Structural and functional insight into serine hydroxymethyltransferase from Helicobacter pylori

PLoS One. 2018 Dec 14;13(12):e0208850. doi: 10.1371/journal.pone.0208850. eCollection 2018.


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacterial Proteins* / chemistry
  • Bacterial Proteins* / genetics
  • Bacterial Proteins* / metabolism
  • Catalysis
  • Escherichia coli / enzymology
  • Escherichia coli / genetics
  • Folic Acid / chemistry
  • Folic Acid / genetics
  • Folic Acid / metabolism
  • Genetic Complementation Test
  • Glycine / chemistry
  • Glycine / genetics
  • Glycine / metabolism
  • Glycine Hydroxymethyltransferase* / chemistry
  • Glycine Hydroxymethyltransferase* / genetics
  • Glycine Hydroxymethyltransferase* / metabolism
  • Helicobacter pylori* / enzymology
  • Helicobacter pylori* / genetics
  • Protein Domains


  • Bacterial Proteins
  • Folic Acid
  • Glycine Hydroxymethyltransferase
  • Glycine

Grant support

This work was supported by the Agence Nationale de la Recherche grant PCV07_189094 to UL and HM. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.