1l4u: Difference between revisions

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-[[Image:1l4u.gif|left|200px]]
- {{Structure
+==CRYSTAL STRUCTURE OF SHIKIMATE KINASE FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH MGADP AND PT(II) AT 1.8 ANGSTROM RESOLUTION==
-|PDB= 1l4u |SIZE=350|CAPTION= <scene name='initialview01'>1l4u</scene>, resolution 1.80&Aring;
+<StructureSection load='1l4u' size='340' side='right'caption='[[1l4u]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=ADP:ADENOSINE-5&#39;-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PT:PLATINUM+(II)+ION'>PT</scene>
+<table><tr><td colspan='2'>[[1l4u]] 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=1L4U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1L4U FirstGlance]. <br>
-|ACTIVITY= <span class='plainlinks'>[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] </span>
+</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>
-|GENE= AROK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 Mycobacterium tuberculosis])
+<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=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PT:PLATINUM+(II)+ION'>PT</scene></td></tr>
-|DOMAIN=
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1l4u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l4u OCA], [https://pdbe.org/1l4u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1l4u RCSB], [https://www.ebi.ac.uk/pdbsum/1l4u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1l4u ProSAT]</span></td></tr>
-|RELATEDENTRY=[[1l4y|1L4Y]], [[1shk|1SHK]], [[2shk|2SHK]], [[1e6c|1E6C]]
+</table>
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1l4u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l4u OCA], [http://www.ebi.ac.uk/pdbsum/1l4u PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1l4u RCSB]</span>
+== 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/l4/1l4u_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=1l4u 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.
-'''CRYSTAL STRUCTURE OF SHIKIMATE KINASE FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH MGADP AND PT(II) AT 1.8 ANGSTROM RESOLUTION'''
+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>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1l4u" style="background-color:#fffaf0;"></div>
-==Overview==
+==See Also==
-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.
+*[[Shikimate kinase 3D structures|Shikimate kinase 3D structures]]
+== References ==
-==About this Structure==
+<references/>
-L4U is a [[Single protein]] structure of sequence 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=1L4U OCA].
+__TOC__
+</StructureSection>
-==Reference==
+[[Category: Large Structures]]
-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://www.ncbi.nlm.nih.gov/pubmed/12054870 12054870]
 [[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: drug design]]
-[[Category: phorsphoryl transfer]]
-[[Category: shikimate kinase]]
-[[Category: shikimate pathway]]
-[[Category: x-ray crystallography]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 21:58:01 2008''