Literature summary for 3.1.11.1 extracted from

Korada, S.K.; Johns, T.D.; Smith, C.E.; Jones, N.D.; McCabe, K.A.; Bell, C.E.
Crystal structures of Escherichia coli exonuclease I in complex with single-stranded DNA provide insights into the mechanism of processive digestion (2013), Nucleic Acids Res., 41, 5887-5897.

Cloned(Commentary)

Cloned (Comment)	Organism
recombinant expression of the His-tagged enzyme in Escherichia coli strain BL21(AI)	Escherichia coli

Crystallization (Commentary)

Crystallization (Comment)	Organism
purified enzyme in complex with four different ssDNA substrates, 5'-Cy5-dT13, 5'-Cy5-dA13, dA16 and dT13, hanging drop vapor diffusion, 0.002 ml of 10 mg/ml enzyme in 20 mM Tris, 1 mM DTT, 10 mM EDTA, pH 8.0, with a 1.2 molar excess of oligonucleotide, is mixed with 0.002 ml of reservoir solution containing 0.9-1.5M ammonium sulfate, 3.756.0% 2-propanol and 25% glycerol, 1 week, X-ray diffraction structure determination and analysis at 2.0-3.7 A resolution	Escherichia coli

Crystallization (Comment)

Organism

purified enzyme in complex with four different ssDNA substrates, 5'-Cy5-dT13, 5'-Cy5-dA13, dA16 and dT13, hanging drop vapor diffusion, 0.002 ml of 10 mg/ml enzyme in 20 mM Tris, 1 mM DTT, 10 mM EDTA, pH 8.0, with a 1.2 molar excess of oligonucleotide, is mixed with 0.002 ml of reservoir solution containing 0.9-1.5M ammonium sulfate, 3.756.0% 2-propanol and 25% glycerol, 1 week, X-ray diffraction structure determination and analysis at 2.0-3.7 A resolution

Escherichia coli

Metals/Ions

Metals/Ions	Comment	Organism	Structure
Mg2+	required, binds at the active site, the Mg2+ ion is coordinated with near octahedral geometry to the scissile phosphate, the carboxylate of Asp15 and three water molecules	Escherichia coli

Organism

Organism	UniProt	Comment	Textmining
Escherichia coli	P04995	-	-

Purification (Commentary)

Purification (Comment)	Organism
recombinant His-tagged enzyme from Escherichia coli strain BL21(AI) by nickel affinity chromatography and ultrafiltration	Escherichia coli

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.	Reac.
additional information	exonuclease I digests single-stranded DNA in the 3'-5' direction in a highly processive manner. The interactions at the anchor site, which involve all three domains of the enzyme protein and three consecutive nucleotides of the ssDNA	Escherichia coli	?	-	?

Synonyms

Synonyms	Comment	Organism
Exo1	-	Escherichia coli
exonuclease 1	-	Escherichia coli

Temperature Optimum [°C]

Temperature Optimum [°C]	Temperature Optimum Maximum [°C]	Comment	Organism
37	-	assay at	Escherichia coli

pH Optimum

pH Optimum Minimum	pH Optimum Maximum	Comment	Organism
8.5	-	assay at	Escherichia coli

General Information

General Information	Comment	Organism
evolution	the enzyme is a member of the RAD2 nuclease family	Escherichia coli
additional information	the enzyme crystal structure, in the absence of DNA, shows a C-shaped molecule with three domains that form a central positively charged groove. The active site is at the bottom of the groove, while an extended loop, proposed to encircle the DNA, crosses over the groove. Analysis of the active site structure of enzyme with bound ssDNA nucleotides, overview	Escherichia coli