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EC Tree
IUBMB Comments Also acts slowly with CTP. Catalyses template-independent extension of the 3'- end of a DNA strand by one nucleotide at a time. Cannot initiate a chain de novo. The primer, depending on the source of the enzyme, may be an RNA or DNA fragment, or oligo(A) bearing a 3'-OH terminal group. See also EC 2.7.7.6 DNA-directed RNA polymerase.
The taxonomic range for the selected organisms is: Bos taurus The enzyme appears in selected viruses and cellular organisms
Synonyms
poly(a) polymerase, pap i, fam46c, gld-2, star-pap, fam46a, poly(a) polymerase i, pap ii, papd5, mtpap,
more
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adenosine triphosphate:ribonucleic acid adenylyltransferase
-
-
-
-
AMP polynucleotidylexotransferase
-
-
-
-
ATP-polynucleotide adenylyltransferase
-
-
-
-
ATP:polynucleotidylexotransferase
-
-
-
-
nucleotidyltransferase, polyadenylate
-
-
-
-
poly(A) hydrolase
-
-
-
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poly(A) synthetase
-
-
-
-
polyadenylate nucleotidyltransferase
-
-
-
-
polyadenylate polymerase
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-
-
-
polyadenylate synthetase
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-
-
-
polyadenylic acid polymerase
-
-
-
-
polyadenylic polymerase
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-
-
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RNA adenylating enzyme
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-
-
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RNA formation factors, PF1
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-
-
-
terminal riboadenylate transferase
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-
-
-
PAP
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-
-
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poly(A) polymerase
-
-
-
-
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ATP + RNAn = diphosphate + RNAn+1
ATP + RNAn = diphosphate + RNAn+1
mechanism
-
ATP + RNAn = diphosphate + RNAn+1
binding of enzyme to nuclear poly(A) binding protein results in 80-fold increase in apparent affinity for RNA, mechanism
-
ATP + RNAn = diphosphate + RNAn+1
SN2-in-line-mechanism
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nucleotidyl group transfer
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-
-
-
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ATP:polynucleotide adenylyltransferase
Also acts slowly with CTP. Catalyses template-independent extension of the 3'- end of a DNA strand by one nucleotide at a time. Cannot initiate a chain de novo. The primer, depending on the source of the enzyme, may be an RNA or DNA fragment, or oligo(A) bearing a 3'-OH terminal group. See also EC 2.7.7.6 DNA-directed RNA polymerase.
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ATP + RNA primer
diphosphate + RNA primer-A
in absence of ATP: no activity with 8-Cl-ATP, and 8-amino-ATP results in chain termination, in presence of ATP: polyadenylation of the primer is blocked (inhibited) by 8-amino-ATP and 8-Cl-ATP
-
-
?
adenosine 5'-O-(1-thiotriphosphate) + RNA
diphosphate + ?
-
SP-diastereomer
-
-
?
ATP + myosin short poly(A)
?
-
-
-
-
?
ATP + oligo(A)n
diphosphate + oligo(A)n+1
-
-
-
-
?
ATP + oligoadenylate
?
-
-
-
-
?
ATP + poly(A)n
diphosphate + poly(A)n+1
-
-
-
-
?
ATP + RNA
diphosphate + RNA(A)n
ATP + RNA (A)15
diphosphate + RNA (A)16
-
-
-
-
?
ATP + RNA(A)15
diphosphate + RNA(A)16
-
-
-
-
?
ATP + RNAn
diphosphate + RNAn+1
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adenine can bind in two different configurations in the PAP active site
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-
?
additional information
?
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-
overview on substrates and primers
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-
?
ATP + RNA
?
-
overview of biological function
-
-
?
ATP + RNA
?
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involved in the 3'-end processing of mRNA
-
-
?
ATP + RNA
diphosphate + RNA(A)n
-
-
-
-
?
ATP + RNA
diphosphate + RNA(A)n
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highly specific for ATP
-
?
ATP + RNA
diphosphate + RNA(A)n
-
highly specific for ATP
-
?
