5.4.3.5: D-ornithine 4,5-aminomutase
This is an abbreviated version!
For detailed information about D-ornithine 4,5-aminomutase, go to the full flat file.
Word Map on EC 5.4.3.5
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5.4.3.5
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pyridoxal
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sticklandii
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adocbl
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homolysis
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5'-phosphate
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plp-dependent
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5,6-aminomutase
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aldimine
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rossmann
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radical-based
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stopped-flow
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5\'-deoxyadenosyl
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paramagnetic
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1,2-amino
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deprotonated
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d-lysine
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cobalamin-binding
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rupture
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ribose
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imine
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interconverting
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5\'-deoxyadenosylcobalamin
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multistep
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adocbl-dependent
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isomerization
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pyridoxal-5'-phosphate
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pyridine
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uv-visible
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refolding
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synergy
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b12-dependent
- 5.4.3.5
- pyridoxal
- sticklandii
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adocbl
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homolysis
- 5'-phosphate
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plp-dependent
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5,6-aminomutase
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aldimine
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rossmann
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radical-based
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stopped-flow
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5\'-deoxyadenosyl
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paramagnetic
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1,2-amino
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deprotonated
- d-lysine
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cobalamin-binding
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rupture
- ribose
- imine
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interconverting
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5\'-deoxyadenosylcobalamin
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multistep
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adocbl-dependent
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isomerization
- pyridoxal-5'-phosphate
- pyridine
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uv-visible
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refolding
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synergy
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b12-dependent
Reaction
Synonyms
4,5-OAM, adenosylcobalamin-dependent ornithine 4,5-aminomutase, Aminomutase, D-ornithine 4,5-, D-ornithine aminomutase, OAM, oraE, oraS, ornithine 4,5-aminomutase, ornithine aminomutase
ECTree
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Reaction
Reaction on EC 5.4.3.5 - D-ornithine 4,5-aminomutase
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D-ornithine = (2R,4S)-2,4-diaminopentanoate
catalytic mechanism, overview
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D-ornithine = (2R,4S)-2,4-diaminopentanoate
mechanism, overview, a gradual weakening of the electrostatic energy between the protein and the ribose leads to a progressive increase in the activation energy barrier for adenosylcobalamin Co-C bond homolysis, key role for the conserved polar glutamate residue in controlling the initial generation of radical species
D-ornithine = (2R,4S)-2,4-diaminopentanoate
mechanism, overview, a gradual weakening of the electrostatic energy between the protein and the ribose leads to a progressive increase in the activation energy barrier for adenosylcobalamin Co?C bond homolysis, key role for the conserved polar glutamate residue in controlling the initial generation of radical species
D-ornithine = (2R,4S)-2,4-diaminopentanoate
radical-based catalysis mechanism, closed, active enzyme form modeling, overview
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D-ornithine = (2R,4S)-2,4-diaminopentanoate
radical-based catalysis that is initiated and propagated by the enzyme's adenosylcobalamin and pyridoxal 5'-phosphate cofactors. Following transaldimination, the Co-C bond of adenosylcobalamin undergoes homolytic rupture, generating a highly reactive carbon-centered 5'-deoxyadenosyl radical and cob(II)alamin. The 5'-deoxyadenosyl radical abstracts the C4 hydrogen atom from the D-ornithinyl-pyridoxal 5'-phosphate aldimine producing a substrate radical, which undergoes internal addition to the imine N to form an aziridylcarbinyl-pyridoxal 5'-phosphate radical adduct. Ring opening leads to formation of a product-like radical intermediate 3, which reabstracts a hydrogen atom from 5'-deoxyadenosine. Adenosylcobalamin is reformed with geminate recombination between the 5'-deoxyadenosyl radical and cob(II)alamin. Release of product from pyridoxal 5'-phosphate completes the catalytic cycle
