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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+
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+
Na+
the enzyme exhibits the highest activity in the presence of 100 mm NaCl
NH4Cl
-
enzyme form H2 is mostly inactive at low salt and requires 100-200 mM concentration for maximal activity. NH4Cl is more efficient than NaCl
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+
Ca2+
Halalkalibacterium halodurans
binding structure
Co2+
the enzyme exhibits the highest activity in the presence of 5 mM Mn2+, 1 mM Co2+, or 10 mM Mg2+, respectively. The specific activity of the enzyme determined with 5 mM MnCl2 is slightly higher than that determined with 10 mM MgCl2, and about 2 folds higher than that determined with 1 mM CoCl2
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+
Co2+
-
divalent metal required, optimal concentration: 20 mM, 70% of the activity with Mg2+
Co2+
-
with Co2+ as activator the decreasing order of preference is G, A, U, C
Co2+
-
activates cleavage of only poly(A) hybrids
Co2+
-
cobalt hexaamine activates
Co2+
-
divalent metal ion required. Maximal activity is obtained with 10 mM Mg2+, 5 mM Co2+ or 0.5 mM Mn2+
Co2+
-
10 mM Co2+ supports activity, with only minor inhibition observed at higher concentrations
Co2+
activates, best at 0.5 mM
Co2+
the enzyme cleaves an RNA strand of the 12-bp RNA/DNA hybrid at multiple sites only in the presence of Mn2+, Mg2+, Co2+ or Ni2+, but not in the presence of Cu2+, Ca2+ or Zn2+, or in the absence of divalent metal ions. The enzyme cleaves an RNA/RNA duplex in the presence of Mn2+ or Co2+
K+
the enzyme exhibits the highest activity in the presence of 100 mm KCl
K+
-
optimum KCl concentration of 100-150 mM
KCl
-
-
KCl
-
activates at 50 mM, inhibits at 200 mM
KCl
equally activating as NaCl
KCl
highly activating, best at 100-200 mM salt, KCl is preferred
KCl
-
activity increases with concentrations up to 50 mM
KCl
-
stimulates enzyme HB2
KCl
-
enzyme form H2 is mostly inactive at low salt and requires 100-200 mM concentration for maximal activity. KCl is more efficient than NaCl
KCl
activates best at 110 mM, preferred to NaCl
KCl
activates, best at 50 mM for the full-length enzyme, and at 10 mM for the C-terminal domain
KCl
requires 50 mm KCl for maximal activity
Mg2+
the enzyme exhibits the highest activity in the presence of 5 mM Mn2+, 1 mM Co2+, or 10 mM Mg2+, respectively. The specific activity of the enzyme determined with 5 mM MnCl2 is slightly higher than that determined with 10 mM MgCl2, and about 2 folds higher than that determined with 1 mM CoCl2
Mg2+
highest activity in the presence of 10 mM MgCl2
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+
Mg2+
-
divalent cation required
Mg2+
-
Mn2+ is preferred over Mg2+
Mg2+
-
ribonuclease H IIa activity is preferentially activated by Mn2+ as opposed to Mg2+
Mg2+
-
optimal concentration: 2 mM
Mg2+
-
optimal activity at 10 mM
Mg2+
-
with Mg2+ as activator the decreasing order of preference is A, U/C, G
Mg2+
-
activates cleavage of only the hybrid combinations containing purine ribo strands
Mg2+
-
a divalent metal ion is required, dependent on the isozyme
Mg2+
-
Mg2+-dependent enzyme requires 10-15 mM Mg2+ for optimal activity
Mg2+
-
required, optimal activity at 2-4 mM
Mg2+
-
characterization of the strong magnesium-binding site
Mg2+
-
absolutely dependent on for activity, can be substituted by Mn2+
Mg2+
-
