Information on EC 3.1.16.1 - spleen exonuclease

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The expected taxonomic range for this enzyme is: Eukaryota, Archaea

EC NUMBER
COMMENTARY hide
3.1.16.1
-
RECOMMENDED NAME
GeneOntology No.
spleen exonuclease
-
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
exonucleolytic cleavage in the 5'- to 3'-direction to yield nucleoside 3'-phosphates
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
hydrolysis of phosphoric ester
-
-
-
-
CAS REGISTRY NUMBER
COMMENTARY hide
9068-54-6
-
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
strain FCR-3/C5
SwissProt
Manually annotated by BRENDA team
strain FCR-3/C5
SwissProt
Manually annotated by BRENDA team
strain
SwissProt
Manually annotated by BRENDA team
gene nurA
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
3'-phospho-2'-deoxyribooligonucleotide + H2O
2'-deoxyribonucleoside 3'-phosphate
show the reaction diagram
4-methylumbelliferyl thymidine 3'-phosphate + H2O
thymidine 3'-phosphate + 4-methylumbelliferone
show the reaction diagram
-
-
-
?
4-nitrophenyl phosphate
4-nitrophenol + phosphate
show the reaction diagram
5'-hydroxy oligonucleotides + H2O
nucleoside 3'-oligonucleotides + nucleoside 3'-phosphates
show the reaction diagram
5-'deoxy-5'-chlorothymidine-3'-(4-nitrophenyl)phosphate + H2O
5'-deoxy-5'-chlorothymidine-3'-phosphate
show the reaction diagram
-
-
-
?
bis-(4-nitrophenyl)phosphate + H2O
4-nitrophenyl phosphate + 4-nitrophenol
show the reaction diagram
DNA + H2O
deoxyribonucleoside 3'-phosphate + ?
show the reaction diagram
DNA + H2O
deoxyribonucleoside 3'-phosphates
show the reaction diagram
Flap34endo + H2O
?
show the reaction diagram
mRNA + H2O
?
show the reaction diagram
-
XRNA is important in the degradation of deadenylated mRNAs in trypanosomes
-
-
-
polyadenylic acid + H2O
5'-hydroxy-adenine oligonucleotides + 3'AMP
show the reaction diagram
polyguanylic acid
3'-GMP
show the reaction diagram
-
-
-
?
polyinosinic acid
3'-IMP
show the reaction diagram
-
-
-
?
polynucleotides + H2O
3'-phosphomononucleotides
show the reaction diagram
polynucleotides + H2O
phosphomononucleotides
show the reaction diagram
-
the enzyme contributes to the turnover of messenger RNAs in eukaryotic cells
-
-
?
polyuridylic acid + H2O
3'-UMP
show the reaction diagram
ribonucleotide 3'-alkyl esters + H2O
3'-Ribonucleotides + alkyl alcohol
show the reaction diagram
RNA core + H2O
nucleoside 3'-phosphates
show the reaction diagram
thymidine 3'-(2,4-dinitrophenyl)phosphate + H2O
thymidine 3'-phosphate + 2,4-dinitrophenol
show the reaction diagram
thymidine 3'-(4-nitrophenyl)phosphate + H2O
thymidine 3'-phosphate + 4-nitrophenol
show the reaction diagram
tRNA + H2O
tRNA fragments + nucleoside 3'-phosphates
show the reaction diagram
[PO/Mix-PS]-d[TPOCPOTPOTPOTPOTPOTPSC] + H2O
?
show the reaction diagram
-
21% degraded after 2 hours, 35% degraded after 8 hours
-
-
?
[PO/Mix-PS]-d[TPOTPOTPOTPOTPOTPOTPOTPOTPOTPOTPST] + H2O
?
show the reaction diagram
-
35% degraded after 2 hours, 75% degraded after 8 hours
-
-
?
[PO/RP-PS]-d[TPOCPOTPOTPOTPOTPOTPSC] + H2O
?
show the reaction diagram
-
22% degraded after 2 hours, 45% degraded after 8 hours
-
-
?
[PO/SP-PS]-d[TPOCPOTPOTPOTPOTPOTPSC] + H2O
?
show the reaction diagram
-
20% degraded after 2 hours, 25% degraded after 8 hours
-
-
?
[PS]-d[A6] + H2O
?
show the reaction diagram
-
-
-
-
?
[RP-PS]-d[A12] + H2O
?
show the reaction diagram
-
-
-
-
?
[RP-PS]-d[T12] + H2O
?
show the reaction diagram
-
25% degraded after 2 hours, 75% degraded after 8 hours
-
-
?
[S]-d[A12] + H2O
?
show the reaction diagram
-
-
-
-
?
[S]-d[T12] + H2O
?
show the reaction diagram
-
100% degraded after 2 hours
-
-
?
[S]-d[TCCTCTTTTTTT] + H2O
?
show the reaction diagram
-
-
-
-
?
[S]-d[TCTTTTTC] + H2O
?
show the reaction diagram
-
100% degraded after 2 hours
-
-
?
additional information
?
