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Fe2+
-
required, in [4Fe-4S] clusters, that are bound to the CysB motif in all yeast B family DNA polymerases, assembly of the essential Fe-S cluster is strictly dependent on the function of mitochondrial Nfs1 and cytosolic Nbp35. The C-terminal domain of the catalytic subunit binds the Fe-S cluster in the CysB motif requiring all Cys residues of motif Cysb
MnCl2
-
sustitution of MgCl2 by MnCl2 produces a slight decrease of activity. Optimal activity is obtained in the presence of 0.4 mM MgCl2
NH4+
Tequintavirus T5
-
0.2 M, stimulates phage T5-induced enzyme
NH4Cl
required, optimal at 80 mM
Ca2+
competes with Mg2+ for metal ion binding site(s)
Ca2+
bound to the active site, structure, overview
Ca2+
Ca2+ (but not Ba2+, Co2+, Cu2+, Ni2+, or Zn2+) is a cofactor for Dpo4-catalyzed polymerization with both native and 8-oxoG-containing DNA templates. Both dNTP and ddNTP are substrates of the polymerase in the presence of either Mg2+ or Ca2+. No pyrophosphorolysis occurs in the presence of Ca2+
Ca2+
Salasvirus phi29
causes a concentration-dependent shift in the translocation equilibrium, predominantly by decreasing the forward translocation rate. Decreases the dNTP dissociation rate relative to Mg2+ and increases the dNTP association rate
Co2+
can effectively replace Mg2+. When Mg2+ is replaced with Co2+, the efficiency of incorporation of dTMP opposite dA increases by 5-fold
Co2+
-
can partially replace Mg2+ in activation, optimal concentration: 2.5 mM
DTT
-
-
K+
-
-
K+
-
stimulates at 125 mM, inhibition at higher concentrations
K+
-
optimal concentration: 0.22 mM, DNA polymerase gamma
K+
-
stimulates at 100-200 mM
K+
Herpes simplex virus
-
-
K+
-
pols beta, iota and zeta exhibit maximal activity under conditions of moderate KCl concentrations of 20-60 mM
K+
-
optimal concentration: 0.025 mM
K+
-
100-200 mM KCl, stimulates Novikoff hepatoma DNA polymerase beta 2fold
K+
Ruellia sp.
-
stimulates
K+
over 80% of maximal activity is obtained with KCl concentrations of 50-80 mM, with a maximum at 60 mM
K+
-
stimulates at 10-55 mM KCl
K+
-
optimal concentration for wild-type enzyme: 50 mM, optimal concentration for G418/E507Q mutant: 100 mM
K+
-
optimal concentration: 50 mM
K+
-
stimulates at 100-200 mM
K+
-
stimulates at 50 mM, inhibition at higher concentrations
K+
-
optimal processivity at 100-150 mM
K+
-
stimulates at 100 mM
K+
-
stimulates at 100-200 mM
KCl
-
optimal concentration is 20 mM
KCl
optimum salt concentration is either 50 mM KCl or 75 mM NaCl
KCl
activates best at 10 mM
KCl
required, optimal at 85 mM
KCl
optimal concentration of KCl is 60 mM
KCl
optimal concentration: 40 mM
KCl
optimal concentration: 50-80 mM
KCl
-
increase in KCl concentration from 10 to 75 mM results in a 10fold increase in polymerase activity
KCl
-
optimal concentration of 80 mM
Mg2+
-
-
Mg2+
-
binding of Mg2+-dNTP to Pol X facilitates subsequent formation of the catalytically competent Pol X-DNA-dNTP ternary complex, Pol X prefers an ordered sequential mechanism with Mg2+-dNTP as the first substrate
Mg2+
-
optimal concentration is 3 mM
Mg2+
maximal activity at 4-10 mM Mg2+
Mg2+
divalent cation required. Maximum activity is observed with 6 mM MgCl2, whereas about 50% activity is obtained with MnCl2 at its optimal concentration of 6 mM
Mg2+
-
optimal concentration: 10 mM
Mg2+
-
divalent cation required, Mg2+ or Mn2+
Mg2+
activates, Mn2+ shows a 8.6fold higher catalytic efficiency than Mg2+
Mg2+
-
DNA polymerase alpha: increasing concentrations of Mg2+ lead to a dramatically increased affinity for poly(dT) and poly(dC) polypyrimidines, has little or no effect on the interaction of the enzyme with poly(dA)
Mg2+
-
free Mg2+ competes with primer for enzyme binding, dramatic inhibition at Mg2+ concentration above the optimum, catalytic core binds primer through a Mg2+-chelate, with each of 4 Mg2+ ions acting to coordinate 2 phosphodiester groups
Mg2+
-
divalent cation required, optimal concentration is 5 mm
Mg2+
-
