1X1C

Crystal structure of BchU complexed with S-adenosyl-L-homocysteine and Zn2+

Summary for 1X1C

• Entry DOI: 10.2210/pdb1x1c/pdb
• Related: 1X19 1X1A 1X1B 1X1D
• Descriptor: CrtF-related protein, ZINC ION, SULFATE ION, ... (6 entities in total)
• Functional Keywords: methyltransferase, bacteriochllochlorophyll, bchu, sam, sah, s-adenosylmethyonine, s-adenosylhomocysteine, ado-met, ado-hcy, transferase
• Biological source: Chlorobium tepidum
• Total number of polymer chains: 1
• Total formula weight: 41179.84

Authors

Yamaguchi, H.,Wada, K.,Fukuyama, K. (deposition date: 2005-04-03, release date: 2006-07-18, Last modification date: 2023-10-25)

Primary citation

Wada, K.,Yamaguchi, H.,Harada, J.,Niimi, K.,Osumi, S.,Saga, Y.,Oh-Oka, H.,Tamiaki, H.,Fukuyama, K.
Crystal Structures of BchU, a Methyltransferase Involved in Bacteriochlorophyll c Biosynthesis, and its Complex with S-adenosylhomocysteine: Implications for Reaction Mechanism.
J.Mol.Biol., 360:839-849, 2006

PubMed Abstract: 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.

PubMed: 16797589
DOI: 10.1016/j.jmb.2006.05.057

Experimental method

X-RAY DIFFRACTION (2.85 Å)