2y1t: Difference between revisions
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< | ==Bacillus subtilis prophage dUTPase in complex with dUDP== | ||
<StructureSection load='2y1t' size='340' side='right'caption='[[2y1t]], [[Resolution|resolution]] 1.89Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[2y1t]] is a 6 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=2Y1T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Y1T 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]] 1.89Å</td></tr> | |||
- | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DUD:DEOXYURIDINE-5-DIPHOSPHATE'>DUD</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=2y1t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2y1t OCA], [https://pdbe.org/2y1t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2y1t RCSB], [https://www.ebi.ac.uk/pdbsum/2y1t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2y1t ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/YOSS_BACSU YOSS_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. | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
dUTPases are housekeeping enzymes which catalyse the hydrolysis of dUTP to dUMP in an ion-dependent manner. Bacillus subtilis has both a genomic and an SPbeta prophage homotrimeric dUTPase. Here, structure determination of the prophage apoenzyme and of its complexes with dUDP and dUpNHpp-Mg(2+) is described at 1.75, 1.9 and 2.55 A resolution, respectively. The C-terminal extension, which carries the conserved motif V, is disordered in all three structures. Unlike all other trimeric dUTPases for which structures are available, with the exception of the Bacillus genomic enzyme, the aromatic residue covering the uridine and acting as the Phe-lid is close to motif III in the sequence rather than in motif V. This is in spite of the presence of an aromatic amino acid at the usual Phe-lid position in motif V. The alternative position of the Phe-lid requires a reconsideration of its role in the catalytic cycle of the enzyme. In the dUpNHpp-Mg(2+) complex a water can be seen at the position expected for nucleophilic attack on the alpha-phosphate, in spite of motif V being disordered. Differences in the active site between the free enzyme and the dUDP and dUpNHpp-Mg(2+) complexes shows that the triphosphate moiety needs to be in the gauche conformation to trigger the conformational changes that can be seen in both B. subtilis dUTPases. | |||
The structure of Bacillus subtilis SPbeta prophage dUTPase and its complexes with two nucleotides.,Garcia-Nafria J, Harkiolaki M, Persson R, Fogg MJ, Wilson KS Acta Crystallogr D Biol Crystallogr. 2011 Mar;67(Pt 3):167-75. Epub 2011, Feb 15. PMID:21358047<ref>PMID:21358047</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 2y1t" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[DUTPase 3D structures|DUTPase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
== | |||
[[ | |||
== | |||
< | |||
[[Category: Bacillus subtilis]] | [[Category: Bacillus subtilis]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: Fogg | [[Category: Fogg MJ]] | ||
[[Category: Garcia-Nafria | [[Category: Garcia-Nafria J]] | ||
[[Category: Harkiolaki | [[Category: Harkiolaki M]] | ||
[[Category: Persson | [[Category: Persson R]] | ||
[[Category: Wilson | [[Category: Wilson KS]] | ||
Latest revision as of 13:43, 20 December 2023
Bacillus subtilis prophage dUTPase in complex with dUDPBacillus subtilis prophage dUTPase in complex with dUDP
Structural highlights
FunctionYOSS_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. Publication Abstract from PubMeddUTPases are housekeeping enzymes which catalyse the hydrolysis of dUTP to dUMP in an ion-dependent manner. Bacillus subtilis has both a genomic and an SPbeta prophage homotrimeric dUTPase. Here, structure determination of the prophage apoenzyme and of its complexes with dUDP and dUpNHpp-Mg(2+) is described at 1.75, 1.9 and 2.55 A resolution, respectively. The C-terminal extension, which carries the conserved motif V, is disordered in all three structures. Unlike all other trimeric dUTPases for which structures are available, with the exception of the Bacillus genomic enzyme, the aromatic residue covering the uridine and acting as the Phe-lid is close to motif III in the sequence rather than in motif V. This is in spite of the presence of an aromatic amino acid at the usual Phe-lid position in motif V. The alternative position of the Phe-lid requires a reconsideration of its role in the catalytic cycle of the enzyme. In the dUpNHpp-Mg(2+) complex a water can be seen at the position expected for nucleophilic attack on the alpha-phosphate, in spite of motif V being disordered. Differences in the active site between the free enzyme and the dUDP and dUpNHpp-Mg(2+) complexes shows that the triphosphate moiety needs to be in the gauche conformation to trigger the conformational changes that can be seen in both B. subtilis dUTPases. The structure of Bacillus subtilis SPbeta prophage dUTPase and its complexes with two nucleotides.,Garcia-Nafria J, Harkiolaki M, Persson R, Fogg MJ, Wilson KS Acta Crystallogr D Biol Crystallogr. 2011 Mar;67(Pt 3):167-75. Epub 2011, Feb 15. PMID:21358047[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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