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

Inoguchi, Noriko; Chaiseeda, Kittichai; Yamanishi, Mamoru; Kim, Moon Ki; Jang, Yunho; Bajaj, Mamta; Chia, Catherine P.; Becker, Donald F.; Moriyama, Hideaki

doi:10.1186/s13104-015-1760-1

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

Journal Article · Tue Dec 15 00:00:00 EST 2015 · BMC Research Notes

DOI:https://doi.org/10.1186/s13104-015-1760-1· OSTI ID:1241070

Inoguchi, Noriko ^[1]; Chaiseeda, Kittichai ^[1]; Yamanishi, Mamoru ^[1]; Kim, Moon Ki ^[2]; Jang, Yunho ^[3]; Bajaj, Mamta ^[1]; Chia, Catherine P. ^[1]; Becker, Donald F. ^[1]; Moriyama, Hideaki ^[1]

Univ. of Nebraska, Lincoln, NE (United States)
Sungkyunkwan Univ., Suwon (South Korea)
Centers for Disease Control and Prevention, Atlanta, GA (United States); Univ. of Massachusetts, Amherst, MA (United States)

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. 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. 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.

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Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES). Scientific User Facilities Division

Grant/Contract Number:: AC02-06CH11357

OSTI ID:: 1241070

Journal Information:: BMC Research Notes, Vol. 8, Issue 1; ISSN 1756-0500

Publisher:: BioMed CentralCopyright Statement

Country of Publication:: United States

Language:: ENGLISH

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Enzyme kinetics of dUTPase from the planarian Dugesia ryukyuensis Alam, Md. Shahanoor; Moriyama, Hideaki; Matsumoto, Midori BMC Research Notes, Vol. 12, Issue 1 https://doi.org/10.1186/s13104-019-4191-6	journal	March 2019
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Mitochondrial localization of Dictyostelium discoideum dUTPase mediated by its N-terminus Chia, Catherine P.; Inoguchi, Noriko; Varon, Kyle C. BMC Research Notes, Vol. 13, Issue 1 https://doi.org/10.1186/s13104-019-4879-7	journal	January 2020
Mitochondrial localization of Dictyostelium discoideum dUTPase mediated by its N-terminus Chia, Catherine; Inoguchi, Noriko; Varon, Kyle C. BMC Research Notes https://doi.org/10.21203/rs.2.13015/v1	posted_content	January 2020

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Related Subjects

59 BASIC BIOLOGICAL SCIENCES
Deoxyuridine triphosphate nucleotidohydrolase
Substrate affinity
Drug targets
Arabidopsis thaliana

Structural insights into the mechanism defining substrate affinity in Arabidopsis thaliana dUTPase: the role of tryptophan 93 in ligand orientation Inoguchi, Noriko; Chaiseeda, Kittichai; Yamanishi, Mamoru https://doi.org/10.6084/m9.figshare.c.3633239.v1 The current record is supplemented by this collection	collection	January 2015
MOESM3 of Structural insights into the mechanism defining substrate affinity in Arabidopsis thaliana dUTPase: the role of tryptophan 93 in ligand orientation Inoguchi, Noriko; Chaiseeda, Kittichai; Yamanishi, Mamoru https://doi.org/10.6084/m9.figshare.c.3633239_d1 The current record is supplemented by this text	text	January 2015
MOESM2 of Structural insights into the mechanism defining substrate affinity in Arabidopsis thaliana dUTPase: the role of tryptophan 93 in ligand orientation Inoguchi, Noriko; Chaiseeda, Kittichai; Yamanishi, Mamoru https://doi.org/10.6084/m9.figshare.c.3633239_d3 The current record is supplemented by this text	text	January 2015
MOESM1 of Structural insights into the mechanism defining substrate affinity in Arabidopsis thaliana dUTPase: the role of tryptophan 93 in ligand orientation Inoguchi, Noriko; Chaiseeda, Kittichai; Yamanishi, Mamoru https://doi.org/10.6084/m9.figshare.c.3633239_d2.v1 The current record is supplemented by this text	text	January 2015
MOESM3 of Structural insights into the mechanism defining substrate affinity in Arabidopsis thaliana dUTPase: the role of tryptophan 93 in ligand orientation Inoguchi, Noriko; Chaiseeda, Kittichai; Yamanishi, Mamoru https://doi.org/10.6084/m9.figshare.c.3633239_d1.v1 The current record is supplemented by this text	text	January 2015
Structural insights into the mechanism defining substrate affinity in Arabidopsis thaliana dUTPase: the role of tryptophan 93 in ligand orientation Inoguchi, Noriko; Chaiseeda, Kittichai; Yamanishi, Mamoru https://doi.org/10.6084/m9.figshare.c.3633239 The current record is supplemented by this collection	collection	January 2015
MOESM2 of Structural insights into the mechanism defining substrate affinity in Arabidopsis thaliana dUTPase: the role of tryptophan 93 in ligand orientation Inoguchi, Noriko; Chaiseeda, Kittichai; Yamanishi, Mamoru https://doi.org/10.6084/m9.figshare.c.3633239_d3.v1 The current record is supplemented by this text	text	January 2015
MOESM1 of Structural insights into the mechanism defining substrate affinity in Arabidopsis thaliana dUTPase: the role of tryptophan 93 in ligand orientation Inoguchi, Noriko; Chaiseeda, Kittichai; Yamanishi, Mamoru https://doi.org/10.6084/m9.figshare.c.3633239_d2 The current record is supplemented by this text	text	January 2015