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Literature summary for 5.4.3.3 extracted from

  • Chen, Y.H.; Maity, A.N.; Frey, P.A.; Ke, S.C.
    Mechanism-based inhibition reveals transitions between two conformational states in the action of lysine 5,6-aminomutase: a combination of electron paramagnetic resonance spectroscopy, electron nuclear double resonance spectroscopy, and density functional (2013), J. Am. Chem. Soc., 135, 788-794.
    View publication on PubMed

Inhibitors

Inhibitors Comment Organism Structure
additional information homologues of substrate D-lysine, D-2,5-diaminopentanoic acid, 2,4-diaminobutyric acid, and D-2,3-diaminopropionic acid bind to pyridoxal 5'-phosphate as an external aldimine and elicit the 5'-deoxyadenosylcobalamin Co-C bond homolysis and the accumulations of cob(II)alamin and analogue-based radicals. The position for hydrogen atom abstraction from D-2,5-diaminopentanoic acid and 2,4-diaminobutyric acid by the 5'-deoxyadenosyl radical occurs at the carbon adjacent to the imine, resulting in overstabilized radicals by spin delocalization through the imine into the pyridine ring of pyridoxal 5'-phosphate. These radicals block the active site, inhibit the enzyme, and poise the enzyme into two distinct conformations: for even-numbered analogues, the cob(II)alamin remains proximal to and spin-coupled with the analogue-based radical in the closed state while odd-numbered analogues trigger the transition to the open state of the enzyme, inactivation mechanism, overview Acetoanaerobium sticklandii
additional information homologues of substrate D-lysine, D-2,5-diaminopentanoic acid, 2,4-diaminobutyric acid, and D-2,3-diaminopropionic acid bind to pyridoxal 5'-phosphate as an external aldimine and elicit the 5'-deoxyadenosylcobalamin Co-C bond homolysis and the accumulations of cob(II)alamin and analogue-based radicals. The position for hydrogen atom abstraction from D-2,5-diaminopentanoic acid and 2,4-diaminobutyric acid by the 5'-deoxyadenosyl radical occurs at the carbon adjacent to the imine, resulting in overstabilized radicals by spin delocalization through the imine into the pyridine ring of pyridoxal 5'-phosphate. These radicals block the active site, inhibit the enzyme, and poise the enzyme into two distinct conformations: for even-numbered analogues, the cob(II)alamin remains proximal to and spin-coupled with the analogue-based radical in the closed state while odd-numbered analogues trigger the transition to the open state of the enzyme, inactivation mechanism, overview Propionibacterium freudenreichii

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
(3S)-3,6-diaminohexanoate Acetoanaerobium sticklandii
-
(3S,5S)-3,5-diaminohexanoate
-
r
(3S)-3,6-diaminohexanoate Propionibacterium freudenreichii
-
(3S,5S)-3,5-diaminohexanoate
-
r
(3S)-3,6-diaminohexanoate Propionibacterium freudenreichii ATCC 9614
-
(3S,5S)-3,5-diaminohexanoate
-
r
(3S)-3,6-diaminohexanoate Acetoanaerobium sticklandii StadtmanHF
-
(3S,5S)-3,5-diaminohexanoate
-
r
D-lysine Acetoanaerobium sticklandii
-
2,5-diaminohexanoate
-
r
D-lysine Propionibacterium freudenreichii
-
2,5-diaminohexanoate
-
r
D-lysine Propionibacterium freudenreichii ATCC 9614
-
2,5-diaminohexanoate
-
r
D-lysine Acetoanaerobium sticklandii StadtmanHF
-
2,5-diaminohexanoate
-
r

Organism

Organism UniProt Comment Textmining
Acetoanaerobium sticklandii
-
-
-
Acetoanaerobium sticklandii StadtmanHF
-
-
-
Propionibacterium freudenreichii
-
subsp. shermanii
-
Propionibacterium freudenreichii ATCC 9614
-
subsp. shermanii
-

Reaction

Reaction Comment Organism Reaction ID
(3S)-3,6-diaminohexanoate = (3S,5S)-3,5-diaminohexanoate catalytic mechanism, the closed-state of the enzyme is required to bring the cofactors adenosylcobalamin and pyridoxal 5'-phosphate and the substrate into proximity for the radical-mediated 1,2-amino group migration. This process is achieved by transaldimination of the pyridoxal 5'-phosphate-Lys144beta internal aldimine with the pyridoxal 5'-phosphate-substrate external aldimine Acetoanaerobium sticklandii
(3S)-3,6-diaminohexanoate = (3S,5S)-3,5-diaminohexanoate catalytic mechanism, the closed-state of the enzyme is required to bring the cofactors adenosylcobalamin and pyridoxal 5'-phosphate and the substrate into proximity for the radical-mediated 1,2-amino group migration. This process is achieved by transaldimination of the pyridoxal 5'-phosphate-Lys144beta internal aldimine with the pyridoxal 5'-phosphate-substrate external aldimine Propionibacterium freudenreichii
D-lysine = (2R,5S)-2,5-diaminohexanoate catalytic mechanism, the closed-state of the enzyme is required to bring the cofactors adenosylcobalamin and pyridoxal 5'-phosphate and the substrate into proximity for the radical-mediated 1,2-amino group migration. This process is achieved by transaldimination of the pyridoxal 5'-phosphate-Lys144beta internal aldimine with the pyridoxal 5'-phosphate-substrate external aldimine Acetoanaerobium sticklandii
D-lysine = (2R,5S)-2,5-diaminohexanoate catalytic mechanism, the closed-state of the enzyme is required to bring the cofactors adenosylcobalamin and pyridoxal 5'-phosphate and the substrate into proximity for the radical-mediated 1,2-amino group migration. This process is achieved by transaldimination of the pyridoxal 5'-phosphate-Lys144beta internal aldimine with the pyridoxal 5'-phosphate-substrate external aldimine Propionibacterium freudenreichii

