Literature summary for 4.1.1.18 extracted from

Sagong, H.Y.; Son, H.F.; Kim, S.; Kim, Y.H.; Kim, I.K.; Kim, K.J.
Crystal structure and pyridoxal 5-phosphate binding property of lysine decarboxylase from Selenomonas ruminantium (2016), PLoS ONE, 11, e0166667 .

Cloned(Commentary)

Cloned (Comment)	Organism
gene Srldc, recombinant expression of His6-tagged enzyme in Escherichia coli strain BL21(DE3)	Selenomonas ruminantium

Crystallization (Commentary)

Crystallization (Comment)	Organism
purified recombinant His6-tagged enzyme, mixing 0.001 ml of 65 mg/ml protein in 40 mM Tris-HCl, pH 8.0, with 0.001 ml of reservoir solution, containing 28% w/v PEG 400, 0.1 M sodium citrate tribasic-citric acid, pH 6.0, and 0.2 M MgCl2, and equilibration against 0.5 ml of reservoir solution, 20°C, the apo-form II crystals of SrLDC are crystallized using a reservoir solution containing 1.15 M sodium citrate and 0.1 M sodium cacodylate, pH 5.0. The crystals of SrLDC complexed with PLP/cadaverine are crystallized using 50% PEG 200, 0.1 M sodium phosphate, pH 4.2, 0.2 M sodium chloride, and 5 mM PLP, followed by soaking in 10 mM L-lysine solution for 30 min, X-ray diffraction structure determination and analysis at 2.0-2.9 A resolution, molecular replacement with the structure of L/ODC from Vibrio vulnificus (VvL/ODC, PDB ID 2PLK) as search model, model building	Selenomonas ruminantium

Crystallization (Comment)

Organism

purified recombinant His6-tagged enzyme, mixing 0.001 ml of 65 mg/ml protein in 40 mM Tris-HCl, pH 8.0, with 0.001 ml of reservoir solution, containing 28% w/v PEG 400, 0.1 M sodium citrate tribasic-citric acid, pH 6.0, and 0.2 M MgCl2, and equilibration against 0.5 ml of reservoir solution, 20°C, the apo-form II crystals of SrLDC are crystallized using a reservoir solution containing 1.15 M sodium citrate and 0.1 M sodium cacodylate, pH 5.0. The crystals of SrLDC complexed with PLP/cadaverine are crystallized using 50% PEG 200, 0.1 M sodium phosphate, pH 4.2, 0.2 M sodium chloride, and 5 mM PLP, followed by soaking in 10 mM L-lysine solution for 30 min, X-ray diffraction structure determination and analysis at 2.0-2.9 A resolution, molecular replacement with the structure of L/ODC from Vibrio vulnificus (VvL/ODC, PDB ID 2PLK) as search model, model building

Selenomonas ruminantium

Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.	Reac.
L-lysine	Selenomonas ruminantium	-	cadaverine + CO2	-	?

Organism

Organism	UniProt	Comment	Textmining
Selenomonas ruminantium	O50657	-	-

Purification (Commentary)

Purification (Comment)	Organism
recombinant His6-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography and gel filtration	Selenomonas ruminantium

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.	Reac.
L-lysine	-	Selenomonas ruminantium	cadaverine + CO2	-	?
additional information	substrate and product binding structure and binding mode, overview. A shallow substrate-binding hole is formed at the interface between the sheet domains of two monomers. The epsilon-amino group of the cadaverine product seems to be stabilized by hydroxyl groups of residues Tyr290 and Ser356. Hydrophobic residues such as Tyr298 and Phe360 provide hydrophobicity for the stabilization of five methylene groups of cadaverine. Asp299 also aids the stabilization of hydrophobic parts of cadaverine. Residues Asp324 and Tyr352 are located in the vicinity of the epsilon-amino group of cadaverine	Selenomonas ruminantium	?	-	?

Subunits

Subunits	Comment	Organism
homodimer	2 * 44000, recombinant His-tagged enzyme, SDS-PAGE	Selenomonas ruminantium
More	SrLDC functions as a dimer and each monomer consists of two distinct domains, a pyridoxal 5'-phosphate-binding-barrel domain and a sheet domain. A shallow substrate-binding hole is formed at the interface between the sheet domains of two monomers	Selenomonas ruminantium

Synonyms

Synonyms	Comment	Organism
LDC	-	Selenomonas ruminantium
SrLDC	-	Selenomonas ruminantium

Cofactor

Cofactor	Comment	Organism	Structure
pyridoxal 5'-phosphate	PLP, binding structure and binding mode, overview. The PLP cofactor binds mainly to the pocket formed at the barrel domain, and the catalytic residue Lys51 interacts with the aldehyde group of the pyridoxal ring. The pyridine ring is stabilized by hydrogen bond between N1 of the ring and the acidic residue Glu255. The phosphate moiety of PLP is mainly stabilized by strong hydrogen bonds with the side-chains of His179, Ser182, and Tyr352, and the main chains of Gly219, Gly257, and Arg258 are also involved in the stabilization of the moiety	Selenomonas ruminantium

General Information

General Information	Comment	Organism
additional information	structure of enzyme SrLDC in complex with pyridoxal 5'-phosphate and cadaverine and binding mode of cofactor and substrate, overview	Selenomonas ruminantium