binding involves Asp10 and is pH-dependent, binds in the active site pocket of the natively folded enzyme only, stabilizes the enzyme conformation, effect of metal binding on enzyme folding kinetics
Mg2+
maximal activity at 5 mM, binds to metal ion binding site 1 not 2, required, can substitute for Mn2+
Mg2+
Mn2+ or Mg2+ are required for catalytic activity
Mg2+
-
Mg2+-dependent enzyme requires 15-20 mM Mg2+ for maximal activity
Mg2+
-
optimal activity with 10-15 mM
Mg2+
required, best at 50 mM
Mg2+
required, highest activity at 50 mM
Mg2+
the enzyme requires Mn2+ or Mg2+ ions, Mg2+ is preferred, coordinated with Asp97, Glu98, and Asp202
Mg2+
-
the optimum concentration is 10 mM
Mg2+
Halalkalibacterium halodurans
-
required
Mg2+
Halalkalibacterium halodurans
binding structure
Mg2+
Halalkalibacterium halodurans
the inability of the enzyme to cleave DNA is due to the deviating curvature of the DNA strand relative to the substrate RNA strand and the absence of Mg2+ at the active site
Mg2+
Halalkalibacterium halodurans
the two Mg2+ support the formation of a meta-stable phosphorane intermediate along the reaction
Mg2+
Halalkalibacterium halodurans
required, two Mg2+ ions are located at specific positions in the catalytic site
Mg2+
-
required, four RNaseH active site conserved carboxylates (the DEDD motif) coordinate two divalent cations, usually Mg2+
Mg2+
-
divalent metal ion required. Maximal activity is obtained with 10 mM Mg2+, 5 mM Co2+ or 0.5 mM Mn2+
Mg2+
-
broad optimum around 20 mM
Mg2+
required for catalysis
Mg2+
-
required, best at 10 mM
Mg2+
highest activity in presence of 5-10 mM
Mg2+
-
two Mg2+ ions in the RNase H active site, required. A two-metal ion mechanism requires that metal ion A activates a water molecule as a nucleophile and moves towards ion B, bringing the nucleophile in close proximity to the scissile bond, while metal ion B destabilizes the substrate-enzyme interaction and lowers the energy barrier to product formation
Mg2+
-
Mg2+ best supports the enzyme, with an optimal concentration of 10 mM
Mg2+
-
the enzyme is stabilized in the presence of Mg2+
Mg2+
-
optimal concentrations for the 4 enzyme forms at pH 7.6 and at pH 8.3
Mg2+
-
1:1 binding stoichiometry in absence of substrate at pH 8.0, activates, no binding to the enzyme but still weak activation without substrate at pH 6.5
Mg2+
-
enzyme form H2: requirement for divalent metal ion can be satisfied only by Mg2+. Enzyme form H1: requirement for a divalent metal ion can be satisfied by Mg2+ or with a stronger preference with Mn2+
Mg2+
-
enzyme is stimulated equally well by Mg2+, optimum concentration 5-10 mM, or Mn2+, optimum concentration 0.5-0.6 mM
Mg2+
-
the type 2 RNase H is an Mg2+ and alkaline pH-dependent enzyme
Mg2+
activates reaction with RNA-DNA heteroduplex and RNA-RNA duplex
Mg2+
-
optimal concentration is 6 mM
Mg2+
-
divalent cation required
Mg2+
-
Mg2+ is preferred over Mn2+
Mg2+
-
required, optimal concentration: 10-15 mM Mg2+
Mg2+
-
isoenzyme I and II both require 10-15 mM Mg2+ for maximal activity. Isoenzyme II is maximally activated by Mg2+, some activity with Mn2+
Mg2+
-
required, optimal concentration: 17 mM
Mg2+
-
Mg2+ activates more than Mn2+, RNase H(70)
Mg2+
-
Mn2+ activates more than Mg2+, RNase H(42)
Mg2+
-
absolute requirement for Mg2+, optimal activity at 2-6 mM MgCl2
Mg2+
-
absolute requirement for divalent cations, preferably Mg2+, optimal activity at 25 mM
Mg2+
activates, best at 5 mM
Mg2+
-
RNases hydrolyze RNA/DNA in the presence of various divalent cofactors such as Mg2+ and Mn2+
