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Literature summary extracted from

  • Menon, B.R.; Fisher, K.; Rigby, S.E.; Scrutton, N.S.; Leys, D.
    A conformational sampling model for radical catalysis in pyridoxal phosphate- and cobalamin-dependent enzymes (2014), J. Biol. Chem., 289, 34161-34174 .
    View publication on PubMedView publication on EuropePMC

Cloned(Commentary)

EC Number Cloned (Comment) Organism
5.4.3.5 recombinant expression of wild-type and beta-subunit mutant enzymes Acetoanaerobium sticklandii

Protein Variants

EC Number Protein Variants Comment Organism
5.4.3.5 C700S site-directed mutagenesis, the beta-subunit mutant shows similar kinetics and activity as the wild-type enzyme Acetoanaerobium sticklandii
5.4.3.5 D627A site-directed mutagenesis, the beta-subunit mutant shows similar kinetics and slightly reduced activity compared to the wild-type enzyme Acetoanaerobium sticklandii
5.4.3.5 E338A site-directed mutagenesis, the beta-subunit mutant shows altered kinetics and highly reduced activity compared to the wild-type enzyme Acetoanaerobium sticklandii
5.4.3.5 G128D site-directed mutagenesis, inactive beta-subunit mutant Acetoanaerobium sticklandii
5.4.3.5 G339W site-directed mutagenesis, the beta-subunit mutant shows altered kinetics and highly reduced activity compared to the wild-type enzyme Acetoanaerobium sticklandii
5.4.3.5 I424E site-directed mutagenesis, the beta-subunit mutant shows altered kinetics and reduced activity compared to the wild-type enzyme Acetoanaerobium sticklandii
5.4.3.5 additional information OAM variants are designed to perturb the interface between the cobalamin-binding domain and the pyridoxal 5'-phosphate-binding TIM-barrel domain. Steady-state and single turnover kinetic studies of these variants, combined with pulsed electron-electron double resonance measurements of spin-labeled OAM are used to provide direct evidence for a dynamic interface between the cobalamin and pyridoxal 5'-phosphate-binding domains, overview Acetoanaerobium sticklandii
5.4.3.5 P343W site-directed mutagenesis, the beta-subunit mutant shows altered kinetics and highly reduced activity compared to the wild-type enzyme Acetoanaerobium sticklandii

KM Value [mM]

EC Number KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
5.4.3.5 additional information
-
 additional information steady-state and pre-steady-state kinetics Acetoanaerobium sticklandii
5.4.3.5 0.176
-
 D-ornithine pH 8.5, 25°C, recombinant beta-subunit mutant E338A Acetoanaerobium sticklandii
5.4.3.5 0.185
-
 D-ornithine pH 8.5, 25°C, recombinant beta-subunit mutant I424E Acetoanaerobium sticklandii
5.4.3.5 0.186
-
 D-ornithine pH 8.5, 25°C, recombinant beta-subunit mutant C700S Acetoanaerobium sticklandii
5.4.3.5 0.189
-
 D-ornithine pH 8.5, 25°C, recombinant wild-type enzyme Acetoanaerobium sticklandii
5.4.3.5 0.19
-
 D-ornithine pH 8.5, 25°C, recombinant beta-subunit mutant G339W Acetoanaerobium sticklandii
5.4.3.5 0.193
-
 D-ornithine pH 8.5, 25°C, recombinant beta-subunit mutant D627A Acetoanaerobium sticklandii
5.4.3.5 0.193
-
 D-ornithine pH 8.5, 25°C, recombinant beta-subunit mutant P343W Acetoanaerobium sticklandii

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
-

Purification (Commentary)

EC Number Purification (Comment) Organism
5.4.3.5 recombinant wild-type and beta-subunit mutant enzymes Acetoanaerobium sticklandii

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
5.4.3.5 additional information cobalamin-dependent enzymes enhance the rate of C-Co bond cleavage by up to 1012-fold to generate cob(II)alamin and a transient adenosyl radical. In the case of the pyridoxal 5'-phosphate and cobalamin-dependent enzymes lysine 5,6-aminomutase (EC 5.4.3.3) and ornithine 4,5 aminomutase, it has been proposed that a large scale domain reorientation of the cobalamin-binding domain is linked to radical catalysis Coupled enzyme assay with (2R,4S)-2,4-diaminopentanoate dehydrogenase (DAPDH) from Clostridium difficile Acetoanaerobium sticklandii ?
-
 ?

Synonyms

EC Number Synonyms Comment Organism
5.4.3.5 OAM
-
 Acetoanaerobium sticklandii
5.4.3.5 ornithine 4,5-aminomutase
-
 Acetoanaerobium sticklandii

Temperature Optimum [°C]

EC Number Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
5.4.3.5 25
-
 assay at Acetoanaerobium sticklandii

Turnover Number [1/s]

EC Number Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
5.4.3.5 0.14
-
 D-ornithine pH 8.5, 25°C, recombinant beta-subunit mutant P343W Acetoanaerobium sticklandii
5.4.3.5 0.2
-
 D-ornithine pH 8.5, 25°C, recombinant beta-subunit mutant G339W Acetoanaerobium sticklandii
5.4.3.5 0.24
-
 D-ornithine pH 8.5, 25°C, recombinant beta-subunit mutant E338A Acetoanaerobium sticklandii
5.4.3.5 0.76
-
 D-ornithine pH 8.5, 25°C, recombinant beta-subunit mutant I424E Acetoanaerobium sticklandii
5.4.3.5 2.88
-
 D-ornithine pH 8.5, 25°C, recombinant beta-subunit mutant C700S Acetoanaerobium sticklandii
5.4.3.5 2.89
-
 D-ornithine pH 8.5, 25°C, recombinant beta-subunit mutant D627A Acetoanaerobium sticklandii
5.4.3.5 2.97
-
 D-ornithine pH 8.5, 25°C, recombinant wild-type enzyme Acetoanaerobium sticklandii

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
5.4.3.5 8.5
-
 assay at Acetoanaerobium sticklandii

Cofactor

EC Number Cofactor Comment Organism Structure
5.4.3.5 5'-deoxyadenosylcobalamin
-
 Acetoanaerobium sticklandii
5.4.3.5 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 Acetoanaerobium sticklandii
5.4.3.5 pyridoxal 5'-phosphate
-
 Acetoanaerobium sticklandii

kcat/KM [mM/s]

EC Number kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
5.4.3.5 0.72
-
 D-ornithine pH 8.5, 25°C, recombinant beta-subunit mutant P343W Acetoanaerobium sticklandii
5.4.3.5 1.05
-
 D-ornithine pH 8.5, 25°C, recombinant beta-subunit mutant G339W Acetoanaerobium sticklandii
5.4.3.5 1.36
-
 D-ornithine pH 8.5, 25°C, recombinant beta-subunit mutant E338A Acetoanaerobium sticklandii
5.4.3.5 4.11
-
 D-ornithine pH 8.5, 25°C, recombinant beta-subunit mutant I424E Acetoanaerobium sticklandii
5.4.3.5 14.97
-
 D-ornithine pH 8.5, 25°C, recombinant beta-subunit mutant D627A Acetoanaerobium sticklandii
5.4.3.5 15.48
-
 D-ornithine pH 8.5, 25°C, recombinant beta-subunit mutant C700S Acetoanaerobium sticklandii
5.4.3.5 15.71
-
 D-ornithine pH 8.5, 25°C, recombinant wild-type enzyme Acetoanaerobium sticklandii