1DFO

CRYSTAL STRUCTURE AT 2.4 ANGSTROM RESOLUTION OF E. COLI SERINE HYDROXYMETHYLTRANSFERASE IN COMPLEX WITH GLYCINE AND 5-FORMYL TETRAHYDROFOLATE

1DFO の概要

• エントリーDOI: 10.2210/pdb1dfo/pdb
• 分子名称: SERINE HYDROXYMETHYLTRANSFERASE, N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE], N-[4-({[(6S)-2-amino-5-formyl-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)benzoyl]-L-glutamic acid, ... (4 entities in total)
• 機能のキーワード: alpha plp aspartate, amino transferase, (aat)-like fold, transferase
• 由来する生物種: Escherichia coli
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 184608.50

構造登録者

Scarsdale, J.N.,Radaev, S.,Kazanina, G.,Schirch, V.,Wright, H.T. (登録日: 1999-11-20, 公開日: 1999-12-10, 最終更新日: 2024-02-07)

主引用文献

Scarsdale, J.N.,Radaev, S.,Kazanina, G.,Schirch, V.,Wright, H.T.
Crystal structure at 2.4 A resolution of E. coli serine hydroxymethyltransferase in complex with glycine substrate and 5-formyl tetrahydrofolate.
J.Mol.Biol., 296:155-168, 2000

PubMed Abstract: Serine hydroxymethyltransferase (EC 2.1.2.1), a member of the alpha-class of pyridoxal phosphate enzymes, catalyzes the reversible interconversion of serine and glycine, changing the chemical bonding at the C(alpha)-C(beta) bond of the serine side-chain mediated by the pyridoxal phosphate cofactor. Scission of the C(alpha)-C(beta) bond of serine substrate produces a glycine product and most likely formaldehyde, which reacts without dissociation with tetrahydropteroylglutamate cofactor. Crystal structures of the human and rabbit cytosolic serine hydroxymethyltransferases (SHMT) confirmed their close similarity in tertiary and dimeric subunit structure to each other and to aspartate aminotransferase, the archetypal alpha-class pyridoxal 5'-phosphate enzyme. We describe here the structure at 2.4 A resolution of Escherichia coli serine hydroxymethyltransferase in ternary complex with glycine and 5-formyl tetrahydropteroylglutamate, refined to an R-factor value of 17.4 % and R(free) value of 19.6 %. This structure reveals the interactions of both cofactors and glycine substrate with the enzyme. Comparison with the E. coli aspartate aminotransferase structure shows the distinctions in sequence and structure which define the folate cofactor binding site in serine hydroxymethyltransferase and the differences in orientation of the amino terminal arm, the evolution of which was necessary for elaboration of the folate binding site. Comparison with the unliganded rabbit cytosolic serine hydroxymethyltransferase structure identifies changes in the conformation of the enzyme, similar to those observed in aspartate aminotransferase, that probably accompany the binding of substrate. The tetrameric quaternary structure of liganded E. coli serine hydroxymethyltransferase also differs in symmetry and relative disposition of the functional tight dimers from that of the unliganded eukaryotic enzymes. SHMT tetramers have surface charge distributions which suggest distinctions in folate binding between eukaryotic and E. coli enzymes. The structure of the E. coli ternary complex provides the basis for a thorough investigation of its mechanism through characterization and structure determination of site mutants.

PubMed: 10656824
DOI: 10.1006/jmbi.1999.3453

実験手法

X-RAY DIFFRACTION (2.4 Å)