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Enzyme Nomenclature
Information on EC 3.1.30.2 - Serratia marcescens nuclease
for references in articles please use BRENDA:EC3.1.30.2
Word Map on EC 3.1.30.2
- 3.1.30.2
- repair
-
double-stranded
-
single-stranded
-
nick
-
excision
- chromatin
-
exonuclease
- viral
- phage
-
nucleases
- rnase
- bacteriophage
-
endonucleolytic
-
mismatch
-
editing
-
glycosylase
-
structure-specific
-
restriction-modification
-
homing
-
supercoiled
-
phosphodiester
-
helicase
-
methylase
- fork
-
palindromic
-
internucleosomal
- xeroderma
-
retrotransposons
-
oligonucleosomal
- deoxyribonuclease
-
overhang
- pigmentosum
-
holliday
-
interstrand
-
dsdna
-
endoribonuclease
-
abasic
-
retrotransposition
-
interspaced
-
end-joining
-
caspase-independent
-
nucleolytic
- pvuii
- dicer
-
micrococcal
-
superhelical
- colicins
-
okazaki
- ecorv
- molecular biology
-
resolvase
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The expected taxonomic range for this enzyme is: Eukaryota, Bacteria
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EC NUMBER 
COMMENTARY 
3.1.30.2
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RECOMMENDED NAME
GeneOntology No.
Serratia marcescens nuclease
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
Endonucleolytic cleavage to 5'-phosphomononucleotide and 5'-phosphooligonucleotide end-products
Endonucleolytic cleavage to 5'-phosphomononucleotide and 5'-phosphooligonucleotide end-products
mechanism
-
Endonucleolytic cleavage to 5'-phosphomononucleotide and 5'-phosphooligonucleotide end-products
one-step in line mechanism of enzymatic hydrolysis. The enzyme hydrolyzes internucleotide phosphothioate linkages of Rp configuration with inversion of configuration at the P-atom. The enzyme is stereoselective towards internucleotide phosphothioate linkages of Rp configuration. The involvement of a non-bridging oxygen in contact with a magnesium ion is a critical discriminatory factor for selectivity towards phosphothioate analogues
-
Endonucleolytic cleavage to 5'-phosphomononucleotide and 5'-phosphooligonucleotide end-products
general acid-base catalysis. The enzyme cleaves 3'- and 5'-phosphodiester bonds to form 5'-phosphorylated oligonucleotides. The hydrolysis of the phosphodiester bonds proceeds as a result of the nucleophilic displacement at the phosphorus atom. The enzyme active site is formed at least by 8 amino acid residues, Arg57, Asp86, His89, Gln114, Asn119 and Glu127. Arg57, Asp86, His89 and Glu127 are important for the catalytic activity of the enzyme. His89 is a potential candidate for the function of a general base catalyst that accepts a proton from a solvent H2O molecule, which is the attacking nucleophile. The reaction is accompanied by the inversion of configuration at the phosphorus atom and proceeds in accordance with an in-line mechanism
-
Endonucleolytic cleavage to 5'-phosphomononucleotide and 5'-phosphooligonucleotide end-products
DNA cleavage stereochemistry and mechanism involving interaction of DNA with three zinc ions, the enzyme contains a cocatalytic zinc site
-
Endonucleolytic cleavage to 5'-phosphomononucleotide and 5'-phosphooligonucleotide end-products
catalytic mechanism, enzyme monomer-DNA binding complex, hydration sites and influence of solvent on structure and reaction, active site structure
-
Endonucleolytic cleavage to 5'-phosphomononucleotide and 5'-phosphooligonucleotide end-products
-
-
-
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
hydrolysis of phosphoric ester
hydrolysis of phosphoric ester
-
-
-
-
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CAS REGISTRY NUMBER
COMMENTARY
9025-65-4
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
expression of the enzyme is not under catabolite or substrate regulation. A transcriptional regulator nucC positively regulates the transcription of nucA. Serratia marcescens homologue of the Escherichia coli DinI SOS regulator inhibits the expression of the enzyme
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
the enzyme belongs to the plant S1-like nucleases class of enzymes. Different members of this family are characterized by a surprisingly large variety of catalytic properties, nucleolytic activities of all Arabidopsis thaliana S1-like paralogues, overview. In addition to Zn2+-dependent enzymes, this family also comprises nucleases activated by Ca2+ and Mn2+, which implies that the apparently well-known S1 nuclease active site in plant nucleases is able to cooperate with different activatory ions. Particular members of this class differ in their optimum pH value and substrate specificity. Plant representatives of this family evolve toward an increase in catalytic diversity. Phylogenetic analysis, overview; the enzyme belongs to the plant S1-like nucleases class of enzymes. Different members of this family are characterized by a surprisingly large variety of catalytic properties, nucleolytic activities of all Arabidopsis thaliana S1-like paralogues, overview. In addition to Zn2+-dependent enzymes, this family also comprises nucleases activated by Ca2+ and Mn2+, which implies that the apparently well-known S1 nuclease active site in plant nucleases is able to cooperate with different activatory ions. Particular members of this class differ in their optimum