1nce: Difference between revisions

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-{{Seed}}
-[[Image:1nce.png|left|200px]]
-<!--
+==Crystal structure of a ternary complex of E. coli thymidylate synthase D169C with dUMP and the antifolate CB3717==
-The line below this paragraph, containing "STRUCTURE_1nce", creates the "Structure Box" on the page.
+<StructureSection load='1nce' size='340' side='right'caption='[[1nce]], [[Resolution|resolution]] 2.40&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'>[[1nce]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [https://en.wikipedia.org/wiki/Escherichia_coli_O157:H7 Escherichia coli O157:H7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NCE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NCE 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]] 2.4&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CB3:10-PROPARGYL-5,8-DIDEAZAFOLIC+ACID'>CB3</scene>, <scene name='pdbligand=CXM:N-CARBOXYMETHIONINE'>CXM</scene>, <scene name='pdbligand=UMP:2-DEOXYURIDINE+5-MONOPHOSPHATE'>UMP</scene></td></tr>
-{{STRUCTURE_1nce|  PDB=1nce  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1nce FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nce OCA], [https://pdbe.org/1nce PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nce RCSB], [https://www.ebi.ac.uk/pdbsum/1nce PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nce 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/nc/1nce_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=1nce ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Cysteine is the only variant of D169, a cofactor-binding residue in thymidylate synthase, that shows in vivo activity. The 2.4 A crystal structure of Escherichia coli thymidylate synthase D169C in a complex with dUMP and the antifolate CB3717 shows it to be an asymmetric dimer, with only one active site covalently bonded to dUMP. At the active site with covalently bound substrate, C169 S gamma adopts the roles of both carboxyl oxygens of D169, making a 3.6 A S...H[bond]N hydrogen bond to 3-NH of CB3717 and a 3.4 A water-mediated hydrogen bond to H212. Analogous hydrogen bonds formed during the enzyme reaction are important for cofactor binding and are postulated to contribute to catalysis. The C169 side chain is likely to be ionized, making it a better hydrogen bond acceptor than a neutral sulfhydryl group. At the second active site, C169 S gamma makes a shorter (3 A) hydrogen bond to the 3-NH of CB3717, CB3717 is approximately 1.5 A out of its binding site and there is no covalent bond between dUMP and the catalytic cysteine. Changes to partitioning among productive and non-productive conformations of reaction intermediates may contribute as much, if not more, to the diminished activity of this mutant than reduced stabilization of transition states.
-===Crystal structure of a ternary complex of E. coli thymidylate synthase D169C with dUMP and the antifolate CB3717===
+The only active mutant of thymidylate synthase D169, a residue far from the site of methyl transfer, demonstrates the exquisite nature of enzyme specificity.,Birdsall DL, Finer-Moore J, Stroud RM Protein Eng. 2003 Mar;16(3):229-40. PMID:12702803<ref>PMID:12702803</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1nce" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_12702803}}, adds the Publication Abstract to the page
+*[[Thymidylate synthase 3D structures|Thymidylate synthase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 12702803 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_12702803}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Escherichia coli]]
-NCE is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli,_and_escherichia_coli_o157:h7 Escherichia coli, and escherichia coli o157:h7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NCE OCA].
+[[Category: Escherichia coli O157:H7]]
+[[Category: Large Structures]]
-==Reference==
+[[Category: Birdsall DL]]
-The only active mutant of thymidylate synthase D169, a residue far from the site of methyl transfer, demonstrates the exquisite nature of enzyme specificity., Birdsall DL, Finer-Moore J, Stroud RM, Protein Eng. 2003 Mar;16(3):229-40. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12702803 12702803]
+[[Category: Finer-Moore J]]
-[[Category: Escherichia coli, and escherichia coli o157:h7]]
+[[Category: Stroud RM]]
-[[Category: Single protein]]
-[[Category: Thymidylate synthase]]
-[[Category: Birdsall, D L.]]
-[[Category: Finer-Moore, J.]]
-[[Category: Stroud, R M.]]
-[[Category: Asymmetric dimer]]
-[[Category: Beta-sheet interface]]
-[[Category: Protein-dump-cofactor analog complex]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 08:08:58 2008''