Structural insights into the mechanism defining substrate affinity in Arabidopsis thaliana dUTPase: the role of tryptophan 93 in ligand orientation

Details

• Alternative Title:
  BMC Res Notes
• Personal Author:
  Inoguchi, Noriko ; Chaiseeda, Kittichai ; Yamanishi, Mamoru ; Kim, Moon Ki ; Jang, Yunho ; Bajaj, Mamta ; Chia, Catherine P. ; Becker, Donald F. ; Moriyama, Hideaki
• Description:
  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 α-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. ; Electronic supplementary material ; The online version of this article (doi:10.1186/s13104-015-1760-1) contains supplementary material, which is available to authorized users.
• Subjects:
  • Amino Acid Sequence
  • Arabidopsis
  • Arabidopsis Proteins
  • Binding Sites
  • Binding, Competitive
  • Catalytic Domain
  • Crystallography, X-Ray
  • Hydrophobic and Hydrophilic Interactions
  • Ligands
  • Models, Molecular
  More +
• Source:
  BMC Res Notes. 8.
• Pubmed ID:
  26666293
• Pubmed Central ID:
  PMC4678481
• Document Type:
  Journal Article
• Volume:
  8
• Download URL:
  https://stacks.cdc.gov/view/cdc/36938/cdc_36938_DS1.pdf
• File Type:
  [PDF - 1.64 MB]
• Collection(s):
  CDC Public Access
• Main Document Checksum:
  urn:sha256:00dbda34c940988600cd814cc81f25522022661958bebf428f6dd87beafee738