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| | ==B. subtilis dUTPase YncF in complex with dU, PPi and Mg (P212121)== | | ==B. subtilis dUTPase YncF in complex with dU, PPi and Mg (P212121)== |
| - | <StructureSection load='4aoz' size='340' side='right' caption='[[4aoz]], [[Resolution|resolution]] 2.05Å' scene=''> | + | <StructureSection load='4aoz' size='340' side='right'caption='[[4aoz]], [[Resolution|resolution]] 2.05Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4aoz]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_globigii"_migula_1900 "bacillus globigii" migula 1900]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4AOZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4AOZ FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4aoz]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4AOZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4AOZ FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DUR:2-DEOXYURIDINE'>DUR</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</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]] 2.05Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2xcd|2xcd]], [[2xce|2xce]], [[4aoo|4aoo]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DUR:2-DEOXYURIDINE'>DUR</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/dUTP_diphosphatase dUTP diphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.23 3.6.1.23] </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=4aoz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4aoz OCA], [https://pdbe.org/4aoz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4aoz RCSB], [https://www.ebi.ac.uk/pdbsum/4aoz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4aoz ProSAT]</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=4aoz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4aoz OCA], [http://pdbe.org/4aoz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4aoz RCSB], [http://www.ebi.ac.uk/pdbsum/4aoz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4aoz ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/YNCF_BACSU YNCF_BACSU]] This enzyme is involved in nucleotide metabolism: it produces dUMP, the immediate precursor of thymidine nucleotides and it decreases the intracellular concentration of dUTP so that uracil cannot be incorporated into DNA (By similarity). | + | [https://www.uniprot.org/uniprot/YNCF_BACSU YNCF_BACSU] This enzyme is involved in nucleotide metabolism: it produces dUMP, the immediate precursor of thymidine nucleotides and it decreases the intracellular concentration of dUTP so that uracil cannot be incorporated into DNA (By similarity). |
| | <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== |
| - | *[[Deoxyuridine 5'-triphosphate nucleotidohydrolase|Deoxyuridine 5'-triphosphate nucleotidohydrolase]] | + | *[[DUTPase 3D structures|DUTPase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacillus globigii migula 1900]] | + | [[Category: Bacillus subtilis]] |
| - | [[Category: DUTP diphosphatase]] | + | [[Category: Large Structures]] |
| - | [[Category: Garcia-Nafria, J]] | + | [[Category: Garcia-Nafria J]] |
| - | [[Category: Harrison, C]] | + | [[Category: Harrison C]] |
| - | [[Category: Timm, J]] | + | [[Category: Timm J]] |
| - | [[Category: Turkenburg, J P]] | + | [[Category: Turkenburg JP]] |
| - | [[Category: Wilson, K S]] | + | [[Category: Wilson KS]] |
| - | [[Category: Hydrolase]]
| + | |
| Structural highlights
4aoz is a 3 chain structure with sequence from Bacillus subtilis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 2.05Å |
| Ligands: | , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
YNCF_BACSU This enzyme is involved in nucleotide metabolism: it produces dUMP, the immediate precursor of thymidine nucleotides and it decreases the intracellular concentration of dUTP so that uracil cannot be incorporated into DNA (By similarity).
Publication Abstract from PubMed
Homotrimeric dUTPases contain three active sites, each formed by five conserved sequence motifs originating from all three subunits. The essential fifth motif lies in a flexible C-terminal arm which becomes ordered during catalysis and is disordered in most crystal structures. Previously, it has been shown that the two Bacillus subtilis dUTPases, YncF and YosS, differ from their orthologues in the position in the sequence of the essential Phe-lid residue, which stacks against the uracil base, and in the conformation of the general base aspartate, which points away from the active site. Here, three structures of the complex of YncF with dU-PPi-Mg(2+) and the structure of YosS complexed with dUMP are reported. dU-PPi-Mg(2+) triggers the ordering of both the C-terminal arm and a loop (residues 18-26) which is uniquely disordered in the Bacillus dUTPases. The dUMP complex suggests two stages in substrate release. Limited proteolysis experiments allowed those complexes in which C-terminal cleavage is hindered and those in which it can be assumed to be ordered to be identified. The results lead to the suggestion that dUpNHpp is not a perfect substrate mimic, at least for the B. subtilis enzymes, and provide new insights into the mechanism of these two dUTPases in comparison to their orthologues. The enzyme mechanism is reviewed using the present and previous crystal structures as snapshots along the reaction coordinate.
Tying down the arm in Bacillus dUTPase: structure and mechanism.,Garcia-Nafria J, Timm J, Harrison C, Turkenburg JP, Wilson KS Acta Crystallogr D Biol Crystallogr. 2013 Aug;69(Pt 8):1367-80. doi:, 10.1107/S090744491300735X. Epub 2013 Jul 13. PMID:23897460[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Garcia-Nafria J, Timm J, Harrison C, Turkenburg JP, Wilson KS. Tying down the arm in Bacillus dUTPase: structure and mechanism. Acta Crystallogr D Biol Crystallogr. 2013 Aug;69(Pt 8):1367-80. doi:, 10.1107/S090744491300735X. Epub 2013 Jul 13. PMID:23897460 doi:10.1107/S090744491300735X
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