4ooq: Difference between revisions
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==apo-dUTPase from Arabidopsis thaliana== | ==apo-dUTPase from Arabidopsis thaliana== | ||
<StructureSection load='4ooq' size='340' side='right' caption='[[4ooq]], [[Resolution|resolution]] 2.00Å' scene=''> | <StructureSection load='4ooq' size='340' side='right'caption='[[4ooq]], [[Resolution|resolution]] 2.00Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[4ooq]] is a 3 chain structure. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2p9o 2p9o]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OOQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4OOQ FirstGlance]. <br> | <table><tr><td colspan='2'>[[4ooq]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Arath Arath]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2p9o 2p9o]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OOQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4OOQ FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | ||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4oop|4oop]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4oop|4oop]]</td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">DUT, DUT1, At3g46940, T6H20.30 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</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='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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ooq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ooq OCA], [http://pdbe.org/4ooq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ooq RCSB], [http://www.ebi.ac.uk/pdbsum/4ooq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ooq 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=4ooq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ooq OCA], [http://pdbe.org/4ooq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ooq RCSB], [http://www.ebi.ac.uk/pdbsum/4ooq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ooq ProSAT]</span></td></tr> | ||
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</div> | </div> | ||
<div class="pdbe-citations 4ooq" style="background-color:#fffaf0;"></div> | <div class="pdbe-citations 4ooq" style="background-color:#fffaf0;"></div> | ||
==See Also== | |||
*[[Deoxyuridine 5'-triphosphate nucleotidohydrolase|Deoxyuridine 5'-triphosphate nucleotidohydrolase]] | |||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Arath]] | |||
[[Category: Large Structures]] | |||
[[Category: DUTP diphosphatase]] | [[Category: DUTP diphosphatase]] | ||
[[Category: Bajaj, M]] | [[Category: Bajaj, M]] | ||
Revision as of 11:09, 17 April 2019
apo-dUTPase from Arabidopsis thalianaapo-dUTPase from Arabidopsis thaliana
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 PubMedBACKGROUND: 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 AlsoReferences
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