Literature summary for 5.1.1.7 extracted from

Sagong, H.Y.; Kim, K.J.
Structural basis for redox sensitivity in Corynebacterium glutamicum diaminopimelate epimerase an enzyme involved in L-lysine biosynthesis (2017), Sci. Rep., 7, 42318 .

Application

Application	Comment	Organism
drug development	DapF is considered as an attractive target for the development of antibacterial drugs	Corynebacterium glutamicum

Cloned(Commentary)

Cloned (Comment)	Organism
gene dapF, recombinant expression of seleno-methionine substituted wild-type and mutant enzymes in Escherichia coli strain B834(DE3)	Corynebacterium glutamicum

Crystallization (Commentary)

Crystallization (Comment)	Organism
purified enzyme CgDapF in both oxidized and reduced forms, selenium-substituted crystal, hanging drop vapor diffusion method, mixing of 0.001 ml of 40 mg/ml protein in 40 mM Tris-HCl, pH 8.0, with 0.001 ml of reservoir solution containing 1.6 M ammonium sulfate, and 0.1 M Bis-Tris, pH 5.0, for the oxidized enzyme form and 1.4 M sodium phosphate monobasic/0.9 M potassium phosphate dibasic, 0.1 M CAPS, pH 10.0, 0.2 M lithium sulfate, and 1 mM 1,4-DTT for the reduced enzyme form, the crystals of CgDapF in complex with DL-DAP are crystallized in the condition of 1.3 M sodium citrate, 0.1 M CHES, pH 9.0, and 10 mM DAP isomer, equilibration against 0.5 ml, 20°C, X-ray diffraction structure determination and analysis at 2.0-2.6 A resolution, single-wavelength anomalous dispersion method, molecular replacement	Corynebacterium glutamicum

Crystallization (Comment)

Organism

purified enzyme CgDapF in both oxidized and reduced forms, selenium-substituted crystal, hanging drop vapor diffusion method, mixing of 0.001 ml of 40 mg/ml protein in 40 mM Tris-HCl, pH 8.0, with 0.001 ml of reservoir solution containing 1.6 M ammonium sulfate, and 0.1 M Bis-Tris, pH 5.0, for the oxidized enzyme form and 1.4 M sodium phosphate monobasic/0.9 M potassium phosphate dibasic, 0.1 M CAPS, pH 10.0, 0.2 M lithium sulfate, and 1 mM 1,4-DTT for the reduced enzyme form, the crystals of CgDapF in complex with DL-DAP are crystallized in the condition of 1.3 M sodium citrate, 0.1 M CHES, pH 9.0, and 10 mM DAP isomer, equilibration against 0.5 ml, 20°C, X-ray diffraction structure determination and analysis at 2.0-2.6 A resolution, single-wavelength anomalous dispersion method, molecular replacement

Corynebacterium glutamicum

Protein Variants

Protein Variants	Comment	Organism
C221A	site-directed mutagenesis, nearly inactive mutant	Corynebacterium glutamicum
C83A	site-directed mutagenesis, nearly inactive mutant	Corynebacterium glutamicum
E212A	site-directed mutagenesis, nearly inactive mutant	Corynebacterium glutamicum
N159A	site-directed mutagenesis, nearly inactive mutant	Corynebacterium glutamicum
N15A	site-directed mutagenesis, nearly inactive mutant	Corynebacterium glutamicum
N194A	site-directed mutagenesis, nearly inactive mutant	Corynebacterium glutamicum
N74A	site-directed mutagenesis, nearly inactive mutant	Corynebacterium glutamicum
N85A	site-directed mutagenesis, nearly inactive mutant	Corynebacterium glutamicum
R213A	site-directed mutagenesis, nearly inactive mutant	Corynebacterium glutamicum
T223A	site-directed mutagenesis, nearly inactive mutant	Corynebacterium glutamicum

Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.	Reac.
LL-2,6-Diaminoheptanedioate	Corynebacterium glutamicum	-	meso-Diaminoheptanedioate	-	r
LL-2,6-Diaminoheptanedioate	Corynebacterium glutamicum ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025	-	meso-Diaminoheptanedioate	-	r

Organism

Organism	UniProt	Comment	Textmining
Corynebacterium glutamicum	Q8NP73	-	-
Corynebacterium glutamicum ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025	Q8NP73	-	-

Purification (Commentary)

Purification (Comment)	Organism
recombinant seleno-methionine substituted wild-type and mutant enzymes from Escherichia coli strain B834(DE3)	Corynebacterium glutamicum

Reaction

Reaction	Comment	Organism	Reaction ID
LL-2,6-diaminoheptanedioate = meso-diaminoheptanedioate	molecular mechanism of the enzyme, reversible disulfide bond formation at the active site of CgDapF and disulfide bond-mediated conformational change in CgDapF, domain movement in CgDapF, CgDapF is regulated by redox-switch modulation, via reversible disulfide bond formation, overview	Corynebacterium glutamicum	a

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.	Reac.
LL-2,6-Diaminoheptanedioate	-	Corynebacterium glutamicum	meso-Diaminoheptanedioate	-	r
LL-2,6-Diaminoheptanedioate	-	Corynebacterium glutamicum ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025	meso-Diaminoheptanedioate	-	r

Subunits

Subunits	Comment	Organism
dimer	CgDapF functions as a dimer and the asymmetric unit contains a CgDapF dimer, the dimerization interface is mainly constituted by the contacts between beta16 from both monomers, and contact between two beta-strands connects the two beta-sheets of the N-terminal domains (NTDs) from both monomers. Contacts between the connecting loops (alpha1-beta3) from both monomers also mediate dimerization of the protein. Each CgDapF monomer consists of two distinct domains: an NTD (Met1-Asp131 and Gly268-Ile277) and a C-terminal domain (CTD, Met132-Thr267). Each domain contains a set of five-stranded and three-stranded antiparallel beta-sheets and two alpha-helices. One alpha-helix of each domain (alpha2 in the NTD and alpha4 in the CTD) is sandwiched between the five-stranded and three-stranded beta-sheets, whereas the other helix lies on the surface of the protein. The NTD and the CTD are structurally homologous to each other, structure comparisons of DAP epimerases, overview	Corynebacterium glutamicum

Synonyms

Synonyms	Comment	Organism
CgDapF	-	Corynebacterium glutamicum
DAP epimerase	-	Corynebacterium glutamicum
DapF	-	Corynebacterium glutamicum

Temperature Optimum [°C]

Temperature Optimum [°C]	Temperature Optimum Maximum [°C]	Comment	Organism
22	-	assay at room temperature	Corynebacterium glutamicum

pH Optimum

pH Optimum Minimum	pH Optimum Maximum	Comment	Organism
8	-	assay at	Corynebacterium glutamicum

General Information

General Information	Comment	Organism
metabolism	the enzyme is involved in L-lysine biosynthesis, where it converts LL-diaminopimelate (LL-DAP) into DL-DAP. In the succinylase pathway, LL-diaminopimelate is synthesized from THDP by succinylation, transamination, and desuccinylation steps, LL-DAP is converted to DL-DAP by the action of DAP epimerase. In contrast, in the mDAP dehydrogenase pathway, DAP dehydrogenase converts THDP into DL-DAP in one step, DAP decarboxylase subsequently catalyzes the decarboxylation of DL-DAP to form L-lysine	Corynebacterium glutamicum
additional information	C83 and C221 are catalytic residues	Corynebacterium glutamicum
physiological function	redox-mediated modification of cellular proteins confers a respose to changes in the environmental redox potential. CgDapF is regulated by redox-switch modulation, via reversible disulfide bond formation	Corynebacterium glutamicum