2bng: Difference between revisions

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-{{Seed}}
-[[Image:2bng.png|left|200px]]
-<!--
+==Structure of an M.tuberculosis LEH-like epoxide hydrolase==
-The line below this paragraph, containing "STRUCTURE_2bng", creates the "Structure Box" on the page.
+<StructureSection load='2bng' size='340' side='right'caption='[[2bng]], [[Resolution|resolution]] 2.50&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'>[[2bng]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis_H37Rv Mycobacterium tuberculosis H37Rv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BNG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BNG 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]] 2.5&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-{{STRUCTURE_2bng|  PDB=2bng  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2bng FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bng OCA], [https://pdbe.org/2bng PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2bng RCSB], [https://www.ebi.ac.uk/pdbsum/2bng PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2bng ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/EPHG_MYCTU EPHG_MYCTU] Epoxide hydrolase capable of hydrolyzing long or bulky lipophilic epoxides such as 9,10-epoxystearic acid and cholesterol 5,6-oxide in vitro. The physiological substrates have yet to be identified, but could be fatty acid or steroid derivatives.<ref>PMID:16051262</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/bn/2bng_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=2bng ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Epoxide hydrolases are vital to many organisms by virtue of their roles in detoxification, metabolism and processing of signaling molecules. The Mycobacterium tuberculosis genome encodes an unusually large number of epoxide hydrolases, suggesting that they might be of particular importance to these bacteria. We report here the first structure of an epoxide hydrolase from M.tuberculosis, solved to a resolution of 2.5 A using single-wavelength anomalous dispersion (SAD) from a selenomethionine-substituted protein. The enzyme features a deep active-site pocket created by the packing of three helices onto a curved six-stranded beta-sheet. This structure is similar to a previously described limonene-1,2-epoxide hydrolase from Rhodococcus erythropolis and unlike the alpha/beta-hydrolase fold typical of mammalian epoxide hydrolases (EH). A number of changes in the mycobacterial enzyme create a wider and deeper substrate-binding pocket than is found in its Rhodococcus homologue. Interestingly, each structure contains a different type of endogenous ligand of unknown origin bound in its active site. As a consequence of its wider substrate-binding pocket, the mycobacterial EH is capable of hydrolyzing long or bulky lipophilic epoxides such as 10,11-epoxystearic acid and cholesterol 5,6-oxide at appreciable rates, suggesting that similar compound(s) will serve as its physiological substrate(s).
-===STRUCTURE OF AN M.TUBERCULOSIS LEH-LIKE EPOXIDE HYDROLASE===
+Structure of an atypical epoxide hydrolase from Mycobacterium tuberculosis gives insights into its function.,Johansson P, Unge T, Cronin A, Arand M, Bergfors T, Jones TA, Mowbray SL J Mol Biol. 2005 Sep 2;351(5):1048-56. PMID:16051262<ref>PMID:16051262</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_16051262}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 2bng" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 16051262 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_16051262}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-BNG is a 3 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=2BNG OCA].
+[[Category: Mycobacterium tuberculosis H37Rv]]
+[[Category: Arand M]]
-==Reference==
+[[Category: Bergfors T]]
-<ref group="xtra">PMID:16051262</ref><references group="xtra"/>
+[[Category: Johansson P]]
-[[Category: Limonene-1,2-epoxide hydrolase]]
+[[Category: Jones TA]]
-[[Category: Mycobacterium tuberculosis]]
+[[Category: Mowbray SL]]
-[[Category: Arand, M.]]
+[[Category: Unge T]]
-[[Category: Bergfors, T.]]
-[[Category: Johansson, P.]]
-[[Category: Jones, T A.]]
-[[Category: Mowbray, S L.]]
-[[Category: SPINE, Structural Proteomics in Europe.]]
-[[Category: Unge, T.]]
-[[Category: Epoxide hydrolase]]
-[[Category: Hydrolase]]
-[[Category: Limonene]]
-[[Category: M tuberculosis]]
-[[Category: Spine]]
-[[Category: Structural genomic]]
-[[Category: Structural proteomics in europe]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 09:37:09 2009''