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Li+
-
less effective in activation than K+
MgCl2
-
optimal activity at 5 mM
Pb2+
-
Pb2+ can replace Mg2+
Sr2+
-
Mg2+, Ca2+, Sr2+, and, to a lesser extent, Mn2+ can perform the electrostatic shielding function and preserve the structural properties of the two RNA molecules necessary to keep the substrate and enzyme in appropriate conformations
Ca2+
-
much less efficiently than Mg2+ or Mn2+
Ca2+
-
suppresses enzyme activity, but supports RNA folding and substrate binding, used for binding assays
Ca2+
-
presence of the protein cofactor increases and equalizes substrate affinity and abolishes the substrate affinity differences seen for Escherichia coli relative to Bacillus subtilis P RNA
Ca2+
-
stabilizes RNase P folding and substrate binding with little activation of catalytic activity. Affinity of RNase P for A(-4) pre-tRNA increases 4fold as the Ca2+ concentration increases from 2 mM to 5 mM. Affinity for the G(-4) substrate increases 65fold over the same range
Ca2+
-
time courses for fluorescein-labeled pre-tRNA binding to RNase P are biphasic in the presence of both Ca2+ and Mg2+II, requiring a minimal two-step association mechanism. With Ca2+, pre-tRNA cleavage is slow
Ca2+
-
a divalent cation stabilizes the active conformation of the RNase P-pre-tRNA complex, a role for an inner-sphere metal ion, Mg2+ or Ca2+, in the enzyme. Structural changes that occur upon binding Ca(II) to the ES complex are determined by time-resolved FRET measurements of the distances between donor/acceptor fluorophores introduced at specific locations on the P protein and pre-tRNA 5' leader. The value of KD,obs has an apparent hyperbolic dependence on the concentration of calcium with an apparent dissociation constant for Ca(II) of 0.04 mM
Ca2+
-
metal-stabilized conformational change in RNase P that accompanies substrate binding and is essential for efficient catalysis
Ca2+
-
Mg2+, Ca2+, Sr2+, and, to a lesser extent, Mn2+ can perform the electrostatic shielding function and preserve the structural properties of the two RNA molecules necessary to keep the substrate and enzyme in appropriate conformations
Ca2+
-
presence of the protein cofactor increases and equalized substrate affinity and abolishes the substrate affinity differences seen for Escherichia coli relative to Bacillus subtilis P RNA
Ca2+
-
Ca2+ can replace Mg2+
Cd2+
-
changes the cleavage pattern
Cd2+
-
changes the cleavage pattern
Cs+
-
less effective in activation than K+
Cs+
-
supports activity at 100-200 mM
Cu2+
-
changes the cleavage pattern
Cu2+
-
changes the cleavage pattern
K+
-
optimal concentration 40-60 mM
K+
-
optimal activity at 0.3-1 M NH4Cl or KCl
K+
-
optimal activity in presence of 5 mM KCl or 10 mM NH4Cl
K+
-
monovalent cation required, K+ is most effective
K+
-
monovalent cation required: Na+, K+ or NH4+
K+
-
stimulates at less than 30 mM
K+
-
optimal activity at 150-200 mM KCl
K+
-
maximal activity at 0.1-0.2 M
KCl
-
activates, best at 200 mM
KCl
-
optimal concentration: 200 mM
Mg2+
-
-
Mg2+
activates, the enzyme requires at least two Mg2+ ions for optimal catalysis. Mg2+ ions bind cooperatively to PRORP1
Mg2+
-
10-15 mM required for optimal activity
Mg2+
-
optimal concentration: 60-90 mM
Mg2+
-
optimal activity at 20-200 mM MgCl2
Mg2+
-
strict requirement for a divalent cation, Mg2+ or Mn2+. Hexacoordinated Mg2+ binds to the catalytic site on M1 RNA
Mg2+
-
required for catalysis
Mg2+
-
absolutely required, optimal at about 20 mM, for catalysis and substrate shape recognition, influences substrate binding affinity
Mg2+
-
best metal ion, required for folding of the RNA, for binding of protein and substrate, and for catalytic activity
Mg2+
-
interaction with the helix P4
Mg2+
-
potential catalytic transition state structure including 3 required divalent metal ions, coordinated to nonbinding phosphate group oxygens
Mg2+
-
preferred metal ion, absolutely required
Mg2+
-
enzymatic activity depends on the presence of divalent metal ions such as Mg2+
Mg2+
-
60 mM is optimal for the holoenzyme
Mg2+
-
