PDBsum entry 6uxh

Plant protein, transferase

PDB id: 6uxh

Contents

Protein chains

462 a.a.

Ligands

EDO

Waters ×382

PDB id:

6uxh

Name:

Plant protein, transferase

Title:

Structure of serine hydroxymethyltransferase 8 from glycine max cultivar essex complexed with plp

Structure:

Serine hydroxymethyltransferase. Chain: a, b. Engineered: yes

Source:

Glycine max. Soybean. Organism_taxid: 3847. Gene: shmt. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.86Å R-factor: 0.201 R-free: 0.231

Authors:

D.A.Korasick,J.J.Tanner,L.J.Beamer

Key ref:

D.A.Korasick et al. (2020). Impaired folate binding of serine hydroxymethyltransferase 8 from soybean underlies resistance to the soybean cyst nematode. J Biol Chem, 295, 3708-3718. PubMed id: 32014996 DOI: 10.1074/jbc.RA119.012256

Date:

07-Nov-19 Release date: 12-Feb-20

Protein chains

A0A0R0IK90  (A0A0R0IK90_SOYBN) -  Serine hydroxymethyltransferase from Glycine max

Seq: 541 a.a.

Struc: 462 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

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 (Bound ligand (Het Group name = EDO) matches with 50.00% similarity) + H2O = (6S)- 5,6,7,8-tetrahydrofolate + L-serine

• Cofactor: Pyridoxal 5'-phosphate

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

reference

DOI no: 10.1074/jbc.RA119.012256

J Biol Chem 295:3708-3718 (2020)

PubMed id: 32014996

Impaired folate binding of serine hydroxymethyltransferase 8 from soybean underlies resistance to the soybean cyst nematode.

D.A.Korasick, P.K.Kandoth, J.J.Tanner, M.G.Mitchum, L.J.Beamer.

ABSTRACT

Management of the agricultural pathogen soybean cyst nematode (SCN) relies on the use of SCN-resistant soybean cultivars, a strategy that has been failing in recent years. An underutilized source of resistance in the soybean genotype Peking is linked to two polymorphisms in serine hydroxy-methyltransferase 8 (SHMT8). SHMT is a pyridoxal 5'-phosphate-dependent enzyme that converts l-serine and (6S)-tetrahydrofolate to glycine and 5,10-methylenetetrahydrofolate. Here, we determined five crystal structures of the 1884-residue SHMT8 tetramers from the SCN-susceptible cultivar (cv.) Essex and the SCN-resistant cv. Forrest (whose resistance is derived from the SHMT8 polymorphisms in Peking); the crystal structures were determined in complex with various ligands at 1.4-2.35 Å resolutions. We find that the two Forrest-specific polymorphic substitutions (P130R and N358Y) impact the mobility of a loop near the entrance of the (6S)-tetrahydrofolate-binding site. Ligand-binding and kinetic studies indicate severely reduced affinity for folate and dramatically impaired enzyme activity in Forrest SHMT8. These findings imply widespread effects on folate metabolism in soybean cv. Forrest that have implications for combating the widespread increase in virulent SCN.