1tuh: Difference between revisions

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-[[Image:1tuh.gif|left|200px]]<br /><applet load="1tuh" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="1tuh, resolution 1.85&Aring;" />
-'''Structure of Bal32a from a Soil-Derived Mobile Gene Cassette'''<br />
-==Overview==
+==Structure of Bal32a from a Soil-Derived Mobile Gene Cassette==
-The wide-ranging physiology and large genetic variability observed for prokaryotes is largely attributed, not to the prokaryotic genome itself, but rather to mechanisms of lateral gene transfer. Cassette PCR has been used to sample the integron/gene cassette metagenome from different natural environments without laboratory cultivation of the host organism, and without prior knowledge of any target protein sequence. Since over 90% of cassette genes are unrelated to any sequence in the current databases, it is not clear whether these genes code for folded functional proteins. We have selected a sample of eight cassette-encoded genes with no known homologs; five have been isolated as soluble protein products and shown by biophysical techniques to be folded. In solution, at least three of these proteins organise as stable oligomeric assemblies. The tertiary structure of one of these, Bal32a derived from a contaminated soil site, has been solved by X-ray crystallography to 1.8 A resolution. From the three-dimensional structure, Bal32a is found to be a member of the highly adaptable alpha+beta barrel family of transport proteins and enzymes. In Bal32a, the barrel cavity is unusually deep and inaccessible to solvent. Polar side-chains in its interior are reminiscent of catalytic sites of limonene-1,2-epoxide hydrolase and nogalonic acid methyl ester cyclase. These studies demonstrate the viability of direct sampling of mobile DNA as a route for the discovery of novel proteins.
+<StructureSection load='1tuh' size='340' side='right'caption='[[1tuh]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
+== Structural highlights ==
-==About this Structure==
+<table><tr><td colspan='2'>[[1tuh]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Uncultured_bacterium Uncultured bacterium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TUH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1TUH FirstGlance]. <br>
-TUH is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Uncultured_bacterium Uncultured bacterium] with <scene name='pdbligand=ACT:'>ACT</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TUH OCA].
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.85&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene></td></tr>
-==Reference==
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1tuh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tuh OCA], [https://pdbe.org/1tuh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1tuh RCSB], [https://www.ebi.ac.uk/pdbsum/1tuh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1tuh ProSAT]</span></td></tr>
-Integron-associated mobile gene cassettes code for folded proteins: the structure of Bal32a, a new member of the adaptable alpha+beta barrel family., Robinson A, Wu PS, Harrop SJ, Schaeffer PM, Dosztanyi Z, Gillings MR, Holmes AJ, Nevalainen KM, Stokes HW, Otting G, Dixon NE, Curmi PM, Mabbutt BC, J Mol Biol. 2005 Mar 11;346(5):1229-41. Epub 2004 Dec 31. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15713477 15713477]
+</table>
-[[Category: Single protein]]
+== Function ==
+[https://www.uniprot.org/uniprot/Q99IU3_9BACT Q99IU3_9BACT]
+== 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/tu/1tuh_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=1tuh ConSurf].
+<div style="clear:both"></div>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Uncultured bacterium]]
-[[Category: Curmi, P M.G.]]
+[[Category: Curmi PMG]]
-[[Category: Dixon, N E.]]
+[[Category: Dixon NE]]
-[[Category: Gillings, M R.]]
+[[Category: Gillings MR]]
-[[Category: Harrop, S J.]]
+[[Category: Harrop SJ]]
-[[Category: Holmes, A J.]]
+[[Category: Holmes AJ]]
-[[Category: Mabbutt, B C.]]
+[[Category: Mabbutt BC]]
-[[Category: Nevalainen, K M.H.]]
+[[Category: Nevalainen KMH]]
-[[Category: Otting, G.]]
+[[Category: Otting G]]
-[[Category: Robinson, A.]]
+[[Category: Robinson A]]
-[[Category: Schaeffer, P M.]]
+[[Category: Schaeffer PM]]
-[[Category: Stokes, H W.]]
+[[Category: Stokes HW]]
-[[Category: Wu, P S.C.]]
+[[Category: Wu PS-C]]
-[[Category: ACT]]
-[[Category: uncultured]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 15:17:29 2008''