pH value and substrate specificity. Plant representatives of this family evolve toward an increase in catalytic diversity. Phylogenetic analysis, overview; the enzyme belongs to the plant S1-like nucleases class of enzymes. Different members of this family are characterized by a surprisingly large variety of catalytic properties, nucleolytic activities of all Arabidopsis thaliana S1-like paralogues, overview. In addition to Zn2+-dependent enzymes, this family also comprises nucleases activated by Ca2+ and Mn2+, which implies that the apparently well-known S1 nuclease active site in plant nucleases is able to cooperate with different activatory ions. Particular members of this class differ in their optimum pH value and substrate specificity. Plant representatives of this family evolve toward an increase in catalytic diversity. Phylogenetic analysis, overview; the enzyme belongs to the plant S1-like nucleases class of enzymes. Different members of this family are characterized by a surprisingly large variety of catalytic properties, nucleolytic activities of all Arabidopsis thaliana S1-like paralogues, overview. In addition to Zn2+-dependent enzymes, this family also comprises nucleases activated by Ca2+ and Mn2+, which implies that the apparently well-known S1 nuclease active site in plant nucleases is able to cooperate with different activatory ions. Particular members of this class differ in their optimum pH value and substrate specificity. Plant representatives of this family evolve toward an increase in catalytic diversity. Phylogenetic analysis, overview
malfunction
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Deficiencies in FEN1 function or deletion of the fen1 gene have profound biological effects, including the suppression of repair of DNA damage incurred from the action of various genotoxic agents
physiological function
additional information
physiological function
-
role of FEN1 in replication, recombination, DNA repair and maintenance of telomeres. FEN1 exhibits distinct activity on G4 DNA substrates representative of intermediates in immunoglobulin class switch recombination. hFEN1 but not hEXO1 cleaves substrates bearing telomeric G4 DNA 5'-flaps, consistent with the requirement for FEN1 in telomeric lagging strand replication. FEN1 can create ssDNA at uncapped telomere ends thereby contributing to recombination
physiological function
-
flap endonuclease 1 is a key enzyme in DNA repair and DNA replication. It is a structure-specific nuclease that removes 5'-overhanging flaps and the RNA/DNA primer during maturation of the Okazaki fragment
physiological function
-
Flap endonuclease, FEN1, is essential for DNA replication and repair, and removes RNA and DNA 5' flaps. Structural and functional analyses of human FEN1:DNA complexes show structure-specific, sequence-independent recognition for nicked dsDNA bent 100° with unpaired 3' and 5' flaps. dsDNA binding and bending, the ssDNA gateway, and double-base unpairing flanking the scissile phosphate control precise flap incision by the two-metal-ion active site
physiological function
-
Flap endonuclease 1 plays critical roles in both DNA replication and repair. Human FEN1 endonuclease, an enzyme involved in excising single-stranded DNA flaps that arise during Okazaki fragment processing and base excision repair, cleaves model flap substrates assembled into nucleosomes. Orienting the flap substrate toward the histone octamer does not significantly alter the rotational orientation of two different nucleosome positioning sequences on the surface of the histone octamer but does cause minor perturbation of nucleosome structure. In contrast, neither flaps oriented toward nor away from the nucleosome surface are cleaved by the enzyme in nucleosomes containing the high-affinity 601 nucleosome positioning sequence. Sequence-dependent motility of DNA on the nucleosome is a major determinant of FEN1 activity
physiological function
-
the Dna2 enzyme is at the center of both DNA replication and DNA damage repair, acting in conjunction with flap endonuclease 1 and replication protein A in DNA lagging strand replication and with BLM/Sgs1 and MRN/X in double strand break repair. Dna2 shows helicase and flap endo/exonuclease activities requiring an unblocked 5' single-stranded DNA end to unwind or cleave DNA, but Dna2 in fact can create 5' single-stranded DNA ends. Both endonuclease and flap endo/exonuclease are abolished by the Dna2-K677R mutation, implicating the same active site in catalysis. ATP-dependent flap endo/exonuclease activity is observed only in the presence of Mn2+. The endonuclease is blocked by ATP and is thus experimentally distinguishable from the flap endo/exonuclease function. Mechanism of action of Dna2 in multiprotein complexes, overview
physiological function
-
FEN1, a key participant in DNA replication and repair, is the major human flap endonuclease that recognizes and cleaves flap DNA structures
physiological function
involvement of isozyme ENDO1 in endosperm senescence. Plant S1-like nucleases are the main class of enzymes involved in nucleic acid degradation during plant programmed cell death; plant S1-like nucleases are the main class of enzymes involved in nucleic acid degradation during plant programmed cell death; plant S1-like nucleases are the