significant association of Mg2+ ions at the P4 major groove of RNase P near the flexible pivot point (A5, G22, and G23)
Mg2+
-
time courses for fluorescein-labeled pre-tRNA binding to RNase P are biphasic in the presence of both Ca2+ and Mg2+II, requiring a minimal two-step association mechanism. Cleavage rate constants are significantly higher in the presence of the physiologically important metal cofactor magnesium
Mg2+
-
a divalent cation stabilizes the active conformation of the RNase P-pre-tRNA complex, a role for an inner-sphere metal ion, Mg2+ or Ca2+, in the enzyme. A second, lower affinity Mg(II) activates cleavage catalyzed by the enzyme
Mg2+
-
metal-stabilized conformational change in RNase P that accompanies substrate binding and is essential for efficient catalysis
Mg2+
-
enzymatic activity depends on the presence of divalent metal ions such as Mg2+
Mg2+
-
the RNA subunit requires 20 mM Mg2+ for optimal activity
Mg2+
-
preferred metal ion, absolutely required
Mg2+
-
optimal activity in presence of 5 mM MgCl2
Mg2+
-
required for activity
Mg2+
-
required for activation
Mg2+
-
the only metal ion that can act as cofactor for activity of M1 RNA
Mg2+
-
Mg2+, Ca2+, Sr2+, and, to a lesser extent, Mn2+ can perform the electrostatic shielding function and preserve the structural properties of the two RNA molecules necessary to keep the substrate and enzyme in appropriate conformations
Mg2+
-
can substitute for the C5 protein as a cofactor, since M1 RNA alone can carry out the catalytic reaction in the buffer that contains more than 20 mM Mg2+
Mg2+
-
strict requirement for a divalent cation, Mg2+ or Mn2+. Hexacoordinated Mg2+ binds to the catalytic site on M1 RNA
Mg2+
-
required for efficient cleavage at the correct position. Essential for the folding of the active conformation of RNase P RNA
Mg2+
-
absolutely required, optimal at about 10 mM, for catalysis and substrate shape recognition, influences substrate binding affinity
Mg2+
-
best metal ion, required for folding of the RNA, for binding of protein and substrate, and for catalytic activity
Mg2+
-
coordination to nucleotide A67 of the enzymes RNA
Mg2+
-
interaction with the helix P4
Mg2+
-
potential catalytic transition state structure including 3 required divalent metal ions, coordinated to nonbinding phosphate group oxygens
Mg2+
-
preferred metal ion, absolutely required
Mg2+
-
required for hyperprocessing reaction, at about 10 mM
Mg2+
-
replacement, deletion, or insertion (except at G63G64) of bases of the J3/4 domain of Escherichia coli ribonuclease P, can be compensated for by the presence of a high concentration of magnesium ions above 20 mM
Mg2+
-
essential for activity, the ribozyme prefers the wild type pre-tRNA (A7) substrate at low Mg2+
Mg2+
-
10 mM is optimal for the holoenzyme
Mg2+
-
for the LNA variant, parallel pathways leading to cleavage at the c0 and m+1 sites have different pH profiles, with a higher Mg2+ requirement for c0 versus m+1 cleavage. The strong catalytic defect for LNA and 2'-OCH3 supports a model where the extra methylene (LNA) or methyl group (2'-OCH3) causes a steric interference with a nearby bound catalytic Mg2+ during its recoordination on the way to the transition state for cleavage. Presence of the protein cofactor suppresses the ground state binding defects, but not the catalytic defects
Mg2+
-
required, the requirement of Mg2+ for catalysis varies with the substrate. Deletion of the S-domain changes the Mg2+ requirement
Mg2+
-
required for folding, substrate binding, and catalysis
Mg2+
-
optimal concentration is 55 mM
Mg2+
-
optimal activity at 5 mM
Mg2+
-
is the most effective cofactor, can be replaced by Mn2+
Mg2+
-
preferred metal ion, absolutely required
Mg2+
-
required, optimal cleavage at 20 mM for the reconstituted mini-enzyme, reduced activity at 40-100 mM, the wild-type enzyme shows no activity at 100 mM
Mg2+
-
dependent on, the optimum is at 5 mM MgCl2, when reactions are carried out at pH 7.5 and 37°C
Mg2+
-
enzymatic activity depends on the presence of divalent metal ions such as Mg2+
Mg2+
-
mitochondrial RNase P requires divalent metal ions, preferably Mg2+, for cleavage
Mg2+
-
maximally active at 2.5-30 mM MgCl2
