5m4z: Difference between revisions
No edit summary |
No edit summary |
||
| Line 3: | Line 3: | ||
<StructureSection load='5m4z' size='340' side='right'caption='[[5m4z]], [[Resolution|resolution]] 1.18Å' scene=''> | <StructureSection load='5m4z' size='340' side='right'caption='[[5m4z]], [[Resolution|resolution]] 1.18Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[5m4z]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/ | <table><tr><td colspan='2'>[[5m4z]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Trichinella_spiralis Trichinella spiralis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5M4Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5M4Z FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=7K8:[(2~{R},3~{S},5~{R})-5-[(4~{E})-4-hydroxyimino-2-oxidanylidene-1,3-diazinan-1-yl]-3-oxidanyl-oxolan-2-yl]methyl+dihydrogen+phosphate'>7K8</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.179Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=7K8:[(2~{R},3~{S},5~{R})-5-[(4~{E})-4-hydroxyimino-2-oxidanylidene-1,3-diazinan-1-yl]-3-oxidanyl-oxolan-2-yl]methyl+dihydrogen+phosphate'>7K8</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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=5m4z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5m4z OCA], [https://pdbe.org/5m4z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5m4z RCSB], [https://www.ebi.ac.uk/pdbsum/5m4z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5m4z ProSAT]</span></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=5m4z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5m4z OCA], [https://pdbe.org/5m4z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5m4z RCSB], [https://www.ebi.ac.uk/pdbsum/5m4z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5m4z ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/Q9NDD3_TRISP Q9NDD3_TRISP] | |||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
| Line 26: | Line 27: | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: | [[Category: Trichinella spiralis]] | ||
[[Category: Dowiercial A]] | |||
[[Category: Dowiercial | [[Category: Jarmula A]] | ||
[[Category: Jarmula | [[Category: Maj P]] | ||
[[Category: Maj | [[Category: Rode W]] | ||
[[Category: Rode | [[Category: Wilk P]] | ||
[[Category: Wilk | |||
Latest revision as of 21:26, 1 November 2023
Crystal structure of the complex of T.spiralis thymidylate synthase with N(4)-hydroxy-2'-deoxycytidine-5'-monophosphate, crystallized in the presence of N(5,10)-methylenetetrahydrofolateCrystal structure of the complex of T.spiralis thymidylate synthase with N(4)-hydroxy-2'-deoxycytidine-5'-monophosphate, crystallized in the presence of N(5,10)-methylenetetrahydrofolate
Structural highlights
FunctionPublication Abstract from PubMedNovel evidence is presented allowing further clarification of the mechanism of the slow-binding thymidylate synthase (TS) inhibition by N(4)-hydroxy-dCMP (N(4)-OH-dCMP). Spectrophotometric monitoring documented time- and temperature-, and N(4)-OH-dCMP-dependent TS-catalyzed dihydrofolate production, accompanying the mouse enzyme incubation with N(4)-OH-dCMP and N(5,10)-methylenetetrahydrofolate, known to inactivate the enzyme by the covalent binding of the inhibitor, suggesting the demonstrated reaction to be uncoupled from the pyrimidine C(5) methylation. The latter was in accord with the hypothesis based on the previously presented structure of mouse TS (cf. PDB ID: 4EZ8), and with conclusions based on the present structure of the parasitic nematode Trichinella spiralis, both co-crystallized with N(4)-OH-dCMP and N(5,10)-methylenetetrahdrofolate. The crystal structure of the mouse TS-N(4)-OH-dCMP complex soaked with N(5,10)-methylenetetrahydrofolate revealed the reaction to run via a unique imidazolidine ring opening, leaving the one-carbon group bound to the N(10) atom, thus too distant from the pyrimidine C(5) atom to enable the electrophilic attack and methylene group transfer. Molecular Mechanism of Thymidylate Synthase Inhibition by N(4)-Hydroxy-dCMP in View of Spectrophotometric and Crystallographic Studies.,Maj P, Jarmula A, Wilk P, Prokopowicz M, Rypniewski W, Zielinski Z, Dowiercial A, Bzowska A, Rode W Int J Mol Sci. 2021 Apr 30;22(9). pii: ijms22094758. doi: 10.3390/ijms22094758. PMID:33946210[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
|
| ||||||||||||||||||