Literature summary for 2.7.1.74 extracted from

Sabini, E.; Hazra, S.; Konrad, M.; Burley, S.K.; Lavie, A.
Structural basis for activation of the therapeutic L-nucleoside analogs 3TC and troxacitabine by human deoxycytidine kinase (2007), Nucleic Acids Res., 35, 186-192.

Cloned(Commentary)

Cloned (Comment)	Organism
mutant protein expressed in Escherichia coli	Homo sapiens

Crystallization (Commentary)

Crystallization (Comment)	Organism
hanging drop vapour diffusion method, mutant enzyme crystallized in complex with its substrates (-)-beta-2,3-dideoxy-3-thiacytidine and troxacitabine	Homo sapiens
mutant C9S/C45S/C59S/C146S in complex with L-nucleosides (-)-beta-2',3'-dideoxy-3'-thiacytidine and troxacitabine. The nucleoside binding-site tolerates substrates with different chiral configurations by maintaining virtually all of the protein-ligand interactions responsible for productive substrate positioning. The pseudo-symmetry of nucleosides and nucleoside analogs in combination with their conformational flexibility allows the L- and D-enantiomeric forms to adopt similar shapes when bound to the enzyme	Homo sapiens

Crystallization (Comment)

Organism

hanging drop vapour diffusion method, mutant enzyme crystallized in complex with its substrates (-)-beta-2,3-dideoxy-3-thiacytidine and troxacitabine

Homo sapiens

mutant C9S/C45S/C59S/C146S in complex with L-nucleosides (-)-beta-2',3'-dideoxy-3'-thiacytidine and troxacitabine. The nucleoside binding-site tolerates substrates with different chiral configurations by maintaining virtually all of the protein-ligand interactions responsible for productive substrate positioning. The pseudo-symmetry of nucleosides and nucleoside analogs in combination with their conformational flexibility allows the L- and D-enantiomeric forms to adopt similar shapes when bound to the enzyme

Homo sapiens

Protein Variants

Protein Variants	Comment	Organism
C9S/C45S/C59S/C146S	engineered protein has a significantly improved crystallization behaviour compared with the wild type protein	Homo sapiens
C9S/C45S/C59S/C146S	mutation of the four surface-exposed Cys residues, constructued for crystallization. Mutant displays moderate kinetic differences in the catalytic efficiency when compared with wild-type	Homo sapiens

KM Value [mM]

KM Value [mM]	KM Value Maximum [mM]	Substrate	Comment	Organism
0.003	-	(-)-beta-2',3'-dideoxy-3'-thiacytidine	wild type enzyme with ATP as phosphate donor, 37°C, pH 7.5	Homo sapiens
0.0034	-	ATP	cosubstrate (-)-beta-2',3'-dideoxy-3'-thiacytidine, wild-type, 37°C, pH 7.5	Homo sapiens
0.008	-	(-)-beta-2',3'-dideoxy-3'-thiacytidine	C9S/C45S/C59S/C146S mutant enzyme with ATP as phosphate donor, 37°C, pH 7.5	Homo sapiens
0.008	-	(-)-beta-2',3'-dideoxy-3'-thiacytidine	wild type enzyme with UTP as phosphate donor, 37°C, pH 7.5	Homo sapiens
0.008	-	UTP	cosubstrate (-)-beta-2',3'-dideoxy-3'-thiacytidine, wild-type, 37°C, pH 7.5	Homo sapiens
0.0084	-	ATP	cosubstrate (-)-beta-2',3'-dideoxy-3'-thiacytidine, mutant C9S/C45S/C59S/C146S, 37°C, pH 7.5	Homo sapiens
0.0106	-	UTP	cosubstrate troxacitabine, wild-type, 37°C, pH 7.5	Homo sapiens
0.011	-	troxacitabine	wild type enzyme with UTP as phosphate donor, 37°C, pH 7.5	Homo sapiens
0.013	-	troxacitabine	wild type enzyme with ATP as phosphate donor, 37°C, pH 7.5	Homo sapiens
0.0132	-	ATP	cosubstrate troxacitabine, wild-type, 37°C, pH 7.5	Homo sapiens
0.0149	-	UTP	cosubstrate (-)-beta-2',3'-dideoxy-3'-thiacytidine, mutant C9S/C45S/C59S/C146S, 37°C, pH 7.5	Homo sapiens
0.015	-	(-)-beta-2',3'-dideoxy-3'-thiacytidine	C9S/C45S/C59S/C146S mutant enzyme with UTP as phosphate donor, 37°C, pH 7.5	Homo sapiens
0.0568	-	ATP	cosubstrate troxacitabine, mutant C9S/C45S/C59S/C146S, 37°C, pH 7.5	Homo sapiens
0.057	-	troxacitabine	C9S/C45S/C59S/C146S mutant enzyme with ATP as phosphate donor, 37°C, pH 7.5	Homo sapiens
0.0578	-	UTP	cosubstrate troxacitabine, mutant C9S/C45S/C59S/C146S, 37°C, pH 7.5	Homo sapiens
0.058	-	troxacitabine	C9S/C45S/C59S/C146Smutant enzyme with UTP as phosphate donor, 37°C, pH 7.5	Homo sapiens