Mg2+
-
dependent on, optimal at 2-10 mM
Mg2+
-
dependent on, at least half-maximal activity between 8-80 mM
Mg2+
-
preferred metal ion, absolutely required
Mg2+
the RNA component alone shows activity on pre-tRNAala substrate at high magnesium concentrations (50 mM). The RNA and protein components associate together to manifest catalytic activity at low magnesium concentrations (20 mM)
Mg2+
-
optimal concentration for RNase P RNA activity is 250 mM MgCl2
Mg2+
-
optimal 120 mM RNase P RNA + RNase P protein 21 + RNase P protein 29
Mg2+
-
required for activation
Mg2+
-
the bulge stem-loop structure containing J3/4 and helix P4 is involved in the interaction with Mg2+ ions important for catalysis
Mg2+
-
optimal activity at 1 mM MgCl2
Mg2+
-
optimally at 7.5 mM
Mg2+
-
dependent on, binds to the pro-Rp nonbridging oxygen of the scissile bond, coordination
Mg2+
-
high activation, specific for
Mg2+
-
preferred metal ion, absolutely required
Mg2+
-
required for formation of the Pop6-Pop7-RNA complex
Mg2+
-
strict requirement for a divalent cation, Mg2+ or Mn2+. Hexacoordinated Mg2+ binds to the catalytic site on M1 RNA
Mg2+
-
required at a concentration of at least 2 mM
Mg2+
-
best metal ion, required for folding of the RNA, for binding of protein and substrate, and for catalytic activity
Mg2+
-
optimal at 5-10 mM for the holoenzyme, the RNA subunit alone is active only at 100 mM MgCl2
Mg2+
required, the active site includes at least two metal ions, RNA U52 nucleotide binds a metal ion at the active site
Mn2+
-
-
Mn2+
activates, two manganese ions are bound to the active site interacting with four conserved aspartate residues (D399A, D474A, D475A, and D493A) through both inner and outer sphere interactions
Mn2+
-
strict requirement for a divalent cation, Mg2+ or Mn2+
Mn2+
-
can substitute for Mg2+, slightly lower activity
Mn2+
-
substitution of Mg2+ by Mn2+ can result in miscleavage of the substrate containing a N(-1)/N(73) pair, better sulfur coordination compared to Mg2+
Mn2+
-
Mn2+ paramagnetic line broadening experiments reveal strong metal localization at residues corresponding to G378 and G379
Mn2+
-
can substitute for Mg2+, slightly lower activity
Mn2+
-
effectively substitutes for Mg2+
Mn2+
-
Mg2+, Ca2+, Sr2+, and, to a lesser extent, Mn2+ can perform the electrostatic shielding function and preserve the structural properties of the two RNA molecules necessary to keep the substrate and enzyme in appropriate conformations
Mn2+
-
can promote catalysis
Mn2+
-
strict requirement for a divalent cation, Mg2+ or Mn2+
Mn2+
-
rescues A67Rp- and A67Sp-phosphorothionate modified inactive enzyme at 5 mM completely and partially, respectively
Mn2+
-
substitution of Mg2+ by Mn2+ can result in miscleavage of the substrate containing a N(-1)/N(73) pair, better sulfur coordination compared to Mg2+
Mn2+
-
Mn2+ can replace for Mg2+ in activation
Mn2+
-
Mn2+ can replace Mg2+
Mn2+
-
can substitute for Mg2+, slightly lower activity
Mn2+
-
can substitute for Mg2+, slightly lower activity
Mn2+
-
strict requirement for a divalent cation, Mg2+ or Mn2+
Na+
-
less effective in activation than K+
Na+
-
monovalent cation required: Na+, K+ or NH4+
Na+
-
less effective in activation than K+
Na+
-
supports activity at 100-200 mM
NaCl
-
activates
NaCl
-
optimal concentration: 50 mM
NaCl
-
activates, best at 50 mM
NH4+
-
optimal concentration: 40-60 mM
NH4+
-
optimal concentration: 100-200 mM
NH4+
-
optimal activity at 0.3-1 M NH4Cl or KCl
NH4+
-
800 mM NH4Cl is required for optimal activity. (NH4)2SO4 is significantly more active than NH4Cl
NH4+
-
optimal activity in presence of 5 mM KCl or 10 mM NH4Cl
NH4+
-
stimulates activity of M1 RNA
NH4+
-
monovalent cation required, NH4+ is less effective than K+
NH4+
-
monovalent cation required: Na+, K+ or NH4+. Optimal NH4+ concentration is 200 mM
NH4+
-
dependent on, the optimum is at 70 mM NH4Cl, when reactions are carried out at pH 7.5 and 37°C
NH4+
-
optimal concentration for RNase P RNA activity is 3 M NH4Cl
NH4+
-
supports activity at 300 mM
NH4Cl
-
activates, best at 200-400 mM
NH4Cl
-
optimal concentration: 200-400 mM
Ni2+
activates
