Literature summary for 3.1.26.4 extracted from

Chai, Q.; Qiu, J.; Chapados, B.R.; Shen, B.
Archaeoglobus fulgidus RNase HII in DNA replication: enzymological functions and activity regulation via metal cofactors (2001), Biochem. Biophys. Res. Commun., 286, 1073-1081.

Protein Variants

Protein Variants	Comment	Organism
D101N	mutation results in more than 95% decrease in activity compared to wild-type enzyme	Archaeoglobus fulgidus
D129A	Km-value for the 8-mer RNA-DNA/DNA hybrid substrate is 2.2fold higher than the wild-type value. The turnover number is 30% of the wild-type value	Archaeoglobus fulgidus
D129N	mutation results in about 75% decrease in activity compared to wild-type enzyme. Km-value for the 8-mer RNA-DNA/DNA hybrid substrate is 70% of the wild-type value. The turnover number is 20% of the wild-type value	Archaeoglobus fulgidus
D167A	no loss of activity	Archaeoglobus fulgidus
D37A	mutation results in about 90% decrease in activity compared to wild-type enzyme. Km-value for the 8-mer RNA-DNA/DNA hybrid substrate is 80% of the wild-type value. The turnover number is 5% of the wild-type value	Archaeoglobus fulgidus
D37N	mutation results in about 10% decrease in activity compared to wild-type enzyme. Km-value for the 8-mer RNA-DNA/DNA hybrid substrate is 1.5fold higher than the wild-type value. The turnover number is 40% of the wild-type value	Archaeoglobus fulgidus
D6N	mutation results in more than 95% decrease in activity compared to wild-type enzyme	Archaeoglobus fulgidus
E7Q	mutation results in more than 95% decrease in activity compared to wild-type enzyme	Archaeoglobus fulgidus
K143A	mutation results in about 80% decrease in activity compared to wild-type enzyme. Km-value for the 8-mer RNA-DNA/DNA hybrid substrate is 31.3fold higher than the wild-type value. The turnover number is 150% of the wild-type value	Archaeoglobus fulgidus
K39A	mutation results in about 30% decrease in activity compared to wild-type enzyme	Archaeoglobus fulgidus
L41A	no loss of activity	Archaeoglobus fulgidus
additional information	of the highly conserved residues, mutations at Ser38, Lys39, Leu41, Arg45, Ser139, and Asp167 do not significantly affect the enzyme activity. Conversion of Asp6 to Asn, Glu7 to Gln, or Asp101 to Asn almost completely inactivated the enzyme, suggesting that these carboxylic acid groups of D6, E7, and D101 are essential for catalysis	Archaeoglobus fulgidus
R146A	mutation results in more than 95% decrease in activity compared to wild-type enzyme. Km-value for the 8-mer RNA-DNA/DNA hybrid substrate is 26.7fold higher than the wild-type value. The turnover number is 140% of the wild-type value	Archaeoglobus fulgidus
R188A	no loss of activity	Archaeoglobus fulgidus
R45A	mutation results in about 5% decrease in activity compared to wild-type enzyme	Archaeoglobus fulgidus
R46A	mutation results in about 50% decrease in activity compared to wild-type enzyme. Km-value for the 8-mer RNA-DNA/DNA hybrid substrate is 60fold higher than the wild-type value. The turnover number is 130% of the wild-type value	Archaeoglobus fulgidus
S139A	no loss of activity	Archaeoglobus fulgidus
S139A	mutation results in about 40% decrease in activity compared to wild-type enzyme	Archaeoglobus fulgidus
S38A	mutation results in about 35% decrease in activity compared to wild-type enzyme	Archaeoglobus fulgidus
Y164A	mutation results in more than 95% decrease in activity compared to wild-type enzyme. Km-value for the 8-mer RNA-DNA/DNA hybrid substrate is 44.7fold higher than the wild-type value. The turnover number is 160% of the wild-type value	Archaeoglobus fulgidus

