1l4y: Difference between revisions

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-[[Image:1l4y.gif|left|200px]]<br /><applet load="1l4y" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1l4y, resolution 2.00&Aring;" />
-'''CRYSTAL STRUCTURE OF SHIKIMATE KINASE FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH MGADP AT 2.0 ANGSTROM RESOLUTION'''<br />
-==Overview==
+==CRYSTAL STRUCTURE OF SHIKIMATE KINASE FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH MGADP AT 2.0 ANGSTROM RESOLUTION==
-Shikimate kinase (SK) and other enzymes in the shikimate pathway are, potential targets for developing non-toxic antimicrobial agents, herbicides, and anti-parasite drugs, because the pathway is essential in, the above species but is absent from mammals. The crystal structure of, Mycobacterium tuberculosis SK (MtSK) in complex with MgADP has been, determined at 1.8 A resolution, revealing critical information for the, structure-based design of novel anti-M. tuberculosis agents. MtSK, with a, five-stranded parallel beta-sheet flanked by eight alpha-helices, has, three domains: the CORE domain, the shikimate-binding domain (SB), and the, LID domain. The ADP molecule is bound with its adenine moiety sandwiched, between the side-chains of Arg110 and Pro155, its beta-phosphate group in, the P-loop, and the alpha and beta-phosphate groups hydrogen bonded to the, guanidinium group of Arg117. Arg117 is located in the LID domain, is, strictly conserved in SK sequences, is observed for the first time to, interact with any bound nucleotide, and appears to be important in both, substrate binding and catalysis. The crystal structure of MtSK (this work), and that of Erwinia chrysanthemi SK suggest a concerted conformational, change of the LID and SB domains upon nucleotide binding.
+<StructureSection load='1l4y' size='340' side='right'caption='[[1l4y]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1l4y]] is a 1 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=1L4Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1L4Y 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&#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>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1l4y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l4y OCA], [https://pdbe.org/1l4y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1l4y RCSB], [https://www.ebi.ac.uk/pdbsum/1l4y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1l4y 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/l4/1l4y_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=1l4y ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Shikimate kinase (SK) and other enzymes in the shikimate pathway are potential targets for developing non-toxic antimicrobial agents, herbicides, and anti-parasite drugs, because the pathway is essential in the above species but is absent from mammals. The crystal structure of Mycobacterium tuberculosis SK (MtSK) in complex with MgADP has been determined at 1.8 A resolution, revealing critical information for the structure-based design of novel anti-M. tuberculosis agents. MtSK, with a five-stranded parallel beta-sheet flanked by eight alpha-helices, has three domains: the CORE domain, the shikimate-binding domain (SB), and the LID domain. The ADP molecule is bound with its adenine moiety sandwiched between the side-chains of Arg110 and Pro155, its beta-phosphate group in the P-loop, and the alpha and beta-phosphate groups hydrogen bonded to the guanidinium group of Arg117. Arg117 is located in the LID domain, is strictly conserved in SK sequences, is observed for the first time to interact with any bound nucleotide, and appears to be important in both substrate binding and catalysis. The crystal structure of MtSK (this work) and that of Erwinia chrysanthemi SK suggest a concerted conformational change of the LID and SB domains upon nucleotide binding.
-==About this Structure==
+Crystal structure of shikimate kinase from Mycobacterium tuberculosis reveals the dynamic role of the LID domain in catalysis.,Gu Y, Reshetnikova L, Li Y, Wu Y, Yan H, Singh S, Ji X J Mol Biol. 2002 Jun 7;319(3):779-89. PMID:12054870<ref>PMID:12054870</ref>
-L4Y is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis] with MG, CL and ADP as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Shikimate_kinase Shikimate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.71 2.7.1.71] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1L4Y OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Crystal structure of shikimate kinase from Mycobacterium tuberculosis reveals the dynamic role of the LID domain in catalysis., Gu Y, Reshetnikova L, Li Y, Wu Y, Yan H, Singh S, Ji X, J Mol Biol. 2002 Jun 7;319(3):779-89. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12054870 12054870]
+</div>
+<div class="pdbe-citations 1l4y" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Shikimate kinase 3D structures|Shikimate kinase 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Mycobacterium tuberculosis]]
-[[Category: Shikimate kinase]]
+[[Category: Gu Y]]
-[[Category: Single protein]]
+[[Category: Ji X]]
-[[Category: Gu, Y.]]
+[[Category: Li Y]]
-[[Category: Ji, X.]]
+[[Category: Reshetnikova L]]
-[[Category: Li, Y.]]
+[[Category: Singh S]]
-[[Category: Reshetnikova, L.]]
+[[Category: Wu Y]]
-[[Category: Singh, S.]]
+[[Category: Yan H]]
-[[Category: Wu, Y.]]
-[[Category: Yan, H.]]
-[[Category: ADP]]
-[[Category: CL]]
-[[Category: MG]]
-[[Category: drug design]]
-[[Category: phorsphoryl transfer]]
-[[Category: shikimate kinase]]
-[[Category: shikimate pathway]]
-[[Category: x-ray crystallography]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 20:15:41 2007''