Roles of adenine anchoring and ion pairing at the coenzyme B12-binding site in diol dehydratase catalysis.
The X-ray structure of the diol dehydratase-adeninylpentylcobalamin complex revealed that the adenine moiety of adenosylcobalamin is anchored in the adenine-binding pocket of the enzyme by hydrogen bonding of N3 with the side chain OH group of Seralpha224, and of 6-NH(2), N1 and N7 with main chain amide groups of other residues. A salt bridge is formed between the epsilon-NH(2) group of Lysbeta135 and the phosphate group of cobalamin. To assess the importance of adenine anchoring and ion pairing, Seralpha224 and Lysbeta135 mutants of diol dehydratase were prepared, and their catalytic properties investigated. The Salpha224A, Salpha224N and Kbeta135E mutants were 19-2% as active as the wild-type enzyme, whereas the Kbeta135A, Kbeta135Q and Kbeta135R mutants retained 58-76% of the wild-type activity. The presence of a positive charge at the beta135 residue increased the affinity for cobalamins but was not essential for catalysis, and the introduction of a negative charge there prevented the enzyme-cobalamin interaction. The Salpha224A and Salpha224N mutants showed a k(cat)/k(inact) value that was less than 2% that of the wild-type, whereas for Lysbeta135 mutants this value was in the range 25-75%, except for the Kbeta135E mutant (7%). Unlike the wild-type holoenzyme, the Salpha224N and Salpha224A holoenzymes showed very low susceptibility to oxygen in the absence of substrate. These findings suggest that Seralpha224 is important for cobalt-carbon bond activation and for preventing the enzyme from being inactivated. Upon inactivation of the Salpha224A holoenzyme during catalysis, cob(II)alamin accumulated, and a trace of doublet signal due to an organic radical disappeared in EPR. 5'-Deoxyadenosine was formed from the adenosyl group, and the apoenzyme itself was not damaged. This inactivation was thus considered to be a mechanism-based one.
Ogura
Ken-ichi
K
Department of Bioscience and Biotechnology, Graduate School of Natural Science and Technology, Okayama University, Japan.
Kunita
Shin-ichi
S
Mori
Koichi
K
Tobimatsu
Takamasa
T
Toraya
Tetsuo
T
D000225:Adenine / Q000378:metabolism*; D019943:Amino Acid Substitution; D001665:Binding Sites; D002384:Catalysis; D003038:Cobamides / Q000235:genetics / Q000378:metabolism*; D006860:Hydrogen Bonding; D007700:Kinetics; D008239:Lysine / Q000737:chemistry; D008958:Models, Molecular; D011408:Propanediol Dehydratase / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D011487:Protein Conformation; D011994:Recombinant Proteins / Q000737:chemistry / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000201:enzymology; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D012694:Serine / Q000737:chemistry; D013379:Substrate Specificity; D014805:Vitamin B 12 / Q000378:metabolism
D003038:Cobamides; D011994:Recombinant Proteins; D029701:Saccharomyces cerevisiae Proteins; D012694:Serine; D011408:Propanediol Dehydratase; C000913:cobamamide; D000225:Adenine; D008239:Lysine; D014805:Vitamin B 12