Crystal Structure of the S-Adenosylmethionine Synthetase Ternary Complex:  A Novel Catalytic Mechanism of S-Adenosylmethionine Synthesis from ATP and Met^,

Abstract

S-Adenosylmethionine synthetase (MAT) catalyzes formation of S-adenosylmethionine (SAM) from ATP and l-methionine (Met) and hydrolysis of tripolyphosphate to PP(i) and P(i). Escherichia coli MAT (eMAT) has been crystallized with the ATP analogue AMPPNP and Met, and the crystal structure has been determined at 2.5 A resolution. eMAT is a dimer of dimers and has a 222 symmetry. Each active site contains the products SAM and PPNP. A modeling study indicates that the substrates (AMPPNP and Met) can bind at the same sites as the products, and only a small conformation change of the ribose ring is needed for conversion of the substrates to the products. On the basis of the ternary complex structure and a modeling study, a novel catalytic mechanism of SAM formation is proposed. In the mechanism, neutral His14 acts as an acid to cleave the C5'-O5' bond of ATP while simultaneously a change in the ribose ring conformation from C4'-exo to C3'-endo occurs, and the S of Met makes a nucleophilic attack on the C5' to form SAM. All essential amino acid residues for substrate binding found in eMAT are conserved in the rat liver enzyme, indicating that the bacterial and mammalian enzymes have the same catalytic mechanism. However, a catalytic mechanism proposed recently by González et al. based on the structures of three ternary complexes of rat liver MAT [González, B., Pajares, M. A., Hermoso, J. A., Guillerm, D., Guillerm, G., and Sanz-Aparicio. J. (2003) J. Mol. Biol. 331, 407] is substantially different from our mechanism.

Crystallography captures catalytic steps in human methionine adenosyltransferase enzymes

“…Despite the plethora of MAT structures that have been published (10,11,(21)(22)(23) or deposited in the PDB, to date only one structure of human MATα2 (12) (1.2 Å resolution) and of the MAT(α2) 4 (βV2) 2 complex (4) (2.35-3.3 Å resolution) have been published. The mechanism of MAT enzyme function has been described for eMAT (11), and this has become the accepted mechanism for MAT enzymes.…”

“…The mechanism of MAT enzyme function has been described for eMAT (11), and this has become the accepted mechanism for MAT enzymes. Here we present several highresolution crystallographic structures that support the overall eMAT reaction mechanism but add to it significantly by defining the movements of methionine within the active site during catalysis.…”

“…A diverse series of structures are available for MAT enzymes from bacteria, rat, and human (4,(10)(11)(12), which, supported by a range of biochemical evidence, have provided significant insight into the enzymatic mechanism. SAMe synthesis follows an SN 2 catalytic mechanism (13,14) in which the reaction is initiated through a nucleophilic attack by the sulfur atom of methionine on the C5′ atom of ATP, which produces the intermediate tripolyphosphate (PPPi).…”

“…It has been suggested that when the active site is occupied, the loop is closed like a gate, but when the active site is empty, the loop becomes invisible in the structure, presumably resulting from an open dynamic gate (11). Whether the opening of the loop/gate is required for the entry of substrate and release of products remains unclear.…”

The 4-aza-S-ribosyl-L-homocysteine Derivatives and the Related Gamma-lactam and Azahemiacetal Analogs: Synthesis, Inhibition and Quorum Sensing Activity

“…40 The SAM acts as a methyl donor in the biosynthesis and/or modification of DNA, RNA and various proteins and produces S-adenosylhomocysteine (SAdH).…”