Literature summary for 3.5.2.6 extracted from

Yamaguchi, Y.; Kuroki, T.; Yasuzawa, H.; Higashi, T.; Jin, W.; Kawanami, A.; Yamagata, Y.; Arakawa, Y.; Goto, M.; Kurosaki, H.
Probing the role of Asp-120(81) of metallo-beta-lactamase (IMP-1) by site-directed mutagenesis, kinetic studies, and X-ray crystallography (2005), J. Biol. Chem., 280, 20824-20832.

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Cloned(Commentary)

Cloned (Comment)	Organism
expression in Escherichia coli	Serratia marcescens

Crystallization (Commentary)

Crystallization (Comment)	Organism
hanging-drop vapour diffusion method. Three-dimensional structures of D120A mutant and D120E mutant determined at 2.0 A and 3.0 A resolution, respectively	Serratia marcescens

Protein Variants

Protein Variants	Comment	Organism
D120A	kcat/KM is up to 425000fold lower than the wild-type enzyme. Ki-value for phosphate is 450fold lower than wild-type value	Serratia marcescens
D120E	kcat/KM is up to 136000fold lower than the wild-type enzyme. the Zn-Zn distance is increased by 0.3 A compared with wild-type enzyme	Serratia marcescens

Inhibitors

Inhibitors	Comment	Organism	Structure
phosphate	competitive inhibition. 50 mM, 30% decrease of wild-type activity. 5 mM, 90% decrease of activity of mutant enzyme D120A	Serratia marcescens

KM Value [mM]

KM Value [mM]	KM Value Maximum [mM]	Substrate	Comment	Organism	Structure
0.0012	-	nitrocefin	mutant enzyme D120E	Serratia marcescens
0.0013	-	nitrocefin	mutant enzyme D120A	Serratia marcescens
0.008	-	cephaloridine	wild-type enzyme	Serratia marcescens
0.02	-	nitrocefin	wild-type enzyme	Serratia marcescens
0.027	-	nitrocefin	mutant enzyme D120A, 1 mM Zn(NO3)2 added	Serratia marcescens
0.045	-	Imipenem	wild-type enzyme	Serratia marcescens
0.05	-	nitrocefin	mutant enzyme D120E, 1 mM Zn(NO3)2 added	Serratia marcescens
0.08	-	benzylpenicillin	wild-type enzyme	Serratia marcescens
0.15	-	cephaloridine	mutant enzyme D120A, 1 mM Zn(NO3)2 added	Serratia marcescens
0.2	-	cephaloridine	mutant enzyme D120E	Serratia marcescens
0.2	-	cephaloridine	mutant enzyme D120E, 1 mM Zn(NO3)2 added	Serratia marcescens
0.27	-	cephaloridine	mutant enzyme D120A	Serratia marcescens
0.64	-	Imipenem	mutant enzyme D120A	Serratia marcescens
0.75	-	Imipenem	mutant enzyme D120E	Serratia marcescens
2.6	-	benzylpenicillin	mutant enzyme D120A	Serratia marcescens
3.1	-	Imipenem	mutant enzyme D120A, 1 mM Zn(NO3)2 added	Serratia marcescens
8	-	benzylpenicillin	mutant enzyme D120A, 1 mM Zn(NO3)2 added	Serratia marcescens

Metals/Ions

Metals/Ions	Comment	Organism	Structure
Zinc	the Zn-Zn distance in D120E mutant is increased by 0.3 A compared with wild-type enzyme	Serratia marcescens

Organism

Organism	UniProt	Comment	Textmining
Serratia marcescens	P52699	-	-

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.	Reac.
benzylpenicillin + H2O	-	Serratia marcescens	(2R,4S)-2-[(R)-carboxy(2-phenylacetamido)methyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid	-	?
cephaloridine + H2O	-	Serratia marcescens	(2R)-2-[(R)-carboxy[(thiophen-2-ylacetyl)amino]methyl]-5-(pyridinium-1-ylmethyl)-3,6-dihydro-2H-1,3-thiazine-4-carboxylate	-	?
imipenem + H2O	-	Serratia marcescens	(5R)-5-[(1S,2R)-1-carboxy-2-hydroxypropyl]-3-({2-[(iminomethyl)amino]ethyl}sulfanyl)-4,5-dihydro-1H-pyrrole-2-carboxylic acid	-	?
nitrocefin + H2O	-	Serratia marcescens	(2R)-2-{(R)-carboxy[2-(thiophen-2-yl)acetamido]methyl}-5-[(E)-2-(2,4-dinitrophenyl)ethenyl]-3,6-dihydro-2H-1,3-thiazine-4-carboxylic acid	-	?

Synonyms

Synonyms	Comment	Organism
IMP-1	-	Serratia marcescens
metallo-beta-lactamase IMP-1	-	Serratia marcescens

Turnover Number [1/s]

Turnover Number Minimum [1/s]	Turnover Number Maximum [1/s]	Substrate	Comment	Organism	Structure
0.0035	-	cephaloridine	mutant enzyme D120A, 1 mM Zn(NO3)2 added	Serratia marcescens
0.022	-	cephaloridine	mutant enzyme D120E, 1 mM Zn(NO3)2 added	Serratia marcescens
0.17	-	benzylpenicillin	mutant enzyme D120A, 1 mM Zn(NO3)2 added	Serratia marcescens
0.22	-	cephaloridine	mutant enzyme D120E	Serratia marcescens
0.23	-	cephaloridine	mutant enzyme D120A	Serratia marcescens
0.27	-	nitrocefin	mutant enzyme D120A	Serratia marcescens
0.53	-	benzylpenicillin	mutant enzyme D120A	Serratia marcescens
0.55	-	nitrocefin	mutant enzyme D120E	Serratia marcescens
2.03	-	Imipenem	mutant enzyme D120A	Serratia marcescens
3.17	-	Imipenem	mutant enzyme D120A, 1 mM Zn(NO3)2 added	Serratia marcescens
3.7	-	Imipenem	mutant enzyme D120E	Serratia marcescens
4.17	-	nitrocefin	mutant enzyme D120E, 1 mM Zn(NO3)2 added	Serratia marcescens
7.5	-	nitrocefin	mutant enzyme D120A, 1 mM Zn(NO3)2 added	Serratia marcescens
90	-	cephaloridine	wild-type enzyme	Serratia marcescens
123.3	-	Imipenem	wild-type enzyme	Serratia marcescens
466.7	-	nitrocefin	wild-type enzyme	Serratia marcescens
535	-	nitrocefin	wild-type enzyme	Serratia marcescens
650	-	benzylpenicillin	wild-type enzyme	Serratia marcescens

Ki Value [mM]

Ki Value [mM]	Ki Value maximum [mM]	Inhibitor	Comment	Organism	Structure
0.00032	-	phosphate	mutant enzyme D120A	Serratia marcescens
0.144	-	phosphate	wild-type value	Serratia marcescens

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Release 2023.1 (January 2023)