
+[[Category: Santos DS]]
-[[Category: Faim, L M.]]
+[[Category: Vasconcelos IB]]
-[[Category: Oliveira, J S.de.]]
+[[Category: De Azevedo WF]]
-[[Category: Santos, D S.]]
+[[Category: De Oliveira JS]]
-[[Category: Vasconcelos, I B.]]
-[[Category: Alpha/beta]]
-[[Category: Shikimate pathway]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 07:51:46 2009''