Literature summary for 5.1.1.1 extracted from

Dong, H.; Hu, T.; He, G.; Lu, D.; Qi, J.; Dou, Y.; Long, W.; He, X.; Ju, J.; Su, D.
Structural features and kinetic characterization of alanine racemase from Bacillus pseudofirmus OF4 (2018), Biochem. Biophys. Res. Commun., 497, 139-145 .

Search for more literature for 5.1.1.1

Application

Application	Comment	Organism
drug development	the enzyme is an attractive target for designing antibacterial drugs	Alkalihalophilus pseudofirmus

Cloned(Commentary)

Cloned (Comment)	Organism
gene dadX, recombinant expression of wild-type and mutant enzymes	Alkalihalophilus pseudofirmus

Crystallization (Commentary)

Crystallization (Comment)	Organism
purified enzyme, hanging drop vapour diffusion, method, X-ray diffraction structure determination and analysis at 1.8 A resolution, molecular replacement method using the crystal structure of native alanine racemase from Bacillus stearothermophilus as search model, PDB ID 1SFT	Alkalihalophilus pseudofirmus

Protein Variants

Protein Variants	Comment	Organism
D318K	site-directed mutagenesis, almost inactive mutant, the mutant shows an altered structure compared to the wild-type enzyme	Alkalihalophilus pseudofirmus
D43K	site-directed mutagenesis, the mutant shows an altered structure and reduced activity compared to the wild-type enzyme	Alkalihalophilus pseudofirmus
D70K	site-directed mutagenesis, the mutant shows an altered structure and reduced activity compared to the wild-type enzyme	Alkalihalophilus pseudofirmus
E134K	site-directed mutagenesis, almost inactive mutant, the mutant shows an altered structure compared to the wild-type enzyme	Alkalihalophilus pseudofirmus
E71K	site-directed mutagenesis, almost inactive mutant, the mutant shows an altered structure compared to the wild-type enzyme	Alkalihalophilus pseudofirmus

KM Value [mM]

KM Value [mM]	KM Value Maximum [mM]	Substrate	Comment	Organism	Structure
additional information	-	additional information	enzyme kinetics analysis	Alkalihalophilus pseudofirmus
20.78	-	D-alanine	pH 10.5, 40°C, recombinant wild-type enzyme	Alkalihalophilus pseudofirmus
56.17	-	L-alanine	pH 10.5, 40°C, recombinant wild-type enzyme	Alkalihalophilus pseudofirmus

Molecular Weight [Da]

Molecular Weight [Da]	Molecular Weight Maximum [Da]	Comment	Organism
45000	-	mutant E71K, gel filtration	Alkalihalophilus pseudofirmus
48000	-	mutant E134K, gel filtration	Alkalihalophilus pseudofirmus
49000	-	mutant D318K, gel filtration	Alkalihalophilus pseudofirmus
69000	-	mutant D70K, gel filtration	Alkalihalophilus pseudofirmus
76000	-	mutant D43K, gel filtration	Alkalihalophilus pseudofirmus
78630	-	recombinant wild-type enzyme, gel filtration	Alkalihalophilus pseudofirmus
80640	-	sequence calculation, wild-type enzyme	Alkalihalophilus pseudofirmus

Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.	Reac.
L-alanine	Alkalihalophilus pseudofirmus	-	D-alanine	-	r
L-alanine	Alkalihalophilus pseudofirmus OF4	-	D-alanine	-	r

Organism

Organism	UniProt	Comment	Textmining
Alkalihalophilus pseudofirmus	B3VI72	-	-
Alkalihalophilus pseudofirmus OF4	B3VI72	-	-

Purification (Commentary)

Purification (Comment)	Organism
recombinant wild-type and mutant enzymes	Alkalihalophilus pseudofirmus

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.	Reac.
D-alanine	reversible racemization	Alkalihalophilus pseudofirmus	L-alanine	-	r
D-alanine	reversible racemization	Alkalihalophilus pseudofirmus OF4	L-alanine	-	r
L-alanine	-	Alkalihalophilus pseudofirmus	D-alanine	-	r
L-alanine	reversible racemization	Alkalihalophilus pseudofirmus	D-alanine	-	r
L-alanine	-	Alkalihalophilus pseudofirmus OF4	D-alanine	-	r
L-alanine	reversible racemization	Alkalihalophilus pseudofirmus OF4	D-alanine	-	r

Subunits

Subunits	Comment	Organism
homodimer	enzyme molecular structure analysis, the tertiary structure of DadXOF4 is a homodimer comprised of two monomers that interact in a head-to-tail manner. Each monomer is composed of two domains, an eight-stranded alpha/beta-barrel at the N-terminus and a C-terminal domain essentially composed of beta-strands. The dimer interface of DadXOF4 is formed by five pairs of salt bridges, i.e. Asp43-Lys360', Asp70-Lys2', Glu71-Arg361', Glu134-Arg259', and Asp318-Lys41'	Alkalihalophilus pseudofirmus

Synonyms

Synonyms	Comment	Organism
ALR	-	Alkalihalophilus pseudofirmus
dadXOF4	-	Alkalihalophilus pseudofirmus

Temperature Optimum [°C]

Temperature Optimum [°C]	Temperature Optimum Maximum [°C]	Comment	Organism
40	-	-	Alkalihalophilus pseudofirmus

pH Optimum

pH Optimum Minimum	pH Optimum Maximum	Comment	Organism
10.5	-	-	Alkalihalophilus pseudofirmus

Cofactor

Cofactor	Comment	Organism	Structure
pyridoxal 5'-phosphate	PLP, dependent on	Alkalihalophilus pseudofirmus

General Information

General Information	Comment	Organism
malfunction	enzyme Alr inhibition is lethal to prokaryotes	Alkalihalophilus pseudofirmus
additional information	enzyme molecular structure analysis. The conserved residues at the substrate entryway and the salt bridge at the dimer interface are critical for enzyme activity	Alkalihalophilus pseudofirmus
physiological function	alanine racemase (Alr) is a pyridoxal 5'-phosphate-dependent (PLP) enzyme that catalyzes a reversible racemization between the enantiomers of alanine. D-Alanine is an indispensable constituent in the biosynthesis of bacterial cell-wall peptidoglycan	Alkalihalophilus pseudofirmus

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Release 2023.1 (January 2023)