ATP + RNA
diphosphate + RNA(A)n
-
highly specific for ATP
-
?
ATP + RNA
diphosphate + RNA(A)n
-
highly specific for ATP
-
?
ATP + RNA
diphosphate + RNA(A)n
-
highly specific for ATP
-
?
ATP + RNA
diphosphate + RNA(A)n
-
elongation of the primer is distributive
-
?
ATP + RNA
diphosphate + RNA(A)n
-
primer: viral RNA MS-2 and QB
-
?
ATP + RNA
diphosphate + RNA(A)n
-
no primer: mixture of tRNA
-
?
ATP + RNA
diphosphate + RNA(A)n
-
primer: short poly(U)
-
?
ATP + RNA
diphosphate + RNA(A)n
-
Mg2+-activated enzyme from calf thymus or HeLa cells prefers either longer poly(A) or RNAs rather than shorter oligomers of AMP
-
?
ATP + RNA
diphosphate + RNA(A)n
-
Mn2+-activated enzymes are indifferent to primer length
-
?
ATP + RNA
diphosphate + RNA(A)n
-
primer required
-
?
ATP + RNA
diphosphate + RNA(A)n
-
primer required
-
?
ATP + RNA
diphosphate + RNA(A)n
-
primer required
-
?
ATP + RNA
diphosphate + RNA(A)n
-
primer required
-
?
ATP + RNA
diphosphate + RNA(A)n
-
primer required
-
?
ATP + RNA
diphosphate + RNA(A)n
-
primer required
-
?
ATP + RNA
diphosphate + RNA(A)n
-
primer required
-
?
ATP + RNA
diphosphate + RNA(A)n
-
primer required
-
?
ATP + RNA
diphosphate + RNA(A)n
-
primer required
polyadenylate sequences of 100-200 AMP residues
?
ATP + RNA
diphosphate + RNA(A)n
-
enzyme has no ATPase or poly(A) degrading activity
-
-
?
ATP + RNA
diphosphate + RNA(A)n
-
primer: poly(G,U)
-
?
ATP + RNA
diphosphate + RNA(A)n
-
no specificity for the 3'-terminal nucleotides
-
?
ATP + RNA
diphosphate + RNA(A)n
-
no specificity for the 3'-terminal nucleotides
-
?
ATP + RNA
diphosphate + RNA(A)n
-
no specificity for the 3'-terminal nucleotides when poly(C) and poly(I), but not poly(U), primes poly(A) synthesis with the Mg2+-activated enzyme
-
?
ATP + RNA
diphosphate + RNA(A)n
-
other nucleotides polymerized at less than 1% of the ATP rate
-
?
ATP + RNA
diphosphate + RNA(A)n
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other nucleotides polymerized at less than 1% of the ATP rate
-
?
ATP + RNA
diphosphate + RNA(A)n
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primer: rRNA 16S, E. coli
-
?
ATP + RNA
diphosphate + RNA(A)n
-
primer: rRNA 23S, E. coli
-
?
ATP + RNA
diphosphate + RNA(A)n
-
no primer: phage RNA
-
?
ATP + RNA
diphosphate + RNA(A)n
-
poly(A) is the most effective primer
-
?
ATP + RNA
diphosphate + RNA(A)n
-
influence of shape and size on priming efficiency
polyadenylate sequences of 100-200 AMP residues
?
ATP + RNA
diphosphate + RNA(A)n
-
Mg2+-activated calf thymus enzyme uses poly(A), tRNA, small RNA fragments from calf thymus RNA well, but HeLa 18 and 28S rRNA and MS-1 RNA poorly if at all
-
?
ATP + RNA
diphosphate + RNA(A)n
-
primer: poly(A)
-
?
ATP + RNA
diphosphate + RNA(A)n
-
primer: variety of oligoribonucleotides having free 3'-OH
-
?
ATP + RNA
diphosphate + RNA(A)n
-
rather low specificity for primer
-
?
