1jmh: Difference between revisions

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-[[Image:1jmh.gif|left|200px]]<br />
-<applet load="1jmh" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1jmh, resolution 2.5&Aring;" />
-'''CONTRIBUTIONS OF ORIENTATION AND HYDROGEN BONDING TO CATALYSIS IN ASN-229 MUTANTS OF THYMIDYLATE SYNTHASE'''<br />
-==Overview==
+==CONTRIBUTIONS OF ORIENTATION AND HYDROGEN BONDING TO CATALYSIS IN ASN-229 MUTANTS OF THYMIDYLATE SYNTHASE==
-We have determined structures of binary and ternary complexes of five, Asn229 variants of thymidylate synthase (TS) and related their structures, to the kinetic constants measured previously. Asn229 forms two hydrogen, bonds to the pyrimidine ring of the substrate, 2'-deoxyuridine-5'-monophosphate (dUMP). These hydrogen bonds constrain, the orientation of dUMP in binary complexes with dUMP, and in ternary, complexes with dUMP and the TS cofactor, 5,10-methylene-5,6,7,8-tetrahydrofolate. In N229 mutants, where these, hydrogen bonds cannot be made, dUMP binds in a misoriented or more, disordered fashion. Most N229 mutants exhibit no activity for the, dehalogenation of 5-bromo-dUMP, which requires correct orientation of dUMP, against Cys198. Since bound dUMP forms the binding surface against which, the pterin ring of cofactor binds, misorientation of dUMP results in, higher Km values for cofactor. At the same time, binding of the cofactor, aids in ordering and positioning dUMP for catalysis. Hydrophobic mutants, such as N229I, favor an arrangement of solvent molecules and side-chains, around the ligands similar to that in a proposed transition state for, ternary complex formation in wild-type TS, and kcat values are similar to, the wild-type value. Smaller, more hydrophilic mutants favor arrangements, of the solvent and side-chains surrounding the ligands that do not, resemble the proposed transition state. These changes correspond to, decreases in kcat of up to 2000-fold, with only modest increases in Km or, Kd. These results are consistent with the proposal that the, hydrogen-bonding network between water, dUMP and side-chains in the, active-site cavity contributes to catalysis in TS. Asn229 has the unique, ability to maintain this critical network, without sterically interfering, with dUMP binding.
+<StructureSection load='1jmh' size='340' side='right'caption='[[1jmh]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1jmh]] 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=1JMH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JMH 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=1jmh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jmh OCA], [https://pdbe.org/1jmh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1jmh RCSB], [https://www.ebi.ac.uk/pdbsum/1jmh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1jmh 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/jm/1jmh_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=1jmh ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-JMH 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 UMP 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] Structure known Active Site: CAT. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1JMH OCA].
+*[[Thymidylate synthase 3D structures|Thymidylate synthase 3D structures]]
+__TOC__
-==Reference==
+</StructureSection>
-Contributions of orientation and hydrogen bonding to catalysis in Asn229 mutants of thymidylate synthase., Finer-Moore JS, Liu L, Birdsall DL, Brem R, Apfeld J, Santi DV, Stroud RM, J Mol Biol. 1998 Feb 13;276(1):113-29. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=9514716 9514716]
+[[Category: Lacticaseibacillus casei]]
-[[Category: Lactobacillus casei]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Finer-Moore J]]
-[[Category: Thymidylate synthase]]
+[[Category: Stroud RM]]
-[[Category: Finer-Moore, J.]]
-[[Category: Stroud, R.M.]]
-[[Category: UMP]]
-[[Category: methyltransferase]]
-[[Category: transferase]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Mon Nov  5 12:39:55 2007''