PDBsum entry 6yme

Transferase

PDB id: 6yme

Contents

Protein chain

425 a.a.

Ligands

GOL ×5

PEG

Waters ×473

PDB id:

6yme

Name:

Transferase

Title:

Crystal structure of serine hydroxymethyltransferase from aphanothece halophytica in the plp-internal aldimine state

Structure:

Serine hydroxymethyltransferase. Chain: a. Synonym: serine methylase. Engineered: yes

Source:

Aphanothece halophytica. Organism_taxid: 72020. Gene: glyra, glya. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

1.77Å R-factor: 0.142 R-free: 0.175

Authors:

M.Ruszkowski,B.Sekula,I.Nogues,A.Tramonti,S.Angelaccio,R.Contestabile

Key ref:

I.Nogués et al. (2020). 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. PubMed id: 32417544 DOI: 10.1016/j.ijbiomac.2020.05.081

Date:

08-Apr-20 Release date: 03-Jun-20

Protein chain

I7H6W6  (I7H6W6_APHHA) -  Serine hydroxymethyltransferase from Aphanothece halophytica

Seq: 427 a.a.

Struc: 425 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.2.1.2.1 - glycine hydroxymethyltransferase.
• Pathway: Folate Coenzymes
• Reaction: (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + glycine + H2O = (6S)- 5,6,7,8-tetrahydrofolate + L-serine

(6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + glycine + H2O = (6S)- 5,6,7,8-tetrahydrofolate + L-serine (Bound ligand (Het Group name = GOL) matches with 62.50% similarity)

• Cofactor: Pyridoxal 5'-phosphate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1016/j.ijbiomac.2020.05.081

Int J Biol Macromol 159:517-529 (2020)

PubMed id: 32417544

Structural and kinetic properties of serine hydroxymethyltransferase from the halophytic cyanobacterium Aphanothece halophytica provide a rationale for salt tolerance.

I.Nogués, A.Tramonti, S.Angelaccio, M.Ruszkowski, B.Sekula, R.Contestabile.

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.