D-ornithine = (2R,4S)-2,4-diaminopentanoate
radical-based catalysis that is initiated and propagated by the enzyme's adenosylcobalamin and pyridoxal 5'-phosphate cofactors. Following transaldimination, the Co-C bond of adenosylcobalamin undergoes homolytic rupture, generating a highly reactive carbon-centered 5'-deoxyadenosyl radical and cob(II)alamin. The 5'-deoxyadenosyl radical abstracts the C4 hydrogen atom from the D-ornithinylpyridoxal 5'-phosphate aldimine producing a substrate radical, which undergoes internal addition to the imine N to form an aziridylcarbinyl-pyridoxal 5'-phosphate radical adduct. Ring opening leads to formation of a product-like radical intermediate 3, which reabstracts a hydrogen atom from 5'-deoxyadenosine. Adenosylcobalamin is reformed with geminate recombination between the 5'-deoxyadenosyl radical and cob(II)alamin. Release of product from pyridoxal 5'-phosphate completes the catalytic cycle
D-ornithine = (2R,4S)-2,4-diaminopentanoate
catalytic mechanism of ornithine 4,5-aminomutase. Substrate binding results in formation of a Schiff base between the terminal amino group of the substrate and the imine nitrogen of the PLP cofactor. Subsequent homolysis of the Co-C bond generates cob(II)alamin and the highly reactive 5'-deoxyadenosyl radical, which abstracts a hydrogen atom from the C4 of the substrate. The substrate radical intermediate then rearranges to the product-like radical intermediate via a proposed cyclic intermediate. Re-abstraction of a hydrogen atom from 5'-deoxyadenosine regenerates the 5'-deoxyadenosyl radical. Product release and recombination between cob(II)alamin and the 5'-deoxyadenosyl radical completes the catalytic cycle
D-ornithine = (2R,4S)-2,4-diaminopentanoate
catalytic mechanism, detailed overview. The substrate forms a covalent Schiff base linkage with the imine nitrogen of the pyridoxal 5'-phosphate cofactor. In particular, Tyr187 forms a Pi-stacking interaction with the pyridine ring of pyridoxal 5'-phosphate, the guanidinium side chain of Arg297 forms a salt bridge with the alpha-carboxylate group of the substrate, and residues His225, His182, Asn226, Glu81, and Ser162 provide additional hydrogen bonding interactions with the substrate and cofactor
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
D-ornithine = (2R,4S)-2,4-diaminopentanoate
mechanism, overview, a gradual weakening of the electrostatic energy between the protein and the ribose leads to a progressive increase in the activation energy barrier for adenosylcobalamin Co?C bond homolysis, key role for the conserved polar glutamate residue in controlling the initial generation of radical species
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D-ornithine = (2R,4S)-2,4-diaminopentanoate
radical-based catalysis that is initiated and propagated by the enzyme's adenosylcobalamin and pyridoxal 5'-phosphate cofactors. Following transaldimination, the Co-C bond of adenosylcobalamin undergoes homolytic rupture, generating a highly reactive carbon-centered 5'-deoxyadenosyl radical and cob(II)alamin. The 5'-deoxyadenosyl radical abstracts the C4 hydrogen atom from the D-ornithinylpyridoxal 5'-phosphate aldimine producing a substrate radical, which undergoes internal addition to the imine N to form an aziridylcarbinyl-pyridoxal 5'-phosphate radical adduct. Ring opening leads to formation of a product-like radical intermediate 3, which reabstracts a hydrogen atom from 5'-deoxyadenosine. Adenosylcobalamin is reformed with geminate recombination between the 5'-deoxyadenosyl radical and cob(II)alamin. Release of product from pyridoxal 5'-phosphate completes the catalytic cycle
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D-ornithine = (2R,4S)-2,4-diaminopentanoate
catalytic mechanism of ornithine 4,5-aminomutase. Substrate binding results in formation of a Schiff base between the terminal amino group of the substrate and the imine nitrogen of the PLP cofactor. Subsequent homolysis of the Co-C bond generates cob(II)alamin and the highly reactive 5'-deoxyadenosyl radical, which abstracts a hydrogen atom from the C4 of the substrate. The substrate radical intermediate then rearranges to the product-like radical intermediate via a proposed cyclic intermediate. Re-abstraction of a hydrogen atom from 5'-deoxyadenosine regenerates the 5'-deoxyadenosyl radical. Product release and recombination between cob(II)alamin and the 5'-deoxyadenosyl radical completes the catalytic cycle
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D-ornithine = (2R,4S)-2,4-diaminopentanoate
mechanism, overview, a gradual weakening of the electrostatic energy between the protein and the ribose leads to a progressive increase in the activation energy barrier for adenosylcobalamin Co-C bond homolysis, key role for the conserved polar glutamate residue in controlling the initial generation of radical species
-
-
D-ornithine = (2R,4S)-2,4-diaminopentanoate
radical-based catalysis that is initiated and propagated by the enzyme's adenosylcobalamin and pyridoxal 5'-phosphate cofactors. Following transaldimination, the Co-C bond of adenosylcobalamin undergoes homolytic rupture, generating a highly reactive carbon-centered 5'-deoxyadenosyl radical and cob(II)alamin. The 5'-deoxyadenosyl radical abstracts the C4 hydrogen atom from the D-ornithinyl-pyridoxal 5'-phosphate aldimine producing a substrate radical, which undergoes internal addition to the imine N to form an aziridylcarbinyl-pyridoxal 5'-phosphate radical adduct. Ring opening leads to formation of a product-like radical intermediate 3, which reabstracts a hydrogen atom from 5'-deoxyadenosine. Adenosylcobalamin is reformed with geminate recombination between the 5'-deoxyadenosyl radical and cob(II)alamin. Release of product from pyridoxal 5'-phosphate completes the catalytic cycle
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