The Crystal Structure of MT0146/CbiT Suggests that the Putative Precorrin-8w Decarboxylase Is a Methyltransferase

Abstract

The CbiT and CbiE enzymes participate in the biosynthesis of vitamin B12. They are fused together in some organisms to form a protein called CobL, which catalyzes two methylations and one decarboxylation on a precorrin intermediate. Because CbiE has sequence homology to canonical precorrin methyltransferases, CbiT was hypothesized to catalyze the decarboxylation. We herein present the crystal structure of MT0146, the CbiT homolog from Methanobacterium thermoautotrophicum. The protein shows structural similarity to Rossmann-like S-adenosyl-methionine-dependent methyltransferases, and our 1.9 A cocrystal structure shows that it binds S-adenosyl-methionine in standard geometry near a binding pocket that could accommodate a precorrin substrate. Therefore, MT0146/CbiT probably functions as a precorrin methyltransferase and represents the first enzyme identified with this activity that does not have the canonical precorrin methyltransferase fold.

Many paths to methyltransfer: a chronicle of convergence

“…It could be argued that precorrin MTases have adopted a novel conformation because of their rigid, planar substrates, however, it appears that not all tetrapyrrole biosynthetic MTases are in Class III. Precorrin-C6 MTase CbiT has [53] and protoporphyrin IX O-MTase is predicted to have a Class I structure [54]. Similarly, not all histone-lysine N-MTases contain the Class V SET domain; the Dot1 histone H3-Lys79 N-MTase belongs to Class I [55].…”

Structure/Function Studies on a S-Adenosyl-l-methionine-dependent Uroporphyrinogen III C Methyltransferase (SUMT), a Key Regulatory Enzyme of Tetrapyrrole Biosynthesis

“…5 The responsible SAM-dependent methyltransferases form an extended family of homologous enzymes, which have been structurally designated as class III methyltransferases. 20 It has been suggested that one of these methylations (at C15) is actually undertaken by precorrin-6Y methyltransferase (CbiT), 21 which belongs to a different structural family of methyltransferases, although this has yet to be proven experimentally. For the purposes of this report, we shall exclude CbiT.…”

“…Nineteen conserved residues are involved directly in the binding site of SAH/SAM. Six make up the established glycinerich region GAGPGD (21)(22)(23)(24)(25)(26) and the others are G100, G101, D102, P103, G107, V126, P127, G128, T130, G134, Y183, M184 and P241.…”

Structural Proteomics: Inferring Function from Protein Structure

“…The tetramerization domain in this protein is structurally unique, so that structure solution contributes to understanding protein fold space. Recognition of the precorrin substrate is dependent on oligomerization and so a comparative model of MT0146 would have provided limited information on enzymatic activity (Keller et al, 2002).…”

“…From in silico screening experiments, the authors suggest that proteins of this family may be involved in binding to nucleic acids or proteins. Keller et al (2002) point out that special care should be taken in structural genomics projects to re-evaluate the primary literature on which functional annotation is based. At a minimum, these authors suggest, all functional annotations in databases should cite the papers containing primary experimental data on which the annotation was based.…”