-
NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
polynucleotides + H2O
3'-phosphomononucleotides
show the reaction diagram
polynucleotides + H2O
phosphomononucleotides
show the reaction diagram
-
the enzyme contributes to the turnover of messenger RNAs in eukaryotic cells
-
-
?
additional information
?
-
-
NurA may function closely together with SSB in DNA transactions in archaea
-
-
-
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Ni2+
minimally stimulates activity
additional information
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
5'-Terminal phosphate
-
in tRNA
-
acetylation
-
complete inhibition by acetylation of the 2'-OH of tRNA
-
Ap4A
-
-
arsenite
-
weak inhibitor with RNA core as substrate
ATPgammaS
-
-
Deoxyribonucleoside 3'-phosphates
-
-
Dihydroxyuridine
-
in tRNA
-
dimethyl sulfate
-
inhibition after methylation of 2'-deoxyribooligonucleotides with dimethyl sulfate
F-
-
weak inhibitor with RNA core as substrate
glycosylation
-
no activity with glycosylated oligonucleotides obtained from T4 phage DNA
-
heparin
-
-
Hg2+
-
with RNA core as substrate
High ionic strength
-
KCl
FEN-1 retains up to approximately 70.0% of its endonuclease at 0-50.0 mM, between 75 and 100 mM FEN-1 displays a significant reduction in activity and at the highest salt concentrations between 125-200 mM almost a complete ablation of activity occurres
Mn2+
-
with RNA core as substrate
p-nitrophenyl-TMP
-
-
Pentamidine
-
endo-exonuclease inhibitor, inhibits DNase activity of CBP-Trm2p
pyridoxal 5'phosphate-6-azophenyl-2',4'-disulfonic acid
-
-
ribo- and deoxyribonucleotides
-
with 5'-phosphomonoester group
-
RNAi
-
down-regulation of expression by tetracycline-inducible RNA interference
-
RP-dATPalphaS
-
-
single-stranded DNA-binding protein
-
i.e. StoSSB, from the hyperthermophilic archaeon Sulfolobus tokodaii, StoSSB inhibits the exonuclease activity of StoNurA on ssDNA and dsDNA
-
SP-ATPalphaS
-
-
SP-CTPalphaS
-
-
SP-dATPalphaS
-
-
UDP-glucose
-
-
Zn2+
-
with RNA core as substrate
additional information
-
no inhibition up to 40 mM by lysophosphatidylcholine
-
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
EDTA
-
with RNA core as substrate
sulfhydryl reagents
-
with RNA core as substrate
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.45
4-methylumbelliferyl thymidine 3'-phosphate
-
-
0.5
5'-deoxy-5'-chlorothymidine-3'-(4-nitrophenyl)phosphate
-
-
0.0000038 - 0.0000066
Flap34endo
-
0.04
thymidine 3'-(2,4-dinitrophenyl)phosphate
0.18 - 3
thymidine 3'-(4-nitrophenyl)phosphate
0.173
[RP-PS]-d[T12]
-
-
-
0.0715
[S]-d[A12]
-
-
-
0.016
[S]-d[T12]
-
-
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
1.2 - 9.1
Flap34endo
-
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2
Urea
-
-
IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.037
Ap4A
Homo sapiens
-
inhibition of degradation of [PO]-d[TCCTCTTTTTTT]
0.054
ATP
Homo sapiens
-
inhibition of degradation of [PO]-d[TCCTCTTTTTTT]
0.027
ATPgammaS
Homo sapiens
-
inhibition of degradation of [PO]-d[TCCTCTTTTTTT]
0.027
p-nitrophenyl-TMP
Homo sapiens
-
inhibition of degradation of [PO]-d[TCCTCTTTTTTT]
0.071
pyridoxal 5'phosphate-6-azophenyl-2',4'-disulfonic acid
Homo sapiens
-
inhibition of degradation of [PO]-d[TCCTCTTTTTTT]
0.002 - 0.005
RP-dATPalphaS
0.0002 - 0.002
SP-ATPalphaS
0.0084
SP-CTPalphaS
Homo sapiens
-
inhibition of degradation of [PO]-d[TCCTCTTTTTTT]
0.0015
SP-dATPalphaS
Homo sapiens
-
inhibition of degradation of [PO]-d[TCCTCTTTTTTT]
0.106
UDP-glucose
Homo sapiens
-
inhibition of degradation of [PO]-d[TCCTCTTTTTTT]
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.72
-
with polyadenylic acid as substrate
34
-
with thymidine 3'-(4-nitrophenyl)phosphate as substrate
43.3
-
with 5'-hydroxy-2'deoxy-cytosine oligonucleotide d-CpCpC, lacking terminal phosphomonoester group, as substrate; with 5'-hydroxy-thymidine oligonucleotide TpT, lacking terminal phosphomonoester group, as substrate; with 5'-hydroxy-thymidine oligonucleotide TpTpTpT, lacking terminal phosphomonoester group, as substrate
45
-
with 5'-hydroxy-thymidine oligonucleotide TpTp as substrate
58.3
-
with 5'-hydroxy-adenine oligonucleotide ApApA, lacking terminal phosphomonoester group, as substrate; with 5'-hydroxy-oligonucleotide ApUp as substrate
646
-
with 5-'deoxy-5'-chlorothymidine-3'-(4-nitrophenyl)phosphate as substrate, 1.5 microg/ml commercially available enzyme
855
-
with thymidine 3'-(4-nitrophenyl)phosphate as substrate, 1.5 microg/ml commercially available enzyme
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5 - 5.8
-
-
5
-
with 0.15 M acetate buffer
5.5
-
with 0.1 M acetate or succinate buffer
5.8
-
