Crystal structures of BchU, a methyltransferase involved in bacteriochlorophyll c biosynthesis, and its complex with S-adenosylhomocysteine: implications for reaction mechanism.
BchU plays a role in bacteriochlorophyll c biosynthesis by catalyzing methylation at the C-20 position of cyclic tetrapyrrole chlorin using S-adenosylmethionine (SAM) as a methyl source. This methylation causes red-shifts of the electronic absorption spectrum of the light-harvesting pigment, allowing green photosynthetic bacteria to adapt to low-light environments. We have determined the crystal structures of BchU and its complex with S-adenosylhomocysteine (SAH). BchU forms a dimer and each subunit consists of two domains, an N-terminal domain and a C-terminal domain. Dimerization occurs through interactions between the N-terminal domains and the residues responsible for the catalytic reaction are in the C-terminal domain. The binding site of SAH is located in a large cavity between the two domains, where SAH is specifically recognized by many hydrogen bonds and a salt-bridge. The electron density map of BchU in complex with an analog of bacteriochlorophyll c located its central metal near the SAH-binding site, but the tetrapyrrole ring was invisible, suggesting that binding of the ring to BchU is loose and/or occupancy of the ring is low. It is likely that His290 acts as a ligand for the central metal of the substrate. The orientation of the substrate was predicted by simulation, and allows us to propose a mechanism for the BchU directed methylation: the strictly conserved Tyr246 residue acts catalytically in the direct transfer of the methyl group from SAM to the substrate through an S(N)2-like mechanism.
Wada
Kei
K
Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan.
Yamaguchi
Hitomi
H
Harada
Jiro
J
Niimi
Keiko
K
Osumi
Shigeaki
S
Saga
Yoshitaka
Y
Oh-Oka
Hirozo
H
Tamiaki
Hitoshi
H
Fukuyama
Keiichi
K
D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000096:biosynthesis* / Q000737:chemistry; D001429:Bacteriochlorophylls / Q000096:biosynthesis* / Q000737:chemistry; D001665:Binding Sites; D041883:Chlorobium / Q000201:enzymology*; D018360:Crystallography, X-Ray; D008745:Methylation; D008780:Methyltransferases / Q000737:chemistry* / Q000378:metabolism*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D020836:Protein Structure, Quaternary; D017434:Protein Structure, Tertiary; D012435:S-Adenosylhomocysteine / Q000378:metabolism*; D012436:S-Adenosylmethionine / Q000378:metabolism; D016415:Sequence Alignment; D013379:Substrate Specificity; D045725:Tetrapyrroles / Q000737:chemistry; D015032:Zinc / Q000378:metabolism
D001426:Bacterial Proteins; D001429:Bacteriochlorophylls; D045725:Tetrapyrroles; C002084:bacteriochlorophyll c; D012436:S-Adenosylmethionine; D012435:S-Adenosylhomocysteine; D008780:Methyltransferases; D015032:Zinc