ATP + RNA
diphosphate + RNA(A)n
-
rather low specificity for primer
-
?
ATP + RNA
diphosphate + RNA(A)n
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no primer: poly(G)
-
?
ATP + RNA
diphosphate + RNA(A)n
-
no primer: poly(C)
-
?
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ATP + RNA
?
-
overview of biological function
-
-
?
ATP + RNA
?
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involved in the 3'-end processing of mRNA
-
-
?
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KCl
-
requirement is dependent on the primer and the divalent cation used
additional information
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overview: ion requirements, poly(A) polymerases purified from different sources, and in some cases even from the same source, respond differently to the presence of Mg2+ and Mn2+
Mg2+
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optimal concentration is about 5 mM
Mg2+
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divalent cation requirement may be fulfilled by Mn2+, Mg2+ or a combination of the two depending on the source of the enzyme
Mg2+
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more active in presence of Mn2+ than Mg2+
Mg2+
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optimal concentration: 4-6 mM
Mg2+
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more active in presence of Mg2+ than Mn2+
Mg2+
-
completely inactive in presence of Mg2+
Mg2+
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one-fifth of the activity of Mg2+ in NTP activation
Mn2+
-
required
Mn2+
-
divalent cation requirement may be fulfilled by Mn2+, Mg2+ or a combination of the two depending on the source of the enzyme
Mn2+
-
more active in presence of Mn2+ than Mg2+
Mn2+
-
more active in presence of Mg2+ than Mn2+
Mn2+
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optimal concentration: 0.5 mM (at 0.5 mM ATP)
Mn2+
-
required for NTP activation
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CaCl2
-
remaining activity 3%
CoCl2
-
remaining activity 75%
CuCl2
-
remaining activity 0.1%
Mn2+
-
high concentrations
N-ethylmaleimide
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inhibits Mn2+-activated enzyme
Polyphosphate
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with 20 nM to 0.002 mM of polyphosphate the length of the products is reduced but inhibition is not complete
Proflavine
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only at very high levels
Ribonucleoside triphosphates other than ATP
-
-
rifamycin AF/013
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O-n-octyloxime of 3-formylrifamycin SV
Zn2+
-
inhibits PAP activity at concentrations above 10 µM in the presence of 5 mM MgCl2
diphosphate
-
-
diphosphate
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noncompetitive to ATP and primer
K+
-
above 50 mM
Na+
-
above 50 mM
NH4+
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ammonium sulfate
additional information
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overview
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additional information
-
not inhibitory: alpha-amanitin
-
additional information
-
not inhibitory: actinomycin D
-
additional information
-
insensitive to high levels of RNA-polymerase inhibitors
-
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0.2
oligoadenylate
-
in presence of Mg2+, pH 9.0, 35°C
additional information
additional information
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-
-
0.05
ATP
-
p(A)3 primer, Mn2+-activated calf thymus enzyme
0.05
ATP
-
oligoadenylate (in presence of Mn2+)
0.154
ATP
-
mutant D167N/N202A
0.229
ATP
-
wild-type, reactions are started with the addition of PAP and incubated at 37 °C for 15 minutes. Reactions are stopped by the addition of 8 microL of stop buffer (formamide with trace amount of bromophenol blue dye)
0.627
ATP
-
mutant D167N/T317G
0.01
oligo(A)n
-
Mn2+-activated enzyme, pH 8.3, 37°C
-
0.3
