1e6c: Difference between revisions

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-[[Image:1e6c.png|left|200px]]
-<!--
+==K15M MUTANT OF SHIKIMATE KINASE FROM ERWINIA CHRYSANTHEMI==
-The line below this paragraph, containing "STRUCTURE_1e6c", creates the "Structure Box" on the page.
+<StructureSection load='1e6c' size='340' side='right'caption='[[1e6c]], [[Resolution|resolution]] 1.80&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'>[[1e6c]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Dickeya_chrysanthemi Dickeya chrysanthemi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1E6C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1E6C 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]] 1.8&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=MRD:(4R)-2-METHYLPENTANE-2,4-DIOL'>MRD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-{{STRUCTURE_1e6c|  PDB=1e6c  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1e6c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e6c OCA], [https://pdbe.org/1e6c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1e6c RCSB], [https://www.ebi.ac.uk/pdbsum/1e6c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1e6c ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/AROL_DICCH AROL_DICCH] Catalyzes the specific phosphorylation of the 3-hydroxyl group of shikimic acid using ATP as a cosubstrate.<ref>PMID:11369852</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/e6/1e6c_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=1e6c ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Shikimate kinase, despite low sequence identity, has been shown to be structurally a member of the nucleoside monophosphate (NMP) kinase family, which includes adenylate kinase. In this paper we have explored the roles of residues in the P-loop of shikimate kinase, which forms the binding site for nucleotides and is one of the most conserved structural features in proteins. In common with many members of the P-loop family, shikimate kinase contains a cysteine residue 2 amino acids upstream of the essential lysine residue; the side chains of these residues are shown to form an ion pair. The C13S mutant of shikimate kinase was found to be enzymatically active, whereas the K15M mutant was inactive. However, the latter mutant had both increased thermostability and affinity for ATP when compared to the wild-type enzyme. The structure of the K15M mutant protein has been determined at 1.8 A, and shows that the organization of the P-loop and flanking regions is heavily disturbed. This indicates that, besides its role in catalysis, the P-loop lysine also has an important structural role. The structure of the K15M mutant also reveals that the formation of an additional arginine/aspartate ion pair is the most likely reason for its increased thermostability. From studies of ligand binding it appears that, like adenylate kinase, shikimate kinase binds substrates randomly and in a synergistic fashion, indicating that the two enzymes have similar catalytic mechanisms.
-===K15M MUTANT OF SHIKIMATE KINASE FROM ERWINIA CHRYSANTHEMI===
+Biochemical and X-ray crystallographic studies on shikimate kinase: the important structural role of the P-loop lysine.,Krell T, Maclean J, Boam DJ, Cooper A, Resmini M, Brocklehurst K, Kelly SM, Price NC, Lapthorn AJ, Coggins JR Protein Sci. 2001 Jun;10(6):1137-49. PMID:11369852<ref>PMID:11369852</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1e6c" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_11369852}}, 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 11369852 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_11369852}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Dickeya chrysanthemi]]
-[[1e6c]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Erwinia_chrysanthemi Erwinia chrysanthemi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1E6C OCA].
+[[Category: Large Structures]]
+[[Category: Coggins JR]]
-==Reference==
+[[Category: Krell T]]
-<ref group="xtra">PMID:11369852</ref><ref group="xtra">PMID:9600856</ref><references group="xtra"/>
+[[Category: Lapthorn AJ]]
-[[Category: Erwinia chrysanthemi]]
+[[Category: Maclean J]]
-[[Category: Shikimate kinase]]
-[[Category: Coggins, J R.]]
-[[Category: Krell, T.]]
-[[Category: Lapthorn, A J.]]
-[[Category: Maclean, J.]]
-[[Category: Adp]]
-[[Category: Mutant shikimate kinase]]
-[[Category: P-loop protein]]
-[[Category: Phosphoryl transfer]]
-[[Category: Shikimate pathway]]
-[[Category: Transferase]]