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
-
rossmann
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radical-based
-
stopped-flow
-
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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Cofactor
Cofactor on EC 5.4.3.5 - D-ornithine 4,5-aminomutase
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5'-deoxyadenosylcobalamin
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shows ability to produce highly reactive 5'-deoxyadenosyl radical in enzymatic environments
adenosylcobalamin
binding analysis with recombinant wild-type and mutant enzymes, overview
adenosylcobalamin
paramagnetic Co2+ metal center of the cob(II)alamin cofactor
pyridoxal 5'-phosphate
covalently bound via a Schiff base (imine) to Lys629
pyridoxal 5'-phosphate
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stabilizes high-energy intermediates for performing challenging 1,2-amino rearrangements between adjacent carbons, binding site structure, overview
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
pyridoxal 5'-phosphate
required, important role of enzyme residue tyrosine 187, which lies planar to the pyridoxal 5'-phosphate pyridine ring. 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
pyridoxal 5'-phosphate
the protonation state of the pyridoxal 5'-phosphate cofactor has less of a role in radical-mediated chemistry compared to electrostatic interactions between the substrate and protein. Binding structure analysis and comparison with lysien 5,6-aminomutase, EC 5.4.3.3
adenosylcobalamin-dependent ornithine 4,5-aminomutase from Clostridium sticklandii utilizes pyridoxal 5'-phosphate to interconvert D-ornithine to 2,4-diaminopentanoate via a multistep mechanism that involves two hydrogen transfer steps
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additional information
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adenosylcobalamin-dependent ornithine 4,5-aminomutase from Clostridium sticklandii utilizes pyridoxal 5'-phosphate to interconvert D-ornithine to 2,4-diaminopentanoate via a multistep mechanism that involves two hydrogen transfer steps
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additional information
ornithine 4,5-aminomutase is a 5'-deoxyadenosylcobalamin and pyridoxal 5'-phosphate co-dependent radical enzyme. Identification of a dynamic interface between the cobalamin and pyridoxal 5'-phosphate-binding domains, overview. Following ligand binding-induced cleavage of the Lys629-pyridoxal 5'-phosphate covalent bond, dynamic motion of the cobalamin-binding domain leads to conformational sampling of the available space. This supports radical catalysis through transient formation of a catalytically competent active state. Crucially, it appears that the formation of the state containing both a substrate/product radical and Co(II) does not restrict cobalamin domain motion
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additional information
ornithine 4,5-aminomutase is a 5'-deoxyadenosylcobalamin and pyridoxal 5'-phosphate co-dependent radical enzyme. The conserved residues include S162 and N226, which form hydrogen bonds to the pyridine nitrogen and the phenolic group of pyridoxal 5'-phosphate, respectively. Other residues include Y187 and Y160, which flank the pyridine ring. The former aromatic side chain also forms a hydrogen bond to the pyridoxal 5'-phosphate phosphate, while the latter side chain forms a hydrogen bond to AdoCbl in a modelled closed conformation of the enzyme
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additional information
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ornithine 4,5-aminomutase is a 5'-deoxyadenosylcobalamin and pyridoxal 5'-phosphate co-dependent radical enzyme. The conserved residues include S162 and N226, which form hydrogen bonds to the pyridine nitrogen and the phenolic group of pyridoxal 5'-phosphate, respectively. Other residues include Y187 and Y160, which flank the pyridine ring. The former aromatic side chain also forms a hydrogen bond to the pyridoxal 5'-phosphate phosphate, while the latter side chain forms a hydrogen bond to AdoCbl in a modelled closed conformation of the enzyme
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