oligo(A)n
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Mg2+-activated enzyme, pH 8.3, 37°C
-
0.0036
poly(A)n
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Mn2+-activated enzyme, pH 8.3, 37°C
-
0.14 - 0.36
poly(A)n
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Mg2+-activated enzyme, pH 8.3, 37°C
-
0.51
RNA (A)15
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mutant A319R
-
0.74
RNA (A)15
-
mutant K232A
-
1.34
RNA (A)15
-
wild-type
-
1.43
RNA (A)15
-
mutant K228A
-
1.47
RNA (A)15
-
mutant V154A
-
1.88
RNA (A)15
-
mutant Q323A
-
2.63
RNA (A)15
-
mutant Y237A
-
2.8
RNA (A)15
-
mutant V206A
-
3.13
RNA (A)15
-
mutant T317G
-
5.31
RNA (A)15
-
mutant K158A
-
6.94
RNA (A)15
-
mutant N239A
-
7.32
RNA (A)15
-
mutant V156A
-
9.85
RNA (A)15
-
mutant V247A
-
10.21
RNA (A)15
-
mutant R199A
-
11.16
RNA (A)15
-
mutant V247R
-
11.44
RNA (A)15
-
mutant N202A
-
12.72
RNA (A)15
-
mutant G203H
-
13.15
RNA (A)15
-
mutant D167N
-
14.37
RNA (A)15
-
mutant F100D
-
16.41
RNA (A)15
-
mutant D167N/N202A
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18.82
RNA (A)15
-
mutant D167N/T317G
-
22.84
RNA (A)15
-
mutant D167N/V247R
-
24.99
RNA (A)15
-
mutant F153A
-
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0.002
ATP
-
mutant V247R
0.006
ATP
-
mutant D167N/N202A
0.007
ATP
-
mutant D167N/T317G
4.203
ATP
-
wild-type, reactions are started with the addition of PAP and incubated at 37 °C for 15 minutes. Reactions are stopped by the addition of 8 microL of stop buffer (formamide with trace amount of bromophenol blue dye)
30
ATP
-
cosubstrates rA(pA)5, pH 9.0, 35°C
0.0025
RNA(A)15
-
mutant D167N/V247R
-
0.006
RNA(A)15
-
mutant G203H
-
0.08
RNA(A)15
-
mutant N202A
-
0.1
RNA(A)15
-
mutant D167N/N202A
-
0.18
RNA(A)15
-
mutant V247R
-
0.26
RNA(A)15
-
mutant D167N/T317G
-
0.39
RNA(A)15
-
mutant V156A
-
0.67
RNA(A)15
-
mutant F100D
-
0.82
RNA(A)15
-
mutant R199A
-
1.43
RNA(A)15
-
mutant D167N
-
6.76
RNA(A)15
-
mutant K228A
-
6.86
RNA(A)15
-
mutant T317G
-
8.18
RNA(A)15
-
mutant K158A
-
10.52
RNA(A)15
-
mutant F153A
-
11.37
RNA(A)15
-
mutant N239A
-
12.58
RNA(A)15
-
mutant V206A
-
19.25
RNA(A)15
-
mutant Y237A
-
19.71
RNA(A)15
-
mutant Q323A
-
20.34
RNA(A)15
-
mutant K232A
-
22.75
RNA(A)15
-
mutant A319R
-
22.78
RNA(A)15
-
wild-type
-
28.96
RNA(A)15
-
mutant V154A
-
34.5
RNA(A)15
-
mutant V247A
-
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additional information
-
-
additional information
-
-
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8
-
Mg2+-activated enzyme
8.3
-
-
8.3
-
Mn2+-activated enzyme
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7 - 8.8
-
about 50% of maximum activity at pH 7.0 and pH 8.8
7 - 9
-
active in this range
7.2 - 9.2
-
pH 7.2: 55% of maximum activity, pH 9.2: 62% of maximum activity
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Uniprot
brenda
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-
brenda
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brenda
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-
brenda
-
-
brenda
-
-
-
brenda
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PAPOA_BOVIN
739
0
82441
Swiss-Prot
other Location (Reliability: 4 )
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120000 - 140000
-
Mg2+-activated enzyme, gel filtration
140000 - 160000
-
gel filtration
76990
-
predicted from nucleotide sequence
82400
-
predicted from nucleotide sequence
85000
-
x * 85000, SDS-PAGE, recombinant enzyme
57000
-
glycerol density gradient centrifugation
57000
-
and 60000, 2 major forms of enzyme, gel filtration
60000
-
Mn2+-activated enzyme, sedimentation analysis, gel filtration
60000
-
and 57000, 2 major forms of enzyme, gel filtration
62000
-
-
62000
-
sucrose density gradient sedimentation, gel filtration
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additional information
-
binding of enzyme to nuclear poly(A) binding protein results in 80-fold increase in apparent affinity for RNA, mechanism
?