Metals/Ions

Metals/Ions	Comment	Organism	Structure
Mg2+	in complex with ATP or UTP	Homo sapiens

Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.
additional information	Homo sapiens	dCK is able to phosphorylate both D- and L-nucleosides and nucleoside analogs	?	-	?
NTP + (-)-beta-2',3'-dideoxy-3'-thiacytidine	Homo sapiens	activation of the clinically relevant substrate	NDP + (-)-beta-2',3'-dideoxy-3'-thiacytidine 5'-phosphate	-	?
NTP + troxacitabine	Homo sapiens	activation of the clinically relevant substrate	?	-	?

Organism

Organism	UniProt	Comment	Textmining
Homo sapiens	-	-	-
Homo sapiens	P27707	-	-

Purification (Commentary)

Purification (Comment)	Organism
recombinant protein from Escherichia coli	Homo sapiens

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.
ATP + (-)-beta-2',3'-dideoxy-3'-thiacytidine	-	Homo sapiens	ADP + (-)-beta-2',3'-dideoxy-3'-thiacytidine 5'-phosphate	-	?
ATP + (-)-beta-2',3'-dideoxy-3'-thiacytidine	i.e. lamivudine	Homo sapiens	ADP + (-)-beta-2',3'-dideoxy-3'-thiacytidine 5'-phosphate	-	?
ATP + D-2'-deoxycytidine	-	Homo sapiens	ADP + D-2'-deoxycytidine 5'-phosphate	-	?
ATP + L-2'-deoxycytidine	-	Homo sapiens	ADP + L-2'-deoxycytidine 5'-phosphate	-	?
ATP + troxacitabine	-	Homo sapiens	ADP + troxacitabine 5'-phosphate	-	?
additional information	dCK is able to phosphorylate both D- and L-nucleosides and nucleoside analogs	Homo sapiens	?	-	?
NTP + (-)-beta-2',3'-dideoxy-3'-thiacytidine	activation of the clinically relevant substrate	Homo sapiens	NDP + (-)-beta-2',3'-dideoxy-3'-thiacytidine 5'-phosphate	-	?
NTP + troxacitabine	activation of the clinically relevant substrate	Homo sapiens	?	-	?
UTP + (-)-beta-2',3'-dideoxy-3'-thiacytidine	-	Homo sapiens	UDP + (-)-beta-2',3'-dideoxy-3'-thiacytidine 5'-phosphate	-	?
UTP + D-2'-deoxycytidine	-	Homo sapiens	UDP + D-2'-deoxycytidine 5'-phosphate	-	?
UTP + L-2'-deoxycytidine	-	Homo sapiens	UDP + L-2'-deoxycytidine 5'-phosphate	-	?
UTP + troxacitabine	-	Homo sapiens	UDP + troxacitabine 5'-phosphate	-	?