Ni2+
-
changes the cleavage pattern
Ni2+
-
changes the cleavage pattern
Zn2+
bound by conserved residues. A putative zinc-finger-like structure is split in two separate motifs. The first motif (CxxC) contains two conserved cysteines upstream of the NYN domain at positions 344 and 347 for PRORP1, whereas the second motif involves a conserved histidine and a cysteine, downstream of the NYN domain, at positions 548 and 565, respectively. The downstream conserved motif has a stronger affinity for the metal than the upstream CxxC coordination element
Zn2+
-
Zn2+ is involved in inner-sphere interactions with the P4 helix mimic of RNase P, the bound Zn2+ exhibits six-coordinate geometry with an average Zn2+-O/N bond distance of 2.08 A
Zn2+
-
Zn2+ can replace Mg2+
additional information
-
divalent metal cations are essential
additional information
-
divalent metal cations are essential for catalysis and stabilize the enzyme conformation and subunit interaction
additional information
-
divalent metal ions are absolutely required, reduced activity with Ca2+
additional information
-
divalent metal ions are important cofactors for the catalytic reaction and for substrate binding at the conserved loops CR-II and CR-III in proximity to the substrate aminoacyl stem, enhancement of substrate affinity by 1000fold
additional information
-
enzyme is dependent on divalent metal ions, enzyme contains a metal binding loop
additional information
-
catalysis of pre-tRNA cleavage by RNase P requires at least one divalent cation capable of forming inner-sphere coordination, such as Mg2+, Mn2+, Zn2+ or Ca2+
additional information
-
divalent metal ions are absolutely required, reduced activity with Ca2+
additional information
-
divalent metal cations are essential
additional information
-
divalent metal ions are important cofactors for the reaction
additional information
-
requires a monovalent and a divalent cation for activity
additional information
-
at least 2 metal ions per enzyme molecule, one catalytically and one structurally important, interactions of divalent metal cations at the pro-Rp and ProSp non-bridging phosphate oxygens with nucleotide A67 in the universally conserved helix p4 are essential for the folding and function of the enzymes' catalytic RNA component, interaction kinetics
additional information
-
divalent metal cations are essential
additional information
-
divalent metal cations are essential for catalysis and stabilize the enzyme conformation and subunit interaction
additional information
-
divalent metal ions are important cofactors for the catalytic reaction and for substrate binding at the conserved loops CR-II and CR-III in proximity to the substrate aminoacyl stem
additional information
-
enzyme is dependent on divalent metal ions
additional information
-
Mn2+, Co2+, Ni2+, Cu2+, Au3+, Pb2+, La3+, Pr3+, Sm3+, Gd3+, Dy3+, Yb3+, and Lu3+ are able to bind to RNase P but are not specific proxies for Mg2+
additional information
-
Ca2+ and Mn2+ cannot substitute for Mg2+
additional information
-
divalent metal cations are essential
additional information
-
divalent metal ions are absolutely required, reduced activity with Ca2+
additional information
-
divalent metal ions are important cofactors for the reaction
additional information
-
divalent metal cations are essential
additional information
-
optimal ionic strength at 800 mM ammonium acetate at 60°C
additional information
-
at least half-maximal activity at 1 M ammonium acetate
additional information
-
divalent metal ions are important cofactors for the reaction
additional information
-
divalent metal cations are essential
additional information
-
requires a monovalent and a divalent cation for activity
additional information
-
divalent metal ions are absolutely required, reduced activity with Ca2+
additional information
-
divalent metal ions are important cofactors for the reaction
additional information
-
Mg2+ is not required for activity
additional information
-
enzyme is dependent on divalent metal ions, enzyme contains a metal binding loop
additional information
-
divalent metal cations are essential