1bp0: Difference between revisions

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-{{Seed}}
-[[Image:1bp0.png|left|200px]]
-<!--
+==THYMIDYLATE SYNTHASE R23I MUTANT==
-The line below this paragraph, containing "STRUCTURE_1bp0", creates the "Structure Box" on the page.
+<StructureSection load='1bp0' size='340' side='right'caption='[[1bp0]], [[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'>[[1bp0]] 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=1BP0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BP0 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=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=UMP:2-DEOXYURIDINE+5-MONOPHOSPHATE'>UMP</scene></td></tr>
-{{STRUCTURE_1bp0|  PDB=1bp0  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1bp0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bp0 OCA], [https://pdbe.org/1bp0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1bp0 RCSB], [https://www.ebi.ac.uk/pdbsum/1bp0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1bp0 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/bp/1bp0_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=1bp0 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+In thymidylate synthase, four conserved arginines provide two hydrogen bonds each to the oxygens of the phosphate group of the substrate, 2'-deoxyuridine-5'-monophosphate. Of these, R23, R178, and R179 are far removed from the site of methyl transfer and contribute to catalysis solely through binding and orientation of ligands. These arginines can be substituted by other residues, while still retaining more than 1% activity of the wild-type enzyme. We compared the kinetics and determined the crystal structures of dUMP complexes of three of the most active, uncharged single mutants of these arginines, R23I, R178T, and R179T, and of double mutants (R23I, R179T) and (R178T, R179T). The dramatically higher K(m) for R178T compared to the other two single mutants arises from the effects of R178 substitution on the orientation of dUMP; 10-15-fold increases in for R23I and R178T reflect the role of these residues in stabilizing the closed conformation of TS in ternary complexes. The free energy for productive dUMP binding, DeltaG(S), increases by at least 1 kcal/mol for each mutant, even when dUMP orientation and mobility in the crystal structure is the same as in wild-type enzyme. Thus, the four arginines do not contribute excess positive charge to the PO(4)(-2) binding site; rather, they ideally complement the charge and geometry of the phosphate moiety. More-than-additive increases in DeltaG(S) seen in the double mutants are consistent with quadratic increases in DeltaG(S) predicted for deviations from ideal electrostatic interactions and may also reflect cooperative binding of the arginines to the phosphate oxygens.
-===THYMIDYLATE SYNTHASE R23I MUTANT===
+Energetic contributions of four arginines to phosphate-binding in thymidylate synthase are more than additive and depend on optimization of "effective charge balance".,Morse RJ, Kawase S, Santi DV, Finer-Moore J, Stroud RM Biochemistry. 2000 Feb 8;39(5):1011-20. PMID:10653645<ref>PMID:10653645</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1bp0" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_10653645}}, 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 10653645 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_10653645}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Lacticaseibacillus casei]]
-BP0 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Lactobacillus_casei Lactobacillus casei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BP0 OCA].
+[[Category: Large Structures]]
+[[Category: Finer-Moore J]]
-==Reference==
+[[Category: Morse R]]
-Energetic contributions of four arginines to phosphate-binding in thymidylate synthase are more than additive and depend on optimization of "effective charge balance"., Morse RJ, Kawase S, Santi DV, Finer-Moore J, Stroud RM, Biochemistry. 2000 Feb 8;39(5):1011-20. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10653645 10653645]
+[[Category: Stroud RM]]
-[[Category: Lactobacillus casei]]
-[[Category: Single protein]]
-[[Category: Thymidylate synthase]]
-[[Category: Finer-Moore, J.]]
-[[Category: Morse, R.]]
-[[Category: Stroud, R M.]]
-[[Category: Methyltransferase]]
-[[Category: Nucleotide biosynthesis]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jun 30 19:28:54 2008''