Metals/Ions

Metals/Ions	Comment	Organism
Ca2+	strictly metal-dependent nuclease. It exhibits activity in the presence of Mg2+, Mn2+, Co2+ or Ni2+, whereas no activity is observed in the absence of these metal ions. Little activity is detected in the presence of other metals including Co3+, Cu2+, Zn2+, and Ca2+	Archaeoglobus fulgidus
Co2+	strictly metal-dependent nuclease. It exhibits activity in the presence of Mg2+, Mn2+, Co2+ or Ni2+, whereas no activity is observed in the absence of these metal ions. Optimum concentration of Co2+ or Ni2+ needed for aRNase HII activity is 1 mM. Little activity is detected in the presence of other metals including Co3+, Cu2+, Zn2+, and Ca2+	Archaeoglobus fulgidus
Co3+	strictly metal-dependent nuclease. It exhibits activity in the presence of Mg2+, Mn2+, Co2+ or Ni2+, whereas no activity is observed in the absence of these metal ions. Little activity is detected in the presence of other metals including Co3+, Cu2+, Zn2+, and Ca2+	Archaeoglobus fulgidus
Cu2+	strictly metal-dependent nuclease. It exhibits activity in the presence of Mg2+, Mn2+, Co2+ or Ni2+, whereas no activity is observed in the absence of these metal ions. Little activity is detected in the presence of other metals including Co3+, Cu2+, Zn2+, and Ca2+	Archaeoglobus fulgidus
Mg2+	strictly metal-dependent nuclease. It exhibits activity in the presence of Mg2+, Mn2+, Co2+ or Ni2+, whereas no activity is observed in the absence of these metal ions. Optimal enzyme activities in the presence of Mg2+ or Mn2+ are 3fold to 7fold higher than that with the other two metals. Maximum aRNase HII activity is observed at concentrations of 6.4 mM Mg2+. The specific activity determined in the presence of 50 mM Mn2+ is 35% of that determined in the presence of 6.4 mM Mg2+. When Mn2+ is added in the presence of 1.6 mM Mg2+, the enzyme activity increases gradually as the Mn2+ concentration reaches 50 mM and decreases after that point. At equal concentrations of Mn2+ and Mg2+ (1.6 mM), the enzyme activity is reduced 10-fold compared to the activity in the presence of only Mg2+. Little activity is detected in the presence of other metals including Co3+, Cu2+, Zn2+, and Ca2+	Archaeoglobus fulgidus
Mn2+	strictly metal-dependent nuclease. It exhibits activity in the presence of Mg2+, Mn2+, Co2+ or Ni2+, whereas no activity is observed in the absence of these metal ions. Optimal enzyme activities in the presence of Mg2+ or Mn2+ are 3fold to 7fold higher than that with the other two metals. Maximum aRNase HII activity is observed at concentrations of 50 mM Mn2+. The specific activity determined in the presence of 50 mM Mn2+ is 35% of that determined in the presence of 6.4 mM Mg2+. Little activity is detected in the presence of other metals including Co3+, Cu2+, Zn2+, and Ca2+	Archaeoglobus fulgidus
Ni2+	strictly metal-dependent nuclease. It exhibits activity in the presence of Mg2+, Mn2+, Co2+ or Ni2+, whereas no activity is observed in the absence of these metal ions. Optimum concentration of Co2+ or Ni2+ needed for aRNase HII activity is 1 mM. Little activity is detected in the presence of other metals including Co3+, Cu2+, Zn2+, and Ca2+	Archaeoglobus fulgidus
Zn2+	strictly metal-dependent nuclease. It exhibits activity in the presence of Mg2+, Mn2+, Co2+ or Ni2+, whereas no activity is observed in the absence of these metal ions. Little activity is detected in the presence of other metals including Co3+, Cu2+, Zn2+, and Ca2+	Archaeoglobus fulgidus

Organism

Organism	UniProt	Comment	Textmining
Archaeoglobus fulgidus	O29634	-	-

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.	Reac.
RNA/DNA hybrid + H2O	model Okazaki fragment 18-mer RNA-DNA/DNA substrate (Q18), RNase H is a structure-specific endonuclease, it cleaves the 25-bp RNA/DNA hybrid at multiple sites, indicating that the enzyme cleaves RNA/DNA in a sequence-independent manner. In the absence of complementary DNA, the chimeric RNA-DNA strand is not cleaved by the enzyme	Archaeoglobus fulgidus	?	-	?

Synonyms

Synonyms	Comment	Organism
aRNase HII	-	Archaeoglobus fulgidus
RNase HII	-	Archaeoglobus fulgidus

General Information

General Information	Comment	Organism
physiological function	the enzyme is involved in RNA primer removal during DNA replication	Archaeoglobus fulgidus