synthesizes DNA processively in the presence of Mn2+ and Mg2+, optimal Mg2+ concentration is 3 mM
Mg2+
-
divalent cation required, Mg2+ or Mn2+
Mg2+
-
required, two metal ion mechanism, nucleotide binds to the enzyme as an Mg–dNTP-2 complex, overview. Mg2+ enforces tetrahedral geometry
Mg2+
-
stimulates at 12 mM, DNA polymerase gamma
Mg2+
polI activity is absolutely dependent on the presence of divalent cations Mg2+ and Mn2+, Mn2+ cannot be replaced with Mg2+ completely, optimal at 8 mM
Mg2+
-
divalent cation required, Mg2+ or Mn2+
Mg2+
-
optimal concentration: 5-30 mM
Mg2+
enzyme prefers Mg2+ over Mn2+
Mg2+
Herpes simplex virus
-
stimulates at 3 mM
Mg2+
-
optimal concentration for polymerase C and N2: 10 mM, optimal concentration for polymerase N1: 20 mM
Mg2+
-
stimulates at 4-8 mM
Mg2+
-
DNA polymerase alpha: increasing concentrations of Mg2+ lead to a dramatically increased affinity for poly(dT) and poly(dC) polypyrimidines, has little or no effect on the interaction of the enzyme with poly(dA)
Mg2+
-
free Mg2+ competes with primer for enzyme binding, dramatic inhibition at Mg2+ concentration above the optimum, catalytic core binds primer through a Mg2+-chelate, with each of 4 Mg2+ ions acting to coordinate 2 phosphodiester groups
Mg2+
-
DNA polymerase lambda is not able to perform de novo DNA synthesis in the absence of a metal ion activator. Synthesis of de novo DNA is much stronger with Mn2+ than with Mg2+
Mg2+
-
maximal activity at 8.75 mM
Mg2+
-
peak activity in the presence of Mg2+ is observed in the range of 0.1-0.5 mM and is significantly reduced at concentrations above 2 mM
Mg2+
-
poly(dA)/oligo(dT)10:1. In the presence of Mn2+, DNA polymerase beta incorporates (biphenylcarbonyl)-4-oxobutyl triphosphate both on an intact template and opposite to an abasic site. DNA polymerase beta incorporates dCTP on the undamaged template, whereas it exclusively incorporates dATP opposite the abasic site. The incorporation efficiency of (biphenylcarbonyl)-4-oxobutyl triphosphate by DNA polymerase beta is 2fold higher in the presence of the undamaged template, with respect to the one carrying an abasic site. When Mn2+ is replaced by Mg2+, this difference becomes even more striking, so that (biphenylcarbonyl)-4-oxobutyl triphosphate can be exclusively incorporated on the undamaged in the presence of Mg2+, the incorporation of (biphenylcarbonyl)-4-oxobutyl triphosphate by DNA polymerase beta becomes strictly dependent on the presence of a templating base. Replacement of Mn2+ with Mg2+, however, greatly enhances the preference for incorporation of dCTP versus (biphenylcarbonyl)-4-oxobutyl triphosphate opposite a template G by DNA polymerase beta, which increases from 23fold to 239fold
Mg2+
DNA polymerase iota contains two catalytic Mg2+ ions in the active site
Mg2+
-
pol zeta functions best in the presence of 1-5mM MgCl2, but exhibits dramatically lower activity in the presence of MnCl2
Mg2+
strongly activated by the presence of Mg2+ at an optimum concentration of 3 mM
Mg2+
-
optimal concentration: 8 mM
Mg2+
-
stimulates at 5-10 mM, polymerase beta
Mg2+
-
divalent cation required, Mg2+ or Mn2+
Mg2+
-
stimulates at 9 mM
Mg2+
-
divalent cation required, Mg2+ or Mn2+
Mg2+
-
stimulates at 4 mM
Mg2+
optimal concentration: 3 mM
Mg2+
oprtimal concentration: 15-20 mM
Mg2+
-
varying magnesium concentration affects both slippage and overall DNA synthesisof DNA polymerase PolB and PolD. There is almost no synthesis by PolB, PolD or their exo-forms at low magnesium concentrations (0.1–0.5 mM). Synthesis is also inhibited at 15–20 mM. Parental molecules are readily detectable together with heteroduplex molecules at low to medium magnesium concentrations (1–5 mM)
Mg2+
optimal magnesium concentration is 17.5 mM
Mg2+
the negative charge and the side-chain length of D259 might play a supporting role in coordinating the conserved Mg2+ to the correct position at the active center in the exonuclease domain
Mg2+
-
required, substrate-like inhibition by Mg2+ occur
Mg2+
Ruellia sp.
