3tms: Difference between revisions

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

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-[[Image:3tms.jpg|left|200px]]<br /><applet load="3tms" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="3tms, resolution 2.1&Aring;" />
-'''PLASTIC ADAPTATION TOWARD MUTATIONS IN PROTEINS: STRUCTURAL COMPARISON OF THYMIDYLATE SYNTHASES'''<br />
-==Overview==
+==PLASTIC ADAPTATION TOWARD MUTATIONS IN PROTEINS: STRUCTURAL COMPARISON OF THYMIDYLATE SYNTHASES==
-The structure of thymidylate synthase (TS) from Escherichia coli was, solved from cubic crystals with a = 133 A grown under reducing conditions, at pH 7.0, and refined to R = 22% at 2.1 A resolution. The structure is, compared with that from Lactobacillus casei solved to R = 21% at 2.3 A, resolution. The structures are compared using a difference distance, matrix, which identifies a common core of residues that retains the same, relationship to one another in both species. After subtraction of the, effects of a 50 amino acid insert present in Lactobacillus casei, differences in position of atoms correlate with temperature factors and, with distance from the nearest substituted residue. The dependence of, structural difference on thermal factor is parameterized and reflects both, errors in coordinates that correlate with thermal factor, and the, increased width of the energy well in which atoms of high thermal factor, lie. The dependence of structural difference on distance from the nearest, substitution also depends on thermal factors and shows an exponential, dependence with half maximal effect at 3.0 A from the substitution. This, represents the plastic accommodation of the protein which is parameterized, in terms of thermal B factor and distance from a mutational change.
+<StructureSection load='3tms' size='340' side='right'caption='[[3tms]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[3tms]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TMS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3TMS 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]] 2.1&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=3tms FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tms OCA], [https://pdbe.org/3tms PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3tms RCSB], [https://www.ebi.ac.uk/pdbsum/3tms PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3tms ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/TYSY_ECOLI TYSY_ECOLI] Provides the sole de novo source of dTMP for DNA biosynthesis. This protein also binds to its mRNA thus repressing its own translation.
+== 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/tm/3tms_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=3tms ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-TMS is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with PO4 as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Thymidylate_synthase Thymidylate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.45 2.1.1.45] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=3TMS OCA].
+*[[Thymidylate synthase 3D structures|Thymidylate synthase 3D structures]]
+__TOC__
-==Reference==
+</StructureSection>
-Plastic adaptation toward mutations in proteins: structural comparison of thymidylate synthases., Perry KM, Fauman EB, Finer-Moore JS, Montfort WR, Maley GF, Maley F, Stroud RM, Proteins. 1990;8(4):315-33. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=2128651 2128651]
 [[Category: Escherichia coli]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Thymidylate synthase]]
+[[Category: Perry KM]]
-[[Category: Perry, K.M.]]
+[[Category: Stroud RM]]
-[[Category: Stroud, R.M.]]
-[[Category: PO4]]
-[[Category: transferase (methyltransferase)]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 19:59:58 2007''