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
(3S)-3,6-diaminohexanoate
-
Acetoanaerobium sticklandii (3S,5S)-3,5-diaminohexanoate
-
r
(3S)-3,6-diaminohexanoate
-
Propionibacterium freudenreichii (3S,5S)-3,5-diaminohexanoate
-
r
(3S)-3,6-diaminohexanoate
-
Propionibacterium freudenreichii ATCC 9614 (3S,5S)-3,5-diaminohexanoate
-
r
(3S)-3,6-diaminohexanoate
-
Acetoanaerobium sticklandii StadtmanHF (3S,5S)-3,5-diaminohexanoate
-
r
D-lysine
-
Acetoanaerobium sticklandii 2,5-diaminohexanoate
-
r
D-lysine
-
Propionibacterium freudenreichii 2,5-diaminohexanoate
-
r
D-lysine
-
Propionibacterium freudenreichii ATCC 9614 2,5-diaminohexanoate
-
r
D-lysine
-
Acetoanaerobium sticklandii StadtmanHF 2,5-diaminohexanoate
-
r
additional information the enzyme can accept D-lysine and L-beta-lysine Acetoanaerobium sticklandii ?
-
?
additional information the enzyme can accept D-lysine and L-beta-lysine Propionibacterium freudenreichii ?
-
?
additional information the enzyme can accept D-lysine and L-beta-lysine Propionibacterium freudenreichii ATCC 9614 ?
-
?
additional information the enzyme can accept D-lysine and L-beta-lysine Acetoanaerobium sticklandii StadtmanHF ?
-
?

Synonyms

Synonyms Comment Organism
5,6-LAM
-
Acetoanaerobium sticklandii
5,6-LAM
-
Propionibacterium freudenreichii
lysine 5,6-aminomutase
-
Acetoanaerobium sticklandii
lysine 5,6-aminomutase
-
Propionibacterium freudenreichii

Cofactor

Cofactor Comment Organism Structure
5'-deoxyadenosylcobalamin dependent on Acetoanaerobium sticklandii
5'-deoxyadenosylcobalamin dependent on Propionibacterium freudenreichii
additional information the closed-state of the enzyme is required to bring the cofactors adenosylcobalamin and pyridoxal 5'-phosphate and the substrate into proximity for the radical-mediated 1,2-amino group migration. This process is achieved by transaldimination of the pyridoxal 5'-phosphate-Lys144beta internal aldimine with the pyridoxal 5'-phosphate-substrate external aldimine Acetoanaerobium sticklandii
additional information the closed-state of the enzyme is required to bring the cofactors adenosylcobalamin and pyridoxal 5'-phosphate and the substrate into proximity for the radical-mediated 1,2-amino group migration. This process is achieved by transaldimination of the pyridoxal 5'-phosphate-Lys144beta internal aldimine with the pyridoxal 5'-phosphate-substrate external aldimine Propionibacterium freudenreichii
additional information the closed-state of the enzyme is required to bring the cofactors adenosylcobalamin and pyridoxal-5'-phosphate and the substrate into proximity for the radical-mediated 1,2-amino group migration. This process is achieved by transaldimination of the pyridoxal 5'-phosphate-Lys144beta internal aldimine with the pyridoxal 5'-phosphate-substrate external aldimine Propionibacterium freudenreichii
pyridoxal 5'-phosphate dependent on Acetoanaerobium sticklandii
pyridoxal 5'-phosphate dependent on Propionibacterium freudenreichii

General Information

General Information Comment Organism
additional information the closed-state of the enzyme is required to bring the cofactors adenosylcobalamin and pyridoxal 5'-phosphate and the substrate into proximity for the radical-mediated 1,2-amino group migration. This process is achieved by transaldimination of the pyridoxal 5'-phosphate-Lys144beta internal aldimine with the pyridoxal 5'-phosphate-substrate external aldimine Acetoanaerobium sticklandii
additional information the closed-state of the enzyme is required to bring the cofactors adenosylcobalamin and pyridoxal 5'-phosphate and the substrate into proximity for the radical-mediated 1,2-amino group migration. This process is achieved by transaldimination of the pyridoxal 5'-phosphate-Lys144beta internal aldimine with the pyridoxal 5'-phosphate-substrate external aldimine Propionibacterium freudenreichii