Literature summary for 2.6.1.83 extracted from

Weatherhead, A.W.; Crowther, J.M.; Horne, C.R.; Meng, Y.; Coombes, D.; Currie, M.J.; Watkin, S.A.J.; Adams, L.E.; Parthasarathy, A.; Dobson, R.C.J.; Hudson, A.O.
Structure-function studies of the antibiotic target L,L-diaminopimelate aminotransferase from Verrucomicrobium spinosum reveal an unusual oligomeric structure (2020), Biochemistry, 59, 2274-2288 .

Cloned(Commentary)

Cloned (Comment)	Organism
gene dapL, functional recombinant expression of the enzyme in Escherichia coli double mutant strain DELTAdapD/E and complementation, and functional recombinant overexpression of the His-tagged enzyme in Escherichia coli strain BL21(DE3)	Verrucomicrobium spinosum

Crystallization (Commentary)

Crystallization (Comment)	Organism
purified recombinant enzyme in presence of malic acid, hanging drop vapor diffusion method, mixing of 200 nl of a protein/inhibitor solution containing 39 mg/ml protein in 100 mM HEPES-KOH, 20 mM NaCl, 1 mM DTT, pH 7.6, and 200 mM malic acid, with 200 nl of reservoir solution containing 60% v/v T-mate, pH 7.0, 20°C, 8 weeks, X-ray diffraction structure determination and analysis at 2.25 A resolution, molecular replacement using the crystal structure of Chlamydomonas reinhardtii LL-diaminopimelate aminotransferase (PDB ID 3QGU) as search model, model building	Verrucomicrobium spinosum

Crystallization (Comment)

Organism

purified recombinant enzyme in presence of malic acid, hanging drop vapor diffusion method, mixing of 200 nl of a protein/inhibitor solution containing 39 mg/ml protein in 100 mM HEPES-KOH, 20 mM NaCl, 1 mM DTT, pH 7.6, and 200 mM malic acid, with 200 nl of reservoir solution containing 60% v/v T-mate, pH 7.0, 20°C, 8 weeks, X-ray diffraction structure determination and analysis at 2.25 A resolution, molecular replacement using the crystal structure of Chlamydomonas reinhardtii LL-diaminopimelate aminotransferase (PDB ID 3QGU) as search model, model building

Verrucomicrobium spinosum

KM Value [mM]

KM Value [mM]	KM Value Maximum [mM]	Substrate	Comment	Organism	Structure
additional information	-	additional information	enzyme VsDapL follows a Michaelis-Menten mechanism, kinetic analysis, overview	Verrucomicrobium spinosum
4	-	LL-2,6-Diaminoheptanedioate	pH 7.6, 30°C	Verrucomicrobium spinosum

Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.	Reac.
LL-2,6-diaminoheptanedioate + 2-oxoglutarate	Verrucomicrobium spinosum	-	(S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate + L-glutamate + H2O	-	r

Organism

Organism	UniProt	Comment	Textmining
Verrucomicrobium spinosum	A0A6P3CW87	-	-

Purification (Commentary)

Purification (Comment)	Organism
recombinant His-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography and gel filtration	Verrucomicrobium spinosum

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.	Reac.
LL-2,6-diaminoheptanedioate + 2-oxoglutarate	-	Verrucomicrobium spinosum	(S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate + L-glutamate + H2O	-	r

Subunits

Subunits	Comment	Organism
homodimer	VsDapL exists in a monomer-dimer self-association, with a KD2-1 of 0.0074 mM, a canonical dimer of chalice-shaped monomers, small-angle X-ray scattering experiments confirm the dimer in solution. Although the dimer interface buries 18% of the total surface area, several loops that contribute to the interface and active site, notably the L1, L2, and L5 loops, are highly mobile, perhaps explaining the unstable dimer and lower catalytic activity	Verrucomicrobium spinosum

Synonyms

Synonyms	Comment	Organism
DapL	-	Verrucomicrobium spinosum
diaminopimelate aminotransferase	-	Verrucomicrobium spinosum
VsDapL	-	Verrucomicrobium spinosum

Temperature Optimum [°C]

Temperature Optimum [°C]	Temperature Optimum Maximum [°C]	Comment	Organism
30	-	assay at	Verrucomicrobium spinosum

Turnover Number [1/s]

Turnover Number Minimum [1/s]	Turnover Number Maximum [1/s]	Substrate	Comment	Organism	Structure
0.46	-	LL-2,6-Diaminoheptanedioate	pH 7.6, 30°C	Verrucomicrobium spinosum

pH Optimum

pH Optimum Minimum	pH Optimum Maximum	Comment	Organism
7.6	-	assay at	Verrucomicrobium spinosum

Cofactor

Cofactor	Comment	Organism	Structure
pyridoxal 5'-phosphate	PLP, dependent on	Verrucomicrobium spinosum

General Information

General Information	Comment	Organism
additional information	DapL enzyme structures comparisons	Verrucomicrobium spinosum
physiological function	the Verrucomicrobium spinosum dapL gene encodes a putative diaminopimelate aminotransferase, the gene expression rescues an Escherichia coli strain that is auxotrophic for meso-diaminopimelate. LL-Diaminopimelate aminotransferase is a pyridoxal 5'-phosphate (PLP)-dependent enzyme that catalyzes the transamination of L-tetrahydrodipicolinate to form LL-diaminopimelate. The reaction proceeds via a bimolecular ping-pong mechanism. First, the amino group from the donor molecule L-glutamate forms a covalent Schiff base with the PLP molecule tethered in the enzyme active site. This is followed by the transfer of the amino group to the acceptor molecule, L-tetrahydrodipicolinate, forming LL-diaminopimelate. Subsequent enzymes catalyze the epimerization to form meso-diaminopimelate and decarboxylation to yield L-lysine	Verrucomicrobium spinosum

kcat/KM [mM/s]

kcat/KM Value [1/mMs^-1]	kcat/KM Value Maximum [1/mMs^-1]	Substrate	Comment	Organism	Structure
0.115	-	LL-2,6-Diaminoheptanedioate	pH 7.6, 30°C	Verrucomicrobium spinosum