2E0K: Crystal Structure Of Cbil, A Methyltransferase Involved In Anaerobic Vitamin B12 Biosynthesis

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.
PDB ID: 2E0KDownload
MMDB ID: 43729
PDB Deposition Date: 2006/10/10
Updated in MMDB: 2012/11
Experimental Method:
x-ray diffraction
Resolution: 2.1  Å
Source Organism:
Similar Structures:
Biological Unit for 2E0K: dimeric; determined by author and by software (PISA)
Molecular Components in 2E0K
Label Count Molecule
Proteins (2 molecules)
Precorrin-2 C20-methyltransferase
Molecule annotation
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Citing MMDB