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| - | [[Image:2tdm.gif|left|200px]]<br /> | |
| - | <applet load="2tdm" size="450" color="white" frame="true" align="right" spinBox="true" | |
| - | caption="2tdm, resolution 2.55Å" /> | |
| - | '''STRUCTURE OF THYMIDYLATE SYNTHASE'''<br /> | |
| | | | |
| - | ==Overview== | + | ==STRUCTURE OF THYMIDYLATE SYNTHASE== |
| - | Crystal structures of two crystal forms of the complex of Lactobacillus, casei (TS) with its substrate dUMP have been solved and refined at 2.55 A, resolution. The two crystal forms differ by approximately 5% in the c-axis, length. The TS-dUMP complexes are symmetric dimers with dUMP bound, equivalently in both active sites. dUMP is non-covalently bound in the, same conformation as in ternary complexes of TS with dUMP and cofactor or, cofactor analogs. The same hydrogen bonds are made between TS and, substrate in the binary and ternary complexes. We have also determined the, 2.36 A crystal structure of phosphate-bound L. casei TS. This structure, has been refined to an R-factor of 19.3% with highly constrained geometry., Refinement has revealed the locations of all residues in the protein, including the disordered residues 90 to 119, which are part of an insert, found only in the L. casei and Staphylococcus aureus transposon Tn4003 TS, sequences. The 2.9 A multiple isomorphous replacement (MIR) structure of, L. casei TS in a complex with its substrate dUMP has been refined to a, crystallographic R-factor of 15.5%. Reducing agents were withheld from, crystallization solutions during MIR structure determination to allow, heavy-metal labeling of the cysteine residues. Therefore, the active-site, cysteine residue in this structure is oxidized and the dUMP is found at, half-occupancy in the active site. No significant conformational, difference was found between the phosphate-bound and dUMP-bound, structures. The TS-dUMP structures were better ordered than the, phosphate-bound TS or the oxidized TS-dUMP, particularly Arg23, which is, clearly hydrogen-bonded to the phosphate group of dUMP. A large and a, small P6(1)22 crystal form are observed for both phosphate-bound and, dUMP-bound L. casei TS. The small cell forms of the phosphate-bound and, dUMP-bound enzyme are isomorphous, whereas the cell constants of the, larger cell form change slightly when dUMP is bound (c = 240 A versus c =, 243 A). For both liganded and unliganded enzyme, conversion from the small, to the large crystal form sometimes occurs spontaneously, and the crystal, packing changes at a single interface. Conversion may be the result of a, small change in pH in the mother liquor surrounding the crystal. A single, intermolecular contact between symmetry-related Asp287 residues is, disrupted on going from the small to the large crystal form.
| + | <StructureSection load='2tdm' size='340' side='right'caption='[[2tdm]], [[Resolution|resolution]] 2.55Å' scene=''> |
| | + | == Structural highlights == |
| | + | <table><tr><td colspan='2'>[[2tdm]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Lacticaseibacillus_casei Lacticaseibacillus casei]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1tdm 1tdm]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2TDM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2TDM 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]] 2.55Å</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=2tdm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2tdm OCA], [https://pdbe.org/2tdm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2tdm RCSB], [https://www.ebi.ac.uk/pdbsum/2tdm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2tdm 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/td/2tdm_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=2tdm ConSurf]. |
| | + | <div style="clear:both"></div> |
| | | | |
| - | ==About this Structure== | + | ==See Also== |
| - | 2TDM 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]. This structure superseeds the now removed PDB entry 1TDM. 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=2TDM OCA].
| + | *[[Thymidylate synthase 3D structures|Thymidylate synthase 3D structures]] |
| - | | + | __TOC__ |
| - | ==Reference==
| + | </StructureSection> |
| - | Refined structures of substrate-bound and phosphate-bound thymidylate synthase from Lactobacillus casei., Finer-Moore J, Fauman EB, Foster PG, Perry KM, Santi DV, Stroud RM, J Mol Biol. 1993 Aug 20;232(4):1101-16. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8371269 8371269]
| + | [[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 18:37:34 2007''
| + | |
