6YMD

Crystal structure of serine hydroxymethyltransferase from Aphanothece halophytica in the covalent complex with malonate

Summary for 6YMD

• Entry DOI: 10.2210/pdb6ymd/pdb
• Descriptor: Serine hydroxymethyltransferase, 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE, 1,2-ETHANEDIOL, ... (6 entities in total)
• Functional Keywords: serine biosynthesis, glycine, plp, one-carbon metabolism, tetrahydrofolate, transferase
• Biological source: Aphanothece halophytica
• Total number of polymer chains: 2
• Total formula weight: 98368.83

Authors

Ruszkowski, M.,Sekula, B.,Nogues, I.,Tramonti, A.,Angelaccio, S.,Contestabile, R. (deposition date: 2020-04-08, release date: 2020-06-03, Last modification date: 2024-01-24)

Primary citation

Nogues, I.,Tramonti, A.,Angelaccio, S.,Ruszkowski, M.,Sekula, B.,Contestabile, R.
Structural and kinetic properties of serine hydroxymethyltransferase from the halophytic cyanobacterium Aphanothece halophytica provide a rationale for salt tolerance.
Int.J.Biol.Macromol., 159:517-529, 2020

PubMed Abstract: Serine hydroxymethyltransferase (SHMT) is a pyridoxal 5'-phosphate-dependent enzyme that plays a pivotal role in cellular one‑carbon metabolism. In plants and cyanobacteria, this enzyme is also involved in photorespiration and confers salt tolerance, as in the case of SHMT from the halophilic cyanobacterium Aphanothece halophytica (AhSHMT). We have characterized the catalytic properties of AhSHMT in different salt and pH conditions. Although the kinetic properties of AhSHMT correlate with those of the mesophilic orthologue from Escherichia coli, AhSHMT appears more catalytically efficient, especially in presence of salt. Our studies also reveal substrate inhibition, previously unobserved in AhSHMT. Furthermore, addition of the osmoprotectant glycine betaine under salt conditions has a distinct positive effect on AhSHMT activity. The crystal structures of AhSHMT in three forms, as internal aldimine, as external aldimine with the l-serine substrate, and as a covalent complex with malonate, give structural insights on the possible role of specific amino acid residues implicated in the halophilic features of AhSHMT. Importantly, we observed that overexpression of the gene encoding SHMT, independently from its origin, increases the capability of E. coli to grow in high salt conditions, suggesting that the catalytic activity of this enzyme in itself plays a fundamental role in salt tolerance.

PubMed: 32417544
DOI: 10.1016/j.ijbiomac.2020.05.081

Experimental method

X-RAY DIFFRACTION (1.25 Å)