Literature summary for 5.4.3.5 extracted from

Menon, B.R.; Menon, N.; Fisher, K.; Rigby, S.E.; Leys, D.; Scrutton, N.S.
Glutamate 338 is an electrostatic facilitator of C-Co bond breakage in a dynamic/electrostatic model of catalysis by ornithine aminomutase (2015), FEBS J., 282, 1242-1255 .

Search for more literature for 5.4.3.5

Cloned(Commentary)

Cloned (Comment)	Organism
genes oraS and oraE encoding the alpha- and beta-subunit, recombinant expression of wild-type and beta-subunit mutant enzymes	Acetoanaerobium sticklandii

Protein Variants

Protein Variants	Comment	Organism
E338A	site-directed mutagenesis, the beta-subunit mutant shows a reduced turnover number compared to wild-type enzyme, while the Km value is similar	Acetoanaerobium sticklandii
E338D	site-directed mutagenesis, the beta-subunit mutant shows a reduced turnover number compared to wild-type enzyme, while the Km value is similar	Acetoanaerobium sticklandii
E338Q	site-directed mutagenesis, the beta-subunit mutant shows a reduced turnover number compared to wild-type enzyme, while the Km value is similar	Acetoanaerobium sticklandii
additional information	analysis of substrate-bound wild-type and beta-subunit mutant enzymes, overview	Acetoanaerobium sticklandii

Inhibitors

Inhibitors	Comment	Organism	Structure
DL-2,4-diaminobutyric acid	DAB, a competitive inhibitor	Acetoanaerobium sticklandii

KM Value [mM]

KM Value [mM]	KM Value Maximum [mM]	Substrate	Comment	Organism	Structure
additional information	-	additional information	steady-state kinetics of wild-type enzyme and beta-subunit mutants, enzyme dynamics and C-Co bond homolysis in single-turnover stopped-flow kinetics	Acetoanaerobium sticklandii

Organism

Organism	UniProt	Comment	Textmining
Acetoanaerobium sticklandii	E3PY95 AND E3PY96	subunits beta and alpha	-

Substrates and Products (Substrate)

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

Synonyms

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

Temperature Optimum [°C]

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

Turnover Number [1/s]

Turnover Number Minimum [1/s]	Turnover Number Maximum [1/s]	Substrate	Comment	Organism	Structure
564	-	D-ornithine	recombinant beta-subunit mutant E338A, pH 8.5, 25°C	Acetoanaerobium sticklandii
608	-	D-ornithine	recombinant beta-subunit mutant E338D, pH 8.5, 25°C	Acetoanaerobium sticklandii
694	-	D-ornithine	recombinant beta-subunit mutant E338Q, pH 8.5, 25°C	Acetoanaerobium sticklandii
1072	-	D-ornithine	recombinant wild-type enzyme, pH 8.5, 25°C	Acetoanaerobium sticklandii

pH Optimum

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

General Information

General Information	Comment	Organism
malfunction	substrate-induced C-Co bond homolysis is compromised in Glu388 variant forms of OAM, although photolysis of the C-Co bond is not affected by the identity of residue 338. Electrostatic interactions of Glu338 with the 5'-deoxyadenosyl group of B12 potentiate C-Co bond homolysis in closed conformations only. These conformations are unlocked by substrate binding. Conformational sampling of the mobile cobalamin-binding domain occurs in the Glu388 variants, but that, in adopting the closed conformation, C-Co bond homolysis is compromised. The population of the closed conformation has an associated lifetime. Each time the closed conformation is populated, there is a higher probability of bond homolysis in wild-type OAM relative to the variant forms because of the electrostatic interactions formed between Glu338 and the cobalamin cofactor that facilitate bond homolysis	Acetoanaerobium sticklandii
additional information	for the pyridoxal 5'-phosphate and cobalamin-dependent enzyme ornithine 4,5-aminomutase, large-scale re-orientation of the cobalamin-binding domain linked to C-Co bond breakage is proposed. In the model, substrate binding triggers dynamic sampling of the B12-binding Rossmann domain to achieve a catalytically competent closed conformational state. In closed conformations of the enzyme, Glu338 is thought to facilitate C-Co bond breakage by close association with the cobalamin adenosyl group. Large-scale motion is required to pre-organize the active site by enabling transient formation of closed conformations of OAM. In closed conformations, Glu338 interacts with the 5'-deoxyadenosyl group of cobalamin. This interaction is required to potentiate C-Co homolysis, and is a crucial component of the approximately 1012 rate enhancement achieved by cobalamin-dependent enzymes for C-Co bond homolysis. Three-dimensional enzyme structure and active site structure analysis, spectral analysis of substrate-bound wild-type and beta-subunit mutant enzymes, overview	Acetoanaerobium sticklandii

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Release 2023.1 (January 2023)