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Structural and functional insight into serine hydroxymethyltransferase from Helicobacter pylori.
PLoS One. 2018; 13(12):e0208850.Plos

Abstract

Serine hydroxymethyltransferase (SHMT), encoded by the glyA gene, is a ubiquitous pyridoxal 5'-phosphate (PLP)-dependent enzyme that catalyzes the formation of glycine from serine. The thereby generated 5,10-methylene tetrahydrofolate (MTHF) is a major source of cellular one-carbon units and a key intermediate in thymidylate biosynthesis. While in virtually all eukaryotic and many bacterial systems thymidylate synthase ThyA, SHMT and dihydrofolate reductase (DHFR) are part of the thymidylate/folate cycle, the situation is different in organisms using flavin-dependent thymidylate synthase ThyX. Here the distinct catalytic reaction directly produces tetrahydrofolate (THF) and consequently in most ThyX-containing organisms, DHFR is absent. While the resulting influence on the folate metabolism of ThyX-containing bacteria is not fully understood, the presence of ThyX may provide growth benefits under conditions where the level of reduced folate derivatives is compromised. Interestingly, the third key enzyme implicated in generation of MTHF, serine hydroxymethyltransferase (SHMT), has a universal phylogenetic distribution, but remains understudied in ThyX-containg bacteria. To obtain functional insight into these ThyX-dependent thymidylate/folate cycles, we characterized the predicted SHMT from the ThyX-containing bacterium Helicobacter pylori. Serine hydroxymethyltransferase activity was confirmed by functional genetic complementation of a glyA-inactivated E. coli strain. A H. pylori ΔglyA strain was obtained, but exhibited markedly slowed growth and had lost the virulence factor CagA. Biochemical and spectroscopic evidence indicated formation of a characteristic enzyme-PLP-glycine-folate complex and revealed unexpectedly weak binding affinity of PLP. The three-dimensional structure of the H. pylori SHMT apoprotein was determined at 2.8Ǻ resolution, suggesting a structural basis for the low affinity of the enzyme for its cofactor. Stabilization of the proposed inactive configuration using small molecules has potential to provide a specific way for inhibiting HpSHMT.

Authors+Show Affiliations

Laboratory of Optics and Biosciences, Ecole polytechnique, CNRS, INSERM, Université Paris Saclay, Palaiseau, France.Institute for Integrative Biology of the Cell, CEA, CNRS, Université Paris Saclay, Gif-sur-Yvette, France.UMR 5086 Molecular Microbiology and Structural Biochemistry, Institut de Biologie et Chimie des Protéines, CNRS, Université de Lyon, Lyon, France.Laboratory of Optics and Biosciences, Ecole polytechnique, CNRS, INSERM, Université Paris Saclay, Palaiseau, France.Laboratory of Optics and Biosciences, Ecole polytechnique, CNRS, INSERM, Université Paris Saclay, Palaiseau, France.Laboratory of Optics and Biosciences, Ecole polytechnique, CNRS, INSERM, Université Paris Saclay, Palaiseau, France.Laboratory of Optics and Biosciences, Ecole polytechnique, CNRS, INSERM, Université Paris Saclay, Palaiseau, France. Department of Biology, Université Paris-Sud, Université Paris Saclay, Orsay, France.Laboratory of Optics and Biosciences, Ecole polytechnique, CNRS, INSERM, Université Paris Saclay, Palaiseau, France.

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

30550583

Citation

Sodolescu, Andreea, et al. "Structural and Functional Insight Into Serine Hydroxymethyltransferase From Helicobacter Pylori." PloS One, vol. 13, no. 12, 2018, pp. e0208850.
Sodolescu A, Dian C, Terradot L, et al. Structural and functional insight into serine hydroxymethyltransferase from Helicobacter pylori. PLoS One. 2018;13(12):e0208850.
Sodolescu, A., Dian, C., Terradot, L., Bouzhir-Sima, L., Lestini, R., Myllykallio, H., Skouloubris, S., & Liebl, U. (2018). Structural and functional insight into serine hydroxymethyltransferase from Helicobacter pylori. PloS One, 13(12), e0208850. https://doi.org/10.1371/journal.pone.0208850
Sodolescu A, et al. Structural and Functional Insight Into Serine Hydroxymethyltransferase From Helicobacter Pylori. PLoS One. 2018;13(12):e0208850. PubMed PMID: 30550583.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Structural and functional insight into serine hydroxymethyltransferase from Helicobacter pylori. AU - Sodolescu,Andreea, AU - Dian,Cyril, AU - Terradot,Laurent, AU - Bouzhir-Sima,Latifa, AU - Lestini,Roxane, AU - Myllykallio,Hannu, AU - Skouloubris,Stéphane, AU - Liebl,Ursula, Y1 - 2018/12/14/ PY - 2018/08/23/received PY - 2018/11/23/accepted PY - 2018/12/15/entrez PY - 2018/12/15/pubmed PY - 2019/5/7/medline SP - e0208850 EP - e0208850 JF - PloS one JO - PLoS One VL - 13 IS - 12 N2 - Serine hydroxymethyltransferase (SHMT), encoded by the glyA gene, is a ubiquitous pyridoxal 5'-phosphate (PLP)-dependent enzyme that catalyzes the formation of glycine from serine. The thereby generated 5,10-methylene tetrahydrofolate (MTHF) is a major source of cellular one-carbon units and a key intermediate in thymidylate biosynthesis. While in virtually all eukaryotic and many bacterial systems thymidylate synthase ThyA, SHMT and dihydrofolate reductase (DHFR) are part of the thymidylate/folate cycle, the situation is different in organisms using flavin-dependent thymidylate synthase ThyX. Here the distinct catalytic reaction directly produces tetrahydrofolate (THF) and consequently in most ThyX-containing organisms, DHFR is absent. While the resulting influence on the folate metabolism of ThyX-containing bacteria is not fully understood, the presence of ThyX may provide growth benefits under conditions where the level of reduced folate derivatives is compromised. Interestingly, the third key enzyme implicated in generation of MTHF, serine hydroxymethyltransferase (SHMT), has a universal phylogenetic distribution, but remains understudied in ThyX-containg bacteria. To obtain functional insight into these ThyX-dependent thymidylate/folate cycles, we characterized the predicted SHMT from the ThyX-containing bacterium Helicobacter pylori. Serine hydroxymethyltransferase activity was confirmed by functional genetic complementation of a glyA-inactivated E. coli strain. A H. pylori ΔglyA strain was obtained, but exhibited markedly slowed growth and had lost the virulence factor CagA. Biochemical and spectroscopic evidence indicated formation of a characteristic enzyme-PLP-glycine-folate complex and revealed unexpectedly weak binding affinity of PLP. The three-dimensional structure of the H. pylori SHMT apoprotein was determined at 2.8Ǻ resolution, suggesting a structural basis for the low affinity of the enzyme for its cofactor. Stabilization of the proposed inactive configuration using small molecules has potential to provide a specific way for inhibiting HpSHMT. SN - 1932-6203 UR - https://www.unboundmedicine.com/medline/citation/30550583/Structural_and_functional_insight_into_serine_hydroxymethyltransferase_from_Helicobacter_pylori_ L2 - https://dx.plos.org/10.1371/journal.pone.0208850 DB - PRIME DP - Unbound Medicine ER -