-
-
?
-
x * 85000, SDS-PAGE, recombinant enzyme
monomer
-
1 * 62000, SDS-PAGE
monomer
-
1 * 57000, SDS-PAGE
monomer
-
1 * 60000, Mn2+-activated enzyme, denaturing gel electrophoresis
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additional information
-
not glycosylated
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in complex with an ATP analog
mutant C36S/C118V/A152C/C160S/C197S/C257S/C293S/C204V in complex with a chemically modified RNA, to 2.25 A resolution
Crystals of PAP complexed to 3'-dATP and Mn2+ are grown from a solution made of 22% (w/v) polyethylene glycol 8000, 100 mM Mes (pH 6), 120 mM ammonium sulfate, 5 mM CaCl2, 2 mM MnCl2, and 2 mM beta-mercaptoethanol. Cocrystallization of PAP with 3'-dATP and MgCl2 is performed under conditions similar to those reported, with the exception that 5 mM MgCl2 is used instead of 2 mM MnCl2. Crystals are of the space group p212121, with one monomer per asymmetric unit and a solvent content of ~55%.
-
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C36S/C118V/A152C/C160S/C197S/C257S/C293S/C204V
introduction of a Cys residue in a mutant lacking all endogenous Cys residues. Mutant achieves maximum specific disulfide cross-linking efficiency. The resulting construct is active and, when mixed with a chemically modified RNA, yields crystals of an enzyme-RNA complex
C36S/C118V/C160S/C197S/C257S/C293S/C204V
mutation of all seven endogenous cysteine residues. Mutant is able to bind RNA at a level similar to that of wild-type, but no longer forms nonspecific disulfide cross-links with the modified RNA
D167N
-
strong reduction of catalytic efficiency
D167N/N202A
-
sharp decrease in catalytic efficiency
D167N/T317G
-
sharp decrease in catalytic efficiency
D167N/V247R
-
sharp decrease in catalytic efficiency
F100D
-
strong reduction of catalytic efficiency
G203H
-
strong reduction of catalytic efficiency
K228A
-
increase in Km for ATP
K232A
-
increase in Km for ATP
N202A
-
high Km value for RNA, strong reduction of catalytic efficiency, incorporates etheno-ATP and N1-methyl-ATP better than wild-type, but incorporates N6-methyl-ATP poorly
N239A
-
kcat for ATP is reduced fourfold
R199A
-
reduces kcat for RNA about 30-fold
T317G
-
increase in Km for ATP, tolerates etheno-ATP and GTP, rejects N6-methyl-ATP
V156A
-
strong reduction of catalytic efficiency
V247R
-
kcat for ATP is reduced 2000-fold, strong reduction of catalytic efficiency
Y237A
-
increase in Km for ATP
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freezing and thawing accelerates inactivation
-
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-20°C, 50% glycerol, 80% inactivation in the first few weeks, the 20% remaining activity is stable for more than 2 years
-
-70°C or under liquid nitrogen, extensive inactivation
-
-80°C, 10-20 mg protein/ml, flash frozen
-
-80°C, storage for 5 days including 2 cycles of freezing and thawing results in 35% inactivation
-
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homogenous preparation of bovine enzyme
-
overview: purification methods
-
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expression in Escherichia coli Rosetta (DE3) pLysS cells
expression in Escherichia coli
-
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Bollum, F.J.; Chang, L.M.S.; Tsiapalis, C.M.; Dorson, J.W.
Nucleotide polymerizing enzymes from calf thymus gland
Methods Enzymol.
29E
70-81
1974
Bos taurus
-
brenda
Edmonds, M.