-
required
Mg2+
-
enzyme prefers Mg2+ over Mn2+
Mg2+
cofactor for both the polymerase and pyrophosphorolysis activities
Mg2+
DNA polymerase Dpo2 and Dpo3 are both more active with Mg2+ than Mn2+. DNA polymerase Dpo1 and Dpo4 are similarly active with Mg2+ or Mn2+
Mg2+
-
Mg2+-dependent DNA-polymerizing activity
Mg2+
-
enzyme prefers Mn2+ over Mg2+ for RTHI activity
Mg2+
-
enzyme prefers Mn2+ over Mg2+ for RTHI nuclease activity
Mg2+
Salasvirus phi29
-
-
Mg2+
Salasvirus phi29
causes a concentration-dependent shift in the translocation equilibrium, predominantly by decreasing the forward translocation rate
Mg2+
-
exonuclease acitivity shows equal efficiency with Mg2+ and Mn2+, mutant D190A shows preference for Mn2+
Mg2+
-
higher polymerase activity with Mg2+ than with Mn2+, exonuclease acitivity shows equal efficiency with Mg2+ and Mn2+
Mg2+
-
divalent cation required, Mg2+ or Mn2+
Mg2+
the enzyme requires an extremely low concentration of Mg+2 cations for activity. A broad plateau is observed between 0.1 and 2 mM MgCl2. Concentrations above 2 mM are inhibitory. 20% of the activity of the plateau value is still observed even if no MgCl2 is added to the assay
Mg2+
activates, optimal concentration is 1.5-2.5 mM
Mg2+
Tequatrovirus T4
-
divalent cation required, Mg2+ or Mn2+
Mg2+
Tequatrovirus T4
-
optimal concentration: 6 mM
Mg2+
Tequintavirus T5
-
divalent cation required, Mg2+ or Mn2+
Mg2+
PI-TfuI utilizes either Mg2+ or Mn2+, PI-TfuII only utilizes Mg2+
Mg2+
activity is dependent on a divalent cation, among which magnesium ion is optimal
Mg2+
1.5-2 mM, optimal activity
Mg2+
requires a divalent cation, optimal activity is obtained with 2.0 mM MgSO4, recombinant enzyme with the nonspecific DNA-binding protein Sso7d from Sulfolobus solfataricus fused to the C-terminus
Mg2+
highly dependent on MgCl2 in the range of 0-20 mM with maximal activity at 14 mM MgCl2 and no detectable activity in the absence of MgCl2
Mg2+
-
highly dependent on MgCl2, with maximal activity at 12 mM MgCl2 and no detectable activity in the absence of MgCl2
Mg2+
-
highly dependent on MgCl2, with maximal activity at 14 mM MgCl2 and no detectable activity in the absence of MgCl2
Mg2+
no activity is detected in the absence of magnesium, activity is maximal between 1.5 and 3.0 mM MgCl2
Mg2+
-
optimal concentration: 2-4 mM
Mg2+
-
MgCl2 is the preferred cofactor compared to MnCl2, CoCl2 and NiCl2
Mg2+
-
optimal concentration: 8 mM
Mg2+
-
optimal concentration: 12 mM
Mg2+
-
divalent cation required, Mg2+ or Mn2+
Mg2+
-
enzyme prefers Mn2+ over Mg2+ for RNase H activity
Mg2+
-
optimal concentration: 20-30 mM
Mg2+
-
optimal concentration: 8 mM
Mg2+
-
PolX has Mg2+-dependent 5'-3' DNA polymerase activity
Mg2+
-
optimal concentration: 6 mM
Mg2+
-
optimal processivity at 6 mM, no synthesis is observed in the absence of Mg2+
Mg2+
-
divalent cation required, Mg2+ or Mn2+
Mg2+
-
optimal concentration: 5-30 mM
Mg2+
-
stimulates at 70 mM
Mg2+
-
divalent cation required, Mg2+ or Mn2+
Mg2+
-
optimal concentration: 5-30 mM
MgCl2
optimal concentration: 10 mM
MgCl2
optimal concentration: 5 mM
MgCl2
-
optimal activity is obtained in the presence of 4 mM MgCl2
Mn2+
-
-
Mn2+
divalent cation required. Maximum activity is observed with 6 mM MgCl2, whereas about 50% activity is obtained with MnCl2 at its optimal concentration of 6 mM
Mn2+
-
divalent cation required, Mn2+ or Mg2+
Mn2+
activates, Mn2+ shows a 8.6fold higher catalytic efficiency than Mg2+
Mn2+
-