Mg2+
the enzyme cleaves an RNA strand of the 12-bp RNA/DNA hybrid at multiple sites only in the presence of Mn2+, Mg2+, Co2+ or Ni2+, but not in the presence of Cu2+, Ca2+ or Zn2+, or in the absence of divalent metal ions
Mg2+
-
Mn2+ or Mg2+ required
Mg2+
the full-length and C-terminally truncated enzymes have similar activity, and both are around 600fold more active in the presence of Mn2+ compared to Mg2+, binding structure and activation mechanism, overview
Mg2+
the optimum concentration is 1 mM
Mg2+
the enzyme (Tma-RNase HI) and the C-terminal RNase H domain (Tma-CD) exhibit the highest activities in the presence of 1 mM MgCl2 and 0.1-5 mM MnCl2. Both proteins exhibit little activity (less than 0.01% of the maximal activity) in the presence of NiCl2, ZnCl2, CoCl2 or CaCl2. Tma-RNase HI prefers Mg2+ to Mn2+ because its maximal Mg2+-dependent activity is higher than its maximal Mn2+-dependent activity by 16fold. The enzyme specifically loses most of the Mg2+-dependent activity on removal of the hybrid binding domain and 87% of it by the mutation at the hybrid binding domain
Mg2+
-
dependent on, can substitute for Mg2+, activates the full length enzyme dependent on the N-terminal 47 amino acids
Mg2+
the enzyme prefers Mg2+ to Mn2+ ions for activity with maximal activity at 10 mM MgCl2
Mn2+
the enzyme exhibits the highest activity in the presence of 5 mM Mn2+, 1 mM Co2+, or 10 mM Mg2+, respectively. The specific activity of the enzyme determined with 5 mM MnCl2 is slightly higher than that determined with 10 mM MgCl2, and about 2 folds higher than that determined with 1 mM CoCl2
Mn2+
highest activity in the presence of 5 mM MnCl2
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+
Mn2+
-
divalent cation required
Mn2+
-
Mn2+ is preferred over Mg2+
Mn2+
-
with Mg2+ as activator the decreasing order of preference is A, U, C, G
Mn2+
-
activates enzymatic cleavage of all hybrid combinations
Mn2+
-
optimal concentration: 25 mM, 40% of the activation with Mg2+
Mn2+
-
optimal activity at 1 mM
Mn2+
-
ribonuclease H IIa activity is preferentially activated by Mn2+ as opposed to Mg2+
Mn2+
-
a divalent metal ion is required, dependent on the isozyme
Mn2+
-
0.4 mM Mn2+ required for optimal activity, some activity with Mg2+
Mn2+
-
absolutely dependent on for activity, can be substituted by Mg2+
Mn2+
required, maximal activity at 0.002-0.005 mM, can substitute for Mg2+, activates up to 0.1 mM, inhibitory above, enzyme contains 2 metal ion binding sites 1 and 2 with regulatory influence on each other, activating metal ion binding site is site 1, inhibitory binding site is site 2, overview, mutants E48A, E48Q, D134A, and D134N have only 1 active Mn2+-binding site
Mn2+
-
activates, two single binding sites: site 1 is formed by Glu48, Asp10, and Asp70, site 2 is formed by Asp10 and Asp134, Glu48 and Asp134 are absolutely required for enzyme activation, binding structure and one-to-two metal mechanism, overview
Mn2+
Mn2+ or Mg2+ are required for catalytic activity
Mn2+
-
0.4 mM Mn2+ required for optimal activity, some activity with Mg2+
Mn2+
less active than Mg2+, best at 10 mM
Mn2+
the enzyme requires Mn2+ or Mg2+ ions, Mg2+ is preferred, coordinated with Asp97, Glu98, and Asp202
Mn2+
-
the optimum concentration is 10 mM
Mn2+
Halalkalibacterium halodurans
required
Mn2+
Halalkalibacterium halodurans
binding structure
Mn2+
-
slightly active with Mn2+
Mn2+
-
divalent metal ion required. Maximal activity is obtained with 10 mM Mg2+, 5 mM Co2+ or 0.5 mM Mn2+
