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Literature summary extracted from

  • Pang, J.; Scrutton, N.S.; Sutcliffe, M.J.
    Quantum mechanics/molecular mechanics studies on the mechanism of action of cofactor pyridoxal 5-phosphate in ornithine 4,5-aminomutase (2014), Chemistry, 20, 11390-11401 .
    View publication on PubMed

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
5.4.3.5 D-ornithine Acetoanaerobium sticklandii
-
 (2R,4S)-2,4-diaminopentanoate
-
 r

Organism

EC Number Organism UniProt Comment Textmining
5.4.3.5 Acetoanaerobium sticklandii E3PY95 AND E3PY96 subunits beta and alpha; i.e. Clostridium sticklandii
-

Reaction

EC Number Reaction Comment Organism Reaction ID
5.4.3.5 D-ornithine = (2R,4S)-2,4-diaminopentanoate the proposed catalytic cycle of OAM starts with substrate binding, which triggers homolytic rupture of the Co-C bond to generate cob(II)alamin and the transient 5'-deoxyadenosyl radical (AdoCH2C), which subsequently abstracts a hydrogen atom from the pyridoxal 5'-phosphate-bound substrate. This results in a pyridoxal 5'-phosphate-bound substrate radical (CYC-1) that isomerises to form a pyridoxal 5'-phosphate-bound product radical (CYC+1) via a cyclic aziridinylcarbinyl intermediate (CYC). Re-abstraction of the hydrogen atom from 5'-deoxyadenosine (AdoCH3) by CYC+1 produces AdoCH2C, which recombines with cob(II)alamin to regenerate the 5'-deoxyadenosylcobalamin Co-C bond Acetoanaerobium sticklandii
a

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
5.4.3.5 D-ornithine
-
 Acetoanaerobium sticklandii (2R,4S)-2,4-diaminopentanoate
-
 r

Synonyms

EC Number Synonyms Comment Organism
5.4.3.5 OAM
-
 Acetoanaerobium sticklandii
5.4.3.5 oraE
-
 Acetoanaerobium sticklandii
5.4.3.5 oraS
-
 Acetoanaerobium sticklandii

Cofactor

EC Number Cofactor Comment Organism Structure
5.4.3.5 5'-deoxyadenosylcobalamin
-
 Acetoanaerobium sticklandii
5.4.3.5 pyridoxal 5'-phosphate quantum mechanics/molecular mechanics (QM/MM) studies on the mechanism of action of cofactor pyridoxal 5'-phosphate in ornithine 4,5-aminomutase, overview Acetoanaerobium sticklandii

General Information

EC Number General Information Comment Organism
5.4.3.5 additional information computational study on the experimentally elusive cyclisation step in the cofactor pyridoxal 5'-phosphate-dependent D-ornithine 4,5-aminomutase-catalysed reaction, quantum mechanics/molecular mechanics (QM/MM) studies on the mechanism of action of cofactor pyridoxal 5-phosphate in ornithine 4,5-aminomutase, modeling, overview. Calculations using both model systems and a combined QM/MM approach suggest that regulation of the cyclic radical intermediate is achieved through the synergy of the intrinsic catalytic power of cofactor pyridoxal 5'-phosphate and enzyme active site. The captodative effect of pyridoxal 5'-phosphate is balanced by an enzyme active site that controls the deprotonation of both the pyridine nitrogen atom (N1) and the Schiff-base nitrogen atom (N2). Electrostatic interactions between the terminal carboxylate and amino groups of the substrate and Arg297 and Glu81 impose substantial strain energy on the orientation of the cyclic intermediate to control its trajectory. In addition the strain energy, which appears to be sensitive to both the number of carbon atoms in the substrate/analogue and the position of the radical intermediates, may play a key role in controlling the transition of the enzyme from the closed to the open state Acetoanaerobium sticklandii