the polymerase activity of PolX is strongly stimulated by Mn2+
Mn2+
-
synthesizes DNA processively in the presence of Mn2+ and Mg2+
Mn2+
activates. When Mg2+ is replaced with Mn2+, the efficiency of incorporation of dTMP opposite dA increases by 3fold
Mn2+
-
divalent cation required, Mn2+ or Mg2+
Mn2+
-
supports chemistry, but leads to markedly decreased fidelity by accelerating the rate of incorporation of mismatches, routinely used to generate random mutations during PCR. Mn2+ accommodates square planar, tetrahedral, and octahedral coordination
Mn2+
-
stimulates at 0.5-0.6 mM, 5fold more effective than optimal Mg2+ concentration
Mn2+
polI activity is absolutely dependent on the presence of divalent cations Mg2+ and Mn2+, Mn2+ cannot be replaced with Mg2+ completely
Mn2+
-
stimulates at 0.4 mM
Mn2+
-
divalent cation required, Mn2+ or Mg2+
Mn2+
enzyme prefers Mg2+ over Mn2+
Mn2+
Herpes simplex virus
-
-
Mn2+
-
DNA polymerase lambda is not able to perform de novo DNA synthesis in the absence of a metal ion activator. Synthesis of de novo DNA is much stronger with Mn2+ than with Mg2+
Mn2+
-
DNA polymerase iota exhibits the greatest activity in the presence of low levels of Mn2+ (0.05-0.25 mM). Mn2+ increases the catalytic activity of DNA polymerase iota by about 30000-60000fold through a strong decrease in the Km value for nucleotide incorporation. Whereas DNA polymerase iota preferentially misinserts G opposite T by a factor of about 1.4-2.5fold over the correct base A in the presence of 0.25 and 5 mM Mg2+, respectively, the correct insertion of A is actually favored 2fold over the misincorporation of guanine in the presence of 0.075 mM Mn2+. Low levels of Mn2+ also dramatically increase the ability of DNA polymerase iota to traverse a variety of DNA lesions in vitro. The cation utilized by DNA polymerase iota in vivo may be Mn2+
Mn2+
-
incorporation of the NNTPs is observed only in the presence of its optimal activator, Mn2+
Mn2+
-
poly(dA)/oligo(dT)10:1. In the presence of Mn2+, DNA polymerase beta incorporates (biphenylcarbonyl)-4-oxobutyl triphosphate both on an intact template and opposite to an abasic site. DNA polymerase beta incorporates dCTP on the undamaged template, whereas it exclusively incorporates dATP opposite the abasic site. The incorporation efficiency of (biphenylcarbonyl)-4-oxobutyl triphosphate by DNA polymerase beta is 2fold higher in the presence of the undamaged template, with respect to the one carrying an abasic site. When Mn2+ is replaced by Mg2+, this difference becomes even more striking, so that (biphenylcarbonyl)-4-oxobutyl triphosphate can be exclusively incorporated on the undamaged in the presence of Mg2+, the incorporation of (biphenylcarbonyl)-4-oxobutyl triphosphate by DNA polymerase beta becomes strictly dependent on the presence of a templating base. Replacement of Mn2+ with Mg2+, however, greatly enhances the preference for incorporation of dCTP versus (biphenylcarbonyl)-4-oxobutyl triphosphate opposite a template G by DNA polymerase beta, which increases from 23fold to 239fold
Mn2+
-
pol iota displays its highest activity in the presence of MnCl2 at low concentrations of 0.05-0.1mM, its activity also peaks at low Mg2+, but is considerably higher in the presence of Mn2+
Mn2+
-
can partially replace Mg2+ in activation
Mn2+
-
optimal concentration: 1 mM, DNA polymerase beta
Mn2+
-
activates DNA polymerase beta
Mn2+
-
stimulates at 0.5 mM, about a third the maximal activity with Mg2+
Mn2+
-
divalent cation required, Mn2+ or Mg2+