Mn2+
0.1-1 mM, 20-30% of maximum activity
Mn2+
-
required, best at 1 mM
Mn2+
-
5 mM Mn2+ supports activity, with only minor inhibition observed at higher concentrations
Mn2+
-
optimal concentrations for the 4 enzyme forms at pH 7.6 and at pH 8.3
Mn2+
-
1:1 binding stoichiometry in absence of substrate at pH 8.0, best activator, maximal activity at 10 mM and pH 8.0
Mn2+
-
enzyme form H1: requirement for a divalent metal ion can be satisfied by Mg2+ or with a stronger preference with Mn2+
Mn2+
-
enzyme is stimulated equally well by Mg2+, optimum concentration 5-10 mM, or Mn2+, optimum concentration 0.5-0.6 mM
Mn2+
wild-type digests RNA-RNA duplexes in presence of Mn2+
Mn2+
the enzyme digests an RNA-RNA duplex in the presence of Mn2+, no activity in presence of Mg2+
Mn2+
-
divalent cation required
Mn2+
-
optimal concentration is 2 mM
Mn2+
-
isoenzyme II is maximally active at 0.4 mM, some activity with Mg2+
Mn2+
-
optimal concentration 0.6 mM
Mn2+
-
Mg2+ is preferred over Mn2+
Mn2+
-
divalent cation required
Mn2+
-
Mn2+ is preferred over Mg2+
Mn2+
-
Mg2+ activates more than Mn2+, RNase H(70)
Mn2+
-
Mn2+ activates more than Mg2+, RNase H(42)
Mn2+
-
cation requirement can be fullfilled to some extent by 2 mM Mn2+
Mn2+
activates, best at 1 mM, strongly preferred divalent cation
Mn2+
-
RNases hydrolyze RNA/DNA in the presence of various divalent cofactors such as Mg2+ and Mn2+
Mn2+
-
the activity of wild-type protein is stimulated by Mn2+, whereas this cation significantly inhibits the activity of C-terminal truncated mutant proteins
Mn2+
the enzyme cleaves an RNA strand of the 12-bp RNA/DNA hybrid at multiple sites only in the presence of Mn2+, Mg2+, Co2+ or Ni2+, but not in the presence of Cu2+, Ca2+ or Zn2+, or in the absence of divalent metal ions. The enzyme cleaves an RNA/RNA duplex in the presence of Mn2+ or Co2+
Mn2+
-
Mn2+ or Mg2+ required
Mn2+
activates, less active than Mg2+
Mn2+
the full-length and C-terminally truncated enzymes have similar activity, and both are around 600fold more active in the presence of Mn2+ compared to Mg2+, binding structure and activation mechanism, overview
Mn2+
the optimum concentration is 1 mM
Mn2+
the enzyme (Tma-RNase HI) and the C-terminal RNase H domain (Tma-CD) exhibit the highest activities in the presence of 1 mM MgCl2 and 0.1-5 mM MnCl2. Both proteins exhibit little activity (less than 0.01% of the maximal activity) in the presence of NiCl2, ZnCl2, CoCl2 or CaCl2. Tma-RNase HI prefers Mg2+ to Mn2+ because its maximal Mg2+-dependent activity is higher than its maximal Mn2+-dependent activity by 16fold
Mn2+
-
can substitute for Mg2+, activates N-terminally truncated mutant RNHIDELTA47 and inhibits the full length enzyme dependent on the presence of the N-terminal 47 amino acids
Mn2+
the enzyme prefers Mg2+ to Mn2+ ions for activity with maximal activity at 0.1 mM MnCl2
Mn2+
-
Mn2+ or Mg2+ required
Mn2+
-
optimal concentration: 1.2 mM
Mn2+
optimal RNase H activity in the presence of Mn2+ and not Mg2+
NaCl
-
activates at 50 mM, inhibits at 200 mM
NaCl
equally activating as KCl
NaCl
activating, best at 100-200 mM salt
NaCl
-
enzyme form H2 is mostly inactive at low salt and requires 100-200 mM concentration for maximal activity. KCl or NH4Cl is more efficient than NaCl
NaCl
activates best at 60 mM
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+
Ni2+
-
exhibits only modest activity as cofactor
Ni2+
