1vzb: Difference between revisions

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-[[Image:1vzb.gif|left|200px]]<br /><applet load="1vzb" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="1vzb, resolution 2.5&Aring;" />
-'''L. CASEI THYMIDYLATE SYNTHASE MUTANT E60Q BINARY COMPLEX WITH DUMP'''<br />
-==Overview==
+==L. CASEI THYMIDYLATE SYNTHASE MUTANT E60Q BINARY COMPLEX WITH DUMP==
-Three steps along the pathway of binding, orientation of substrates and release of products are revealed by X-ray crystallographic structures of ternary complexes of the wild-type Lactobacillus casei thymidylate synthase enzyme. Each complex was formed by diffusion of either the cofactor 5,10-methylene-5,6,7,8-tetrahydrofolate or the folate analog 10-propargyl-5,8-dideazafolate into binary co-crystals of thymidylate synthase with 2'-deoxyuridine-5'-monophosphate. A two-substrate/enzyme complex is formed where the substrates remain unaltered. The imidazolidine ring is unopened and the pterin of the 5,10-methylene-5,6,7,8-tetrahydrofolate cofactor binds at an unproductive "alternate" site. We propose that the presence of the pterin at this site may represent an initial interaction with the enzyme that precedes all catalytic events. The structure of the 2'-deoxyuridine-5'-monophosphate and 10-propargyl-5,8-dideazafolate folate analog complex identifies both ligands in orientations favorable for the initiation of catalysis and resembles the productive complex. A product complex where the ligands have been converted into products of the thymidylate synthase reaction within the crystal, 2'-deoxythymidine-5'-monophosphate and 7,8-dihydrofolate, shows how ligands are situated within the enzyme after catalysis and on the way to product release.
+<StructureSection load='1vzb' size='340' side='right'caption='[[1vzb]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1vzb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Lacticaseibacillus_casei Lacticaseibacillus casei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VZB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VZB 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]] 2.5&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=UMP:2-DEOXYURIDINE+5-MONOPHOSPHATE'>UMP</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=1vzb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vzb OCA], [https://pdbe.org/1vzb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vzb RCSB], [https://www.ebi.ac.uk/pdbsum/1vzb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vzb ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/TYSY_LACCA TYSY_LACCA] Provides the sole de novo source of dTMP for DNA biosynthesis.
+== 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/vz/1vzb_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=1vzb ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-VZB is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Lactobacillus_casei Lactobacillus casei] with <scene name='pdbligand=UMP:'>UMP</scene> 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://oca.weizmann.ac.il/oca-bin/ocashort?id=1VZB OCA].
+*[[Thymidylate synthase 3D structures|Thymidylate synthase 3D structures]]
+__TOC__
-==Reference==
+</StructureSection>
-Entropy in bi-substrate enzymes: proposed role of an alternate site in chaperoning substrate into, and products out of, thymidylate synthase., Birdsall DL, Finer-Moore J, Stroud RM, J Mol Biol. 1996 Jan 26;255(3):522-35. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8568895 8568895]
+[[Category: Lacticaseibacillus casei]]
-[[Category: Lactobacillus casei]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Birdsall DL]]
-[[Category: Thymidylate synthase]]
+[[Category: Finer-Moore J]]
-[[Category: Birdsall, D L.]]
+[[Category: Stroud RM]]
-[[Category: Finer-Moore, J.]]
-[[Category: Stroud, R M.]]
-[[Category: UMP]]
-[[Category: methyltransferase]]
-[[Category: nucleotide synthase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 15:38:51 2008''