Mn2+
-
stimulates at 0.2 mM
Mn2+
-
divalent cation required, Mn2+ or Mg2+
Mn2+
-
enzyme prefers Mg2+ over Mn2+
Mn2+
DNA polymerase Dpo2 and Dpo3 are both more active with Mg2+ than Mn2+. DNA polymerase Dpo1 and Dpo4 are similarly active with Mg2+ or Mn2+
Mn2+
-
enzyme prefers Mn2+ over Mg2+ for RTHI nuclease activity
Mn2+
Salasvirus phi29
-
-
Mn2+
Salasvirus phi29
causes a concentration-dependent shift in the translocation equilibrium, predominantly by decreasing the forward translocation rate. Decreases the dNTP dissociation rate relative to Mg2+
Mn2+
-
exonuclease acitivity shows equal efficiency with Mg2+ and Mn2+, mutant D190A shows preference for Mn2+
Mn2+
-
divalent cation required, Mn2+ or Mg2+
Mn2+
in a MnCl2-soaked crystal, a Mn2+ is bound to one of the oxygens of the Asp111 side chain
Mn2+
optimal Mn2+ concentration is 0.5 mM
Mn2+
Tequatrovirus T4
-
optimal concentration: 0.1 mM
Mn2+
Tequatrovirus T4
-
25% of the activity with Mg2+
Mn2+
Tequatrovirus T4
-
divalent cation required, Mn2+ or Mg2+
Mn2+
Tequintavirus T5
-
divalent cation required, Mn2+ or Mg2+
Mn2+
PI-TfuI utilizes either Mg2+ or Mn2+, PI-TfuII only utilizes Mg2+
Mn2+
-
can partially replace Mg2+ in activation
Mn2+
-
stimulates at 0.4-0.8 mM
Mn2+
-
stimulates at 0.4 mM
Mn2+
-
enzyme prefers Mn2+ over Mg2+ for RNase H activity, optimal concentration: 1.5-2.5 mM
Mn2+
-
divalent cation required, Mn2+ or Mg2+
Mn2+
-
can partially replace Mg2+ in activation
Mn2+
-
divalent cation required, Mn2+ or Mg2+
Mn2+
-
stimulates at 0.4 mM
Mn2+
-
divalent cation required, Mn2+ or Mg2+
Na+
-
pols beta, iota and zeta exhibit maximal activity under conditions of moderate NaCl concentrations of 20-60 mM
Na+
-
50 mM stimulates DNA polymerase beta 2fold
Na+
Tequintavirus T5
-
0.2 M, stimulates phage T5-induced enzyme
NaCl
optimum salt concentration is either 50 mM KCl or 75 mM NaCl
NaCl
activates best at 50 mM
NaCl
required, optimal at 100 mM
NaCl
optimal concentration: 0-75 mM
NaCl
in absence of NaCl, Tga PolB displays 67% polymerization activity. From 50 to 200 mM NaCl, the activity is higher than 90%, but it is significantly reduced at NaCl concentrations above 400 mM
Zn2+
-
-
Zn2+
-
pol I contains one Zn2+ per molecule
Zn2+
-
10-13% of the activity with Mg2+, optimal concentration: 0.3-0.5 mM
Zn2+
-
increases enzymatic activity, no absolute dependence on zinc
Zn2+
-
required, Zn2+ is bound to the CysA motif in yeast B family DNA polymerases
additional information
no activation by Fe2+, Ca2+, Zn2+, Cd2+, Sr2+, Ba2+, Cu2+, and Cr3+. Ca2+ concentration required to obtain the half-maximal incorporation rate under single-turnover conditions was 0.63 mM
additional information
-
no activation by Fe2+, Ca2+, Zn2+, Cd2+, Sr2+, Ba2+, Cu2+, and Cr3+. Ca2+ concentration required to obtain the half-maximal incorporation rate under single-turnover conditions was 0.63 mM
additional information
-
Ca2+ supports nucleotide binding but not catalysis
additional information
polI activity requires the presence of monovalent ions, above 100 mM, monovalent salts become inhibitory for the activity
additional information
-
DNA binding, dNTP binding and catalytic activity of mutant enzyme in the presence of two metal ions, Mg2+ and Mn2+, overview. Amino acid residues D378 and D531 are mainly responsible for the binding of metal chelated substrate dNTP
additional information
-
the PolX catalytic domain exhibits no polymerase activity with 5 mM Zn2+, Ni2+, Ca2+ or Co2+, or without a metal ion