Synonyms

Synonyms	Comment	Organism
dCK	-	Homo sapiens

Turnover Number [1/s]

Turnover Number Minimum [1/s]	Turnover Number Maximum [1/s]	Substrate	Comment	Organism
0.01	-	UTP	cosubstrate L-2'-deoxycytidine, wild-type, 37°C, pH 7.5	Homo sapiens
0.012	-	ATP	cosubstrate L-2'-deoxycytidine, wild-type, 37°C, pH 7.5	Homo sapiens
0.028	-	(-)-beta-2',3'-dideoxy-3'-thiacytidine	C9S/C45S/C59S/C146S mutant enzyme with ATP as phosphate donor, 37°C, pH 7.5	Homo sapiens
0.028	-	ATP	cosubstrate (-)-beta-2',3'-dideoxy-3'-thiacytidine, mutant C9S/C45S/C59S/C146S, 37°C, pH 7.5	Homo sapiens
0.03	-	(-)-beta-2',3'-dideoxy-3'-thiacytidine	wild type enzyme with ATP as phosphate donor, 37°C, pH 7.5	Homo sapiens
0.03	-	ATP	cosubstrate (-)-beta-2',3'-dideoxy-3'-thiacytidine, wild-type, 37°C, pH 7.5	Homo sapiens
0.033	-	ATP	cosubstrate D-2'-deoxycytidine, wild-type, 37°C, pH 7.5	Homo sapiens
0.036	-	ATP	cosubstrate L-2'-deoxycytidine, mutant C9S/C45S/C59S/C146S, 37°C, pH 7.5	Homo sapiens
0.042	-	UTP	cosubstrate L-2'-deoxycytidine, mutant C9S/C45S/C59S/C146S, 37°C, pH 7.5	Homo sapiens
0.049	-	UTP	cosubstrate D-2'-deoxycytidine, wild-type, 37°C, pH 7.5	Homo sapiens
0.072	-	(-)-beta-2',3'-dideoxy-3'-thiacytidine	C9S/C45S/C59S/C146S mutant enzyme with UTP as phosphate donor, 37°C, pH 7.5	Homo sapiens
0.072	-	UTP	cosubstrate (-)-beta-2',3'-dideoxy-3'-thiacytidine, mutant C9S/C45S/C59S/C146S, 37°C, pH 7.5	Homo sapiens
0.095	-	troxacitabine	wild type enzyme with ATP as phosphate donor, 37°C, pH 7.5	Homo sapiens
0.095	-	ATP	cosubstrate troxacitabine, wild-type, 37°C, pH 7.5	Homo sapiens
0.102	-	(-)-beta-2',3'-dideoxy-3'-thiacytidine	wild type enzyme with UTP as phosphate donor, 37°C, pH 7.5	Homo sapiens
0.102	-	UTP	cosubstrate (-)-beta-2',3'-dideoxy-3'-thiacytidine, wild-type, 37°C, pH 7.5	Homo sapiens
0.173	-	ATP	cosubstrate D-2'-deoxycytidine, mutant C9S/C45S/C59S/C146S, 37°C, pH 7.5	Homo sapiens
0.179	-	troxacitabine	wild type enzyme with UTP as phosphate donor, 37°C, pH 7.5	Homo sapiens
0.179	-	UTP	cosubstrate troxacitabine, wild-type, 37°C, pH 7.5	Homo sapiens
0.192	-	troxacitabine	C9S/C45S/C59S/C146S mutant enzyme with ATP as phosphate donor, 37°C, pH 7.5	Homo sapiens
0.192	-	ATP	cosubstrate troxacitabine, mutant C9S/C45S/C59S/C146S, 37°C, pH 7.5	Homo sapiens
0.217	-	UTP	cosubstrate D-2'-deoxycytidine, mutant C9S/C45S/C59S/C146S, 37°C, pH 7.5	Homo sapiens
0.524	-	troxacitabine	C9S/C45S/C59S/C146S mutant enzyme with UTP as phosphate donor, 37°C, pH 7.5	Homo sapiens
0.524	-	UTP	cosubstrate troxacitabine, mutant C9S/C45S/C59S/C146S, 37°C, pH 7.5	Homo sapiens

Cofactor

Cofactor	Comment	Organism	Structure
ATP	-	Homo sapiens
UTP	-	Homo sapiens