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| | ==Arabidopsis thaliana dUTPase with with magnesium and alpha,beta-imido-dUTP== | | ==Arabidopsis thaliana dUTPase with with magnesium and alpha,beta-imido-dUTP== |
| - | <StructureSection load='4oop' size='340' side='right' caption='[[4oop]], [[Resolution|resolution]] 1.50Å' scene=''> | + | <StructureSection load='4oop' size='340' side='right'caption='[[4oop]], [[Resolution|resolution]] 1.50Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4oop]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OOP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4OOP FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4oop]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OOP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4OOP FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DUP:2-DEOXYURIDINE+5-ALPHA,BETA-IMIDO-TRIPHOSPHATE'>DUP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 1.5Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4ooq|4ooq]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DUP:2-DEOXYURIDINE+5-ALPHA,BETA-IMIDO-TRIPHOSPHATE'>DUP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=4oop FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4oop OCA], [https://pdbe.org/4oop PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4oop RCSB], [https://www.ebi.ac.uk/pdbsum/4oop PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4oop 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=4oop FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4oop OCA], [http://pdbe.org/4oop PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4oop RCSB], [http://www.ebi.ac.uk/pdbsum/4oop PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4oop ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/DUT_ARATH DUT_ARATH]] This enzyme is involved in nucleotide metabolism: it produces dUMP, the immediate precursor of thymidine nucleotides and it decreases the intracellular concentration of dUTP, preventing uracil incorporation into DNA.<ref>PMID:20227352</ref> | + | [https://www.uniprot.org/uniprot/DUT_ARATH DUT_ARATH] This enzyme is involved in nucleotide metabolism: it produces dUMP, the immediate precursor of thymidine nucleotides and it decreases the intracellular concentration of dUTP, preventing uracil incorporation into DNA.<ref>PMID:20227352</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </div> | | </div> |
| | <div class="pdbe-citations 4oop" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 4oop" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[DUTPase 3D structures|DUTPase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: DUTP diphosphatase]] | + | [[Category: Arabidopsis thaliana]] |
| - | [[Category: Bajaj, M]] | + | [[Category: Large Structures]] |
| - | [[Category: Inoguchi, N]] | + | [[Category: Bajaj M]] |
| - | [[Category: Moriyama, H]] | + | [[Category: Inoguchi N]] |
| - | [[Category: Dutp]] | + | [[Category: Moriyama H]] |
| - | [[Category: Dutpase]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Hydrolysis]]
| + | |
| Structural highlights
Function
DUT_ARATH This enzyme is involved in nucleotide metabolism: it produces dUMP, the immediate precursor of thymidine nucleotides and it decreases the intracellular concentration of dUTP, preventing uracil incorporation into DNA.[1]
Publication Abstract from PubMed
BACKGROUND: Deoxyuridine triphosphate nucleotidohydrolase (dUTPase) hydrolyzes dUTP to dUMP and pyrophosphate to maintain the cellular thymine-uracil ratio. dUTPase is also a target for cancer chemotherapy. However, the mechanism defining its substrate affinity remains unclear. Sequence comparisons of various dUTPases revealed that Arabidopsis thaliana dUTPase has a unique tryptophan at position 93, which potentially contributes to its degree of substrate affinity. To better understand the roles of tryptophan 93, A. thaliana dUTPase was studied. RESULTS: Enzyme assays showed that A. thaliana dUTPase belongs to a high-affinity group of isozymes, which also includes the enzymes from Escherichia coli and Mycobacterium tuberculosis. Enzymes from Homo sapiens and Saccharomyces cerevisiae are grouped as low-affinity dUTPases. The structure of the homo-trimeric A. thaliana dUTPase showed three active sites, each with a different set of ligand interactions between the amino acids and water molecules. On an alpha-helix, tryptophan 93 appears to keep serine 89 in place via a water molecule and to specifically direct the ligand. Upon being oriented in the active site, the C-terminal residues close the active site to promote the reaction. CONCLUSIONS: In the high-affinity group, the prefixed direction of the serine residues was oriented by a positively charged residue located four amino acids away, while low-affinity enzymes possess small hydrophobic residues at the corresponding sites.
Structural insights into the mechanism defining substrate affinity in Arabidopsis thaliana dUTPase: the role of tryptophan 93 in ligand orientation.,Inoguchi N, Chaiseeda K, Yamanishi M, Kim MK, Jang Y, Bajaj M, Chia CP, Becker DF, Moriyama H BMC Res Notes. 2015 Dec 15;8:784. doi: 10.1186/s13104-015-1760-1. PMID:26666293[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Siaud N, Dubois E, Massot S, Richaud A, Dray E, Collier J, Doutriaux MP. The SOS screen in Arabidopsis: a search for functions involved in DNA metabolism. DNA Repair (Amst). 2010 May 4;9(5):567-78. doi: 10.1016/j.dnarep.2010.02.009., Epub 2010 Mar 12. PMID:20227352 doi:http://dx.doi.org/10.1016/j.dnarep.2010.02.009
- ↑ Inoguchi N, Chaiseeda K, Yamanishi M, Kim MK, Jang Y, Bajaj M, Chia CP, Becker DF, Moriyama H. Structural insights into the mechanism defining substrate affinity in Arabidopsis thaliana dUTPase: the role of tryptophan 93 in ligand orientation. BMC Res Notes. 2015 Dec 15;8:784. doi: 10.1186/s13104-015-1760-1. PMID:26666293 doi:http://dx.doi.org/10.1186/s13104-015-1760-1
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