2e0n: Difference between revisions
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'''Crystal structure of CbiL in complex with S-adenosylhomocysteine, a methyltransferase involved in anaerobic vitamin B12 biosynthesis''' | {{Structure | ||
|PDB= 2e0n |SIZE=350|CAPTION= <scene name='initialview01'>2e0n</scene>, resolution 2.00Å | |||
|SITE= | |||
|LIGAND= <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene> | |||
|ACTIVITY= [http://en.wikipedia.org/wiki/Precorrin-2_C(20)-methyltransferase Precorrin-2 C(20)-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.130 2.1.1.130] | |||
|GENE= cbiL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1097 Chlorobaculum tepidum]) | |||
}} | |||
'''Crystal structure of CbiL in complex with S-adenosylhomocysteine, a methyltransferase involved in anaerobic vitamin B12 biosynthesis''' | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
2E0N is a [ | 2E0N is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Chlorobaculum_tepidum Chlorobaculum tepidum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E0N OCA]. | ||
==Reference== | ==Reference== | ||
Crystal structures of CbiL, a methyltransferase involved in anaerobic vitamin B biosynthesis, and CbiL in complex with S-adenosylhomocysteine--implications for the reaction mechanism., Wada K, Harada J, Yaeda Y, Tamiaki H, Oh-Oka H, Fukuyama K, FEBS J. 2007 Jan;274(2):563-73. PMID:[http:// | Crystal structures of CbiL, a methyltransferase involved in anaerobic vitamin B biosynthesis, and CbiL in complex with S-adenosylhomocysteine--implications for the reaction mechanism., Wada K, Harada J, Yaeda Y, Tamiaki H, Oh-Oka H, Fukuyama K, FEBS J. 2007 Jan;274(2):563-73. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17229157 17229157] | ||
[[Category: Chlorobaculum tepidum]] | [[Category: Chlorobaculum tepidum]] | ||
[[Category: Precorrin-2 C(20)-methyltransferase]] | [[Category: Precorrin-2 C(20)-methyltransferase]] | ||
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[[Category: tetrapyrrole]] | [[Category: tetrapyrrole]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 16:33:48 2008'' | ||
Revision as of 14:33, 20 March 2008
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| 2e0n, resolution 2.00Å | |||||||||||||
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| Ligands: | SAH | ||||||||||||
| Gene: | cbiL (Chlorobaculum tepidum) | ||||||||||||
| Activity: | Precorrin-2 C(20)-methyltransferase, with EC number 2.1.1.130 | ||||||||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||||||||
Crystal structure of CbiL in complex with S-adenosylhomocysteine, a methyltransferase involved in anaerobic vitamin B12 biosynthesis
Overview
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.
About this Structure
2E0N is a Single protein structure of sequence from Chlorobaculum tepidum. Full crystallographic information is available from OCA.
Reference
Crystal structures of CbiL, a methyltransferase involved in anaerobic vitamin B biosynthesis, and CbiL in complex with S-adenosylhomocysteine--implications for the reaction mechanism., Wada K, Harada J, Yaeda Y, Tamiaki H, Oh-Oka H, Fukuyama K, FEBS J. 2007 Jan;274(2):563-73. PMID:17229157
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