Crystal structure of aminomethyltransferase in complex with dihydrolipoyl-H-protein of the glycine cleavage system: implications for recognition of lipoyl protein substrate, disease-related mutations, and reaction mechanism.
Aminomethyltransferase, a component of the glycine cleavage system termed T-protein, reversibly catalyzes the degradation of the aminomethyl moiety of glycine attached to the lipoate cofactor of H-protein, resulting in the production of ammonia, 5,10-methylenetetrahydrofolate, and dihydrolipoate-bearing H-protein in the presence of tetrahydrofolate. Several mutations in the human T-protein gene are known to cause nonketotic hyperglycinemia. Here, we report the crystal structure of Escherichia coli T-protein in complex with dihydrolipoate-bearing H-protein and 5-methyltetrahydrofolate, a complex mimicking the ternary complex in the reverse reaction. The structure of the complex shows a highly interacting intermolecular interface limited to a small area and the protein-bound dihydrolipoyllysine arm inserted into the active site cavity of the T-protein. Invariant Arg(292) of the T-protein is essential for complex assembly. The structure also provides novel insights in understanding the disease-causing mutations, in addition to the disease-related impairment in the cofactor-enzyme interactions reported previously. Furthermore, structural and mutational analyses suggest that the reversible transfer of the methylene group between the lipoate and tetrahydrofolate should proceed through the electron relay-assisted iminium intermediate formation.
Okamura-Ikeda
Kazuko
K
Institute for Enzyme Research, the University of Tokushima, Tokushima 770-8503, Japan. ikeda@ier.tokushima-u.ac.jp
Hosaka
Harumi
H
Maita
Nobuo
N
Fujiwara
Kazuko
K
Yoshizawa
Akiyasu C
AC
Nakagawa
Atsushi
A
Taniguchi
Hisaaki
H
D050960:Aminomethyltransferase / Q000737:chemistry*; D001120:Arginine / Q000737:chemistry; D001426:Bacterial Proteins / Q000737:chemistry*; D002384:Catalysis; D020134:Catalytic Domain; D018360:Crystallography, X-Ray / Q000379:methods; D004252:DNA Mutational Analysis; D004268:DNA-Binding Proteins / Q000737:chemistry*; D019281:Dimerization; D004926:Escherichia coli / Q000378:metabolism; D005492:Folic Acid / Q000737:chemistry; D005998:Glycine / Q000737:chemistry; D006943:Hyperglycemia / Q000378:metabolism; D007097:Imines / Q000737:chemistry; D008958:Models, Molecular; D009154:Mutation
D001426:Bacterial Proteins; D004268:DNA-Binding Proteins; D007097:Imines; C040330:histone-like protein HU, bacteria; D005492:Folic Acid; D001120:Arginine; D050960:Aminomethyltransferase; D005998:Glycine