Crystal structures of CbiL, a methyltransferase involved in anaerobic vitamin B biosynthesis, and CbiL in complex with S-adenosylhomocysteine--implications for the reaction mechanism.
During anaerobic cobalamin (vitamin B12) biosynthesis, CbiL catalyzes methylation at the C-20 position of a cyclic tetrapyrrole ring using S-adenosylmethionine as a methyl group source. This methylation is a key modification for the ring contraction process, by which a porphyrin-type tetrapyrrole ring is converted to a corrin ring through elimination of the modified C-20 and direct bonding of C-1 to C-19. We have determined the crystal structures of Chlorobium tepidum CbiL and CbiL in complex with S-adenosylhomocysteine (the S-demethyl form of S-adenosylmethionine). CbiL forms a dimer in the crystal, and each subunit consists of N-terminal and C-terminal domains. S-Adenosylhomocysteine binds to a cleft between the two domains, where it is specifically recognized by extensive hydrogen bonding and van der Waals interactions. The orientation of the cobalt-factor II substrate was modeled by simulation, and the predicted model suggests that the hydroxy group of Tyr226 is located in close proximity to the C-20 atom as well as the C-1 and C-19 atoms of the tetrapyrrole ring. These configurations allow us to propose a catalytic mechanism: the conserved Tyr226 residue in CbiL catalyzes the direct transfer of a methyl group from S-adenosylmethionine to the substrate through an S(N)2-like mechanism. Furthermore, the structural model of CbiL binding to its substrate suggests the axial residue coordinated to the central cobalt of cobalt-factor II.
Wada
Kei
K
Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Japan. keiwada@bio.sci.osaka-u.ac.jp
Harada
Jiro
J
Yaeda
Yuki
Y
Tamiaki
Hitoshi
H
Oh-Oka
Hirozo
H
Fukuyama
Keiichi
K
D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry*; D041883:Chlorobium / Q000378:metabolism*; D003035:Cobalt / Q000737:chemistry; D018360:Crystallography, X-Ray; D008745:Methylation; D008780:Methyltransferases / Q000737:chemistry* / Q000378:metabolism; D008969:Molecular Sequence Data; D020836:Protein Structure, Quaternary; D017434:Protein Structure, Tertiary; D012435:S-Adenosylhomocysteine / Q000737:chemistry*; D012436:S-Adenosylmethionine / Q000737:chemistry; D017386:Sequence Homology, Amino Acid; D013379:Substrate Specificity; D014803:Vitamin B Complex / Q000096:biosynthesis*
D001426:Bacterial Proteins; D014803:Vitamin B Complex; D003035:Cobalt; D012436:S-Adenosylmethionine; D012435:S-Adenosylhomocysteine; D008780:Methyltransferases