the enzyme cleaves an RNA strand of the 12-bp RNA/DNA hybrid at multiple sites only in the presence of Mn2+, Mg2+, Co2+ or Ni2+, but not in the presence of Cu2+, Ca2+ or Zn2+, or in the absence of divalent metal ions
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+
Zn2+
-
exhibits only modest activity as cofactor
additional information
the enzyme exhibits little activity (less than 0.002% of the maximal activity) in the presence of ZnCl2, CaCl2, CoCl2 and NiCl2
additional information
metal coordination in the active site
additional information
-
metal coordination in the active site
additional information
-
the enzyme exists in two different conformations depending on the type of divalent cation activation
additional information
metal ion binding sites are located in the active site
additional information
-
metal ion binding sites are located in the active site
additional information
-
no activity in absence of Mg2+ or Mn2+, and in presence of 10 mM of Ba2+, Ca2+, Co2+, Zn2+, Cu2+, Fe2+, or Sr2+
additional information
no activation by Ca2+, Zn2+, Ba2+, Ni2+, Cu2+, Fe2+, and Sr2+
additional information
-
no activation by Ca2+, Zn2+, Ba2+, Ni2+, Cu2+, Fe2+, and Sr2+
additional information
RNases H act as dimers, with two Mg2+ or other divalent cations being essential for correct protein structure, stability and enzyme activity
additional information
Mg2+ cannot be substituted by Co2+ and Ni2+, and only partially by Mn2+
additional information
-
Mg2+ cannot be substituted by Co2+ and Ni2+, and only partially by Mn2+
additional information
Halalkalibacterium halodurans
the enzyme performs a two-metal catalysis, with metal A activating the nucleophile and metal B stabilizing the transition state, mechanism and structures, overview
additional information
Halalkalibacterium halodurans
the enzyme uses two-metal ion (Mg2+ or Mn2+) catalysis to cleave nucleic acids
additional information
the enzyme requires either salt or divalent metal ions for folding. The enzyme exhibits activity in the presence of divalent metal ions regardless of the presence or absence of 3 M NaCl. However, higher concentrations of divalent metal ions are required for activity in the absence of salt to facilitate folding
additional information
-
enzyme requires divalent cations
additional information
-
not stimulated by Ca2+
additional information
-
RNases H act as dimers, with two Mg2+ or other divalent cations being essential for correct protein structure, stability and enzyme activity
additional information
-
enzyme is divalent metal ion-dependent, one metal ion binding mechanism, pH-dependence, kinetics, and thermodynamics for Mg2+, Mn2+, wild-type and mutant enzymes, substrate is involved in metal ion positioning and binding, Ca2+ and Ba2+ cannot substitute for Mn2+ or Mg2+
additional information
-
RNases H act as dimers, with two Mg2+ or other divalent cations being essential for correct protein structure, stability and enzyme activity
additional information
-
RNases H act as dimers, with two Mg2+ or other divalent cations being essential for correct protein structure, stability and enzyme activity
additional information
no activation by Ca2+, Zn2+, Ba2+, Ni2+, Cu2+, Fe2+, and Sr2+
additional information
-
type 2 enzyme requires divalent cations
additional information
Tma-RNase HI prefers Mg2+ to Mn2+ for activity, and specifically loses most of the Mg2+-dependent activity on removal of the hybrid binding domain and 87% of it by the mutation at the hybrid binding domain. Activity profiles of different metals and salt concentrations