View source for 4apz


==Structure of B. subtilis genomic dUTPase YncF in complex with dU, PPi and Mg in P1==
<StructureSection load='4apz' size='340' side='right'caption='[[4apz]], [[Resolution|resolution]] 2.01&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[4apz]] is a 48 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=4APZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4APZ 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]] 2.01&#8491;</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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</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=4apz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4apz OCA], [https://pdbe.org/4apz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4apz RCSB], [https://www.ebi.ac.uk/pdbsum/4apz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4apz ProSAT]</span></td></tr>
</table>
== Function ==
[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).
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== 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<ref>PMID:23897460</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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<div class="pdbe-citations 4apz" style="background-color:#fffaf0;"></div>

==See Also==
*[[DUTPase 3D structures|DUTPase 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Bacillus subtilis]]
[[Category: Large Structures]]
[[Category: Garcia-Nafria J]]
[[Category: Harrison C]]
[[Category: Timm J]]
[[Category: Turkenburg JP]]
[[Category: Wilson KS]]