Literature summary for 2.7.2.2 extracted from

Lim, K.; Kulakova, L.; Galkin, A.; Herzberg, O.
Crystal structures of carbamate kinase from Giardia lamblia bound with citric acid and AMP-PNP (2013), PLoS ONE, 8, e64004.

Application

Application	Comment	Organism
drug development	because the L-arginine pathway is essential for Giardia lamblia survival and absent in high eukaryotes including humans, the enzyme is a potential target for drug development	Giardia intestinalis

Cloned(Commentary)

Cloned (Comment)	Organism
gene cbk, recombinant expression in Escherichia coli strain BL21(DE3)Star as a TEV protease-cleavable, His-tagged, maltose binding protein fusion protein	Giardia intestinalis

Crystallization (Commentary)

Crystallization (Comment)	Organism
purified detagged recombinant enzyme in complex with nonhydrolyzable ATP analogue, adenosine 5'-adenylyl-beta,gamma-imidodiphosphate (AMP-PNP), and with citric acid, hanging drop vapor diffusion method, mixing of 30 mg/ml protein in 50 mM Tris-HCl, pH 8.0, 0.1 M NaCl, 5 mM MgCl2, and 1 mM DTT, with an equal volume of mother liquor containing 0.4 M ammonium citrate dibasic, pH 5.0, and 21% w/v PEG 3350, soaking of crystals in 50 mM AMP-PNP, X-ray diffraction structure determination and analysis at 2.1-2.6 A resolution	Giardia intestinalis

Crystallization (Comment)

Organism

purified detagged recombinant enzyme in complex with nonhydrolyzable ATP analogue, adenosine 5'-adenylyl-beta,gamma-imidodiphosphate (AMP-PNP), and with citric acid, hanging drop vapor diffusion method, mixing of 30 mg/ml protein in 50 mM Tris-HCl, pH 8.0, 0.1 M NaCl, 5 mM MgCl2, and 1 mM DTT, with an equal volume of mother liquor containing 0.4 M ammonium citrate dibasic, pH 5.0, and 21% w/v PEG 3350, soaking of crystals in 50 mM AMP-PNP, X-ray diffraction structure determination and analysis at 2.1-2.6 A resolution

Giardia intestinalis

General Stability

General Stability	Organism
DTT is required to prevent the protein from aggregation	Giardia intestinalis

Metals/Ions

Metals/Ions	Comment	Organism	Structure
Mg2+	required	Giardia intestinalis

Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.	Reac.
ATP + NH3 + CO2	Giardia intestinalis	-	ADP + carbamoyl phosphate	-	r

Organism

Organism	UniProt	Comment	Textmining
Giardia intestinalis	O97438	gene cbk	-
no activity in Homo sapiens	-	-	-

Reaction

Reaction	Comment	Organism	Reaction ID
ATP + NH3 + hydrogencarbonate = ADP + carbamoyl phosphate + H2O	the protein residues involved in ligand binding, together with a model of the transition state, suggest that catalysis follows an in-line, predominantly dissociative, phosphotransfer reaction mechanism, and that closure of the flexible auxiliary domain is required to protect the transition state from bulk solvent. Model of the transition state, overview	Giardia intestinalis	a

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.	Reac.
ATP + NH3 + CO2	-	Giardia intestinalis	ADP + carbamoyl phosphate	-	r
additional information	ligand binding involves conformational flexibility of an auxiliary domain (amino acid residues 123-170), which exhibits open or closed conformations or structural disorder, depending on the bound ligand	Giardia intestinalis	?	-	?

Subunits

Subunits	Comment	Organism
More	the enzyme structure shows a core alpha/beta domain. A region comprising 30 amino acid residues flanking the active site is largely disordered in the crystal and has a possible role for enzyme conformational transition during catalysis	Giardia intestinalis

Synonyms

Synonyms	Comment	Organism
Cbk	-	Giardia intestinalis

Cofactor

Cofactor	Comment	Organism
ADP	-	Giardia intestinalis
ATP	-	Giardia intestinalis
additional information	nucleotide binding structure and conformational flexibility analysis, overview	Giardia intestinalis

General Information

General Information	Comment	Organism
metabolism	carbamate kinase catalyzes the last step of the essential L-arginine pathway, converting ADP and carbamoyl phosphate to ATP and ammonium carbamate	Giardia intestinalis