substrate bis-(p-nitrophenyl) phosphate in 0.25 M succinate buffer
5.9 - 6.5
-
5.9 with almost 0.15 M ammonium succinate buffer, 6.5 with almost 0.3 M and thymidine 3'(4-nitrophenyl)phosphate as substrate
6 - 6.5
6.2 - 6.3
-
-
6.6 - 6.8
-
-
6.7
-
-
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
4 - 7
-
poor effect of 0.02 M Mg2+ on pH activity curve at 37°C
6 - 8
-
-
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
22
-
assay at room temperature
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
additional information
-
bloodstream forms and procyclic forms of trypanosomes
Manually annotated by BRENDA team
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
additional information
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
25000
-
alpha2beta2, 2 * 25000 + 2 * 55000, intermolecular disulfide bonds, no activity of subunits alpha or beta, but 3.1 times higher specific activity of tetramer in comparison with alpha,beta dimer, SDS-polyacrylamide gel electrophoresis in presence of mercaptoethanol
46000
C-terminal truncation mutant, Western blot analysis
54500
sequence analysis
55000
-
alpha2beta2, 2 * 25000 + 2 * 55000, intermolecular disulfide bonds, no activity of subunits alpha or beta, but 3.1 times higher specific activity of tetramer in comparison with alpha,beta dimer, SDS-polyacrylamide gel electrophoresis in presence of mercaptoethanol
75000
sequence analysis, Western blot analysis
95000
-
XRNC
98000
-
molecular sieving, SDS gel electrophoresis, sucrose density gradient centrifugation
115000
-
XRNB
125000
-
gel filtration
158000
-
XRNA
160000
-
SDS-polyacrylamide gel electrophoresis
170000
-
gel filtration
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
tetramer
POSTTRANSLATIONAL MODIFICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
glycoprotein
pH STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5 - 7
-
incubation of pure enzyme for 2 h at 4°C, beyond the limits sharp decrease of stability
134134
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
35 - 60
-
incubation at pH 5.7, 10 min: 90% of initial activity at 35°C, 10% at 60°C
45 - 80
-
range of thermal inactivation, 50% of activity at 56°C
61
-
lost of 50% of activity after heating of partially purified enzyme for 5 min
64
-
lost of 50% of activity after heating of partially purified enzyme for 5 min
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-15°C, in 50% glycerol
-
-80°C
-
4°C, lyophilized crude enzyme, more than 1 year, no loss of activity
-
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
by calmodulin affinity chromatography
-
by cation exchange column and on Ni-NTA column
by gel filtration
-
contamination by endonuclease activity
-
FEN-1 purified by cation exchange column followed by a calmodulin affinity resin, more than 95% pure, C-terminal truncation mutant purified on Ni-NTA column and by cation exchange column, more than 95% pure
fractionation of exonucleases A, B and C; no contamination by other phosphohydrolase activities
-
no contamination by other phosphohydrolase activities
-
no endonuclease and phophomonoesterase activities
-
XRND purified by nickel affinity chromatography
-
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
Escherichia coli BL21-Gold DE3 transformed with the plasmid pCBP-TRM2 and pCBP-DTRM2(ctdelta1689-1920nt), also cloned into a GFP vector bearing a GAL1::GFP transcriptional fusion
-
FEN-1 cloned into the pCAL-n-FLAG expression vector and expressed in Escherichia coli BLR(DE3)pLysS cells. C-terminal truncation mutant cloned into pET24d(+) and expressed in Escherichia coli BL21(DE3)CodonPlus-RIL
full-length, sequence verified PCR product cloned into vector pENTR3C, wild type and mutant Ape2 cDNAs in fusion with GST under the control of the Saccharomyces cerevisiae galactose-inducible phosphoglycerate promoter using plasmid pBJ842, resulting in plasmids pIL1047 and pIL1247, respectively, overexpressed in parallel in the protease-deficient BJ5464 yeast strain
-
gene nurA, DNA and amino acid sequence determination and analysis, the nurA gene is arranged in an operon-like structure with mre11, rad50, and herA genes, expression with StoSSB in the two-hybrid system in yeast AH109
-
His-tagged XRND protein expressed in Escherichia coli by cloning into pET3A vector
-
HIS6 tagged gene subcloned into pET24d(+) and expressed in Escherichia coli BL21(DE3)CodonPlus-RIL
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
D277A
-
mutation of the active-site residue, inactivates 3'–5' exonuclease, 3'-phosphodiesterase and AP-endonuclease activities
additional information
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
analysis
additional information