Poly(A) adding enzymes
The Enzymes,3rd Ed. (Boyer,P. D. ,ed. )
15
217-244
1982
Bos taurus, Cricetulus griseus, Coturnix sp., Escherichia coli, Homo sapiens, Mus musculus, Rattus norvegicus, Vaccinia virus
-
brenda
Winters, M.A.; Edmonds, M.
A poly(A) polymerase from calf thymus. Purification and properities of the enzyme
J. Biol. Chem.
248
4756-4762
1973
Bos taurus
brenda
Winters, M.A.; Edmonds, M.
A poly(A) polymerase from calf thymus. Characterization of the reaction product and the primer requirement
J. Biol. Chem.
248
4763-4768
1973
Bos taurus
brenda
Raabe, T.; Bollum, F.J.; Manley, J.L.
Primary structure and expression of bovine poly(A) polymerase
Nature
353
229-234
1991
Bos taurus
brenda
Tsiapalis, C.M.; Dorson, J.W.; Bollum, F.J.
Purification of terminal riboadenylate transferase from calf thymus gland
J. Biol. Chem.
250
4486-4496
1975
Bos taurus
brenda
Wahle, E.; Martin, G.; Schiltz, E.; Keller, W.
Isolation and expression of cDNA clones encoding mammalian poly(A) polymerase
EMBO J.
10
4251-4257
1991
Bos taurus
brenda
Wahle, E.
Purification and characterization of a mammalian polyadenylate polymerase involved in the 3 end processing of messenger RNA precursors
J. Biol. Chem.
266
3131-3139
1991
Bos taurus
brenda
Ohyama, Y.; Fukami, H.; Ohta, T.
Purification and characterization of a poly(A) polymerase from beef liver nuclei
J. Biochem.
88
337-348
1980
Bos taurus
brenda
Martin, G.; Keller, W.; Doublie, S.
Crystal structure of mammalian poly(A) polymerase in complex with an analog of ATP
EMBO J.
19
4193-4203
2000
Bos taurus (P25500), Bos taurus
brenda
Wittmann, T.; Wahle, E.
Purification and characterization of full-length mammalian poly(A) polymerase
Biochim. Biophys. Acta
1350
293-305
1997
Bos taurus
brenda
Kerwitz, Y.; Kuehn, U.; Lilie, H.; Knoth, A.; Scheuermann, T.; Friedrich, H.; Schwarz, E.; Wahle, E.
Stimulation of poly(A) polymerase through a direct interaction with the nuclear poly(A) binding protein allosterically regulated by RNA
EMBO J.
22
3705-3714
2003
Bos taurus
brenda
Martin, G.; Moglich, A.; Keller, W.; Doublie, S.
Biochemical and structural insights into substrate binding and catalytic mechanism of mammalian poly(A) polymerase
J. Mol. Biol.
341
911-925
2004
Bos taurus
brenda
Holbein, S.; Freimoser, F.M.; Werner, T.P.; Wengi, A.; Dichtl, B.
Cordycepin-hypersensitive growth links elevated polyphosphate levels to inhibition of poly(A) polymerase in Saccharomyces cerevisiae
Nucleic Acids Res.
36
353-363
2008
Bos taurus, Saccharomyces cerevisiae, Saccharomyces cerevisiae BY4741
brenda
Chen, L.S.; Du-Cuny, L.; Vethantham, V.; Hawke, D.H.; Manley, J.L.; Zhang, S.; Gandhi, V.
Chain termination and inhibition of mammalian poly(A) polymerase by modified ATP analogues
Biochem. Pharmacol.
79
669-677
2010
Bos taurus (P25500), Bos taurus
brenda
Yang, Q.; Faucher, F.; Coseno, M.; Heckman, J.; Doublie, S.
Purification, crystallization and preliminary X-ray diffraction of a disulfide cross-linked complex between bovine poly(A) polymerase and a chemically modified 15-mer oligo(A) RNA
Acta Crystallogr. Sect. F
67
241-244
2011
Bos taurus (P25500), Bos taurus
brenda