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| | <StructureSection load='5ioq' size='340' side='right'caption='[[5ioq]], [[Resolution|resolution]] 1.93Å' scene=''> | | <StructureSection load='5ioq' size='340' side='right'caption='[[5ioq]], [[Resolution|resolution]] 1.93Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5ioq]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Thema Thema]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IOQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5IOQ FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5ioq]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_maritima_MSB8 Thermotoga maritima MSB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IOQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5IOQ FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DUR:2-DEOXYURIDINE'>DUR</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.93Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5ior|5ior]], [[5ios|5ios]], [[5iot|5iot]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DUR:2-DEOXYURIDINE'>DUR</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">thyX, thy1, TM_0449 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243274 THEMA])</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=5ioq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ioq OCA], [https://pdbe.org/5ioq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ioq RCSB], [https://www.ebi.ac.uk/pdbsum/5ioq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ioq ProSAT]</span></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Thymidylate_synthase_(FAD) Thymidylate synthase (FAD)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.148 2.1.1.148] </span></td></tr> | + | |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ioq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ioq OCA], [http://pdbe.org/5ioq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ioq RCSB], [http://www.ebi.ac.uk/pdbsum/5ioq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ioq ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/THYX_THEMA THYX_THEMA]] Catalyzes the formation of dTMP and tetrahydrofolate from dUMP and methylenetetrahydrofolate. | + | [https://www.uniprot.org/uniprot/THYX_THEMA THYX_THEMA] Catalyzes the formation of dTMP and tetrahydrofolate from dUMP and methylenetetrahydrofolate. |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | | | |
| | ==See Also== | | ==See Also== |
| - | *[[Thymidylate synthase|Thymidylate synthase]] | + | *[[Thymidylate synthase 3D structures|Thymidylate synthase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Thema]] | + | [[Category: Thermotoga maritima MSB8]] |
| - | [[Category: Bernard, S M]] | + | [[Category: Bernard SM]] |
| - | [[Category: Smith, J L]] | + | [[Category: Smith JL]] |
| - | [[Category: Stull, F W]] | + | [[Category: Stull FW]] |
| - | [[Category: Fad-dependent]]
| + | |
| - | [[Category: Nucleotide biosynthesis]]
| + | |
| - | [[Category: Reductive methylation]]
| + | |
| - | [[Category: Transferase]]
| + | |
| Structural highlights
Function
THYX_THEMA Catalyzes the formation of dTMP and tetrahydrofolate from dUMP and methylenetetrahydrofolate.
Publication Abstract from PubMed
Many microorganisms use flavin-dependent thymidylate synthase (FDTS) to synthesize the essential nucleotide 2'-deoxythymidine 5'-monophosphate (dTMP) from 2'-deoxyuridine 5'-monophosphate (dUMP), 5,10-methylenetetrahydrofolate (CH2THF), and NADPH. FDTSs have a structure that is unrelated to the thymidylate synthase used by humans and a very different mechanism. Here we report nuclear magnetic resonance evidence that FDTS ionizes N3 of dUMP using an active-site arginine. The ionized form of dUMP is largely responsible for the changes in the flavin absorbance spectrum of FDTS upon dUMP binding. dUMP analogues also suggest that the phosphate of dUMP acts as the base that removes the proton from C5 of the dUMP-methylene intermediate in the FDTS-catalyzed reaction. These findings establish additional differences between the mechanisms of FDTS and human thymidylate synthase.
Deprotonations in the Reaction of Flavin-Dependent Thymidylate Synthase.,Stull FW, Bernard SM, Sapra A, Smith JL, Zuiderweg ER, Palfey BA Biochemistry. 2016 Jun 14;55(23):3261-9. doi: 10.1021/acs.biochem.6b00510. Epub, 2016 Jun 2. PMID:27214228[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Stull FW, Bernard SM, Sapra A, Smith JL, Zuiderweg ER, Palfey BA. Deprotonations in the Reaction of Flavin-Dependent Thymidylate Synthase. Biochemistry. 2016 Jun 14;55(23):3261-9. doi: 10.1021/acs.biochem.6b00510. Epub, 2016 Jun 2. PMID:27214228 doi:http://dx.doi.org/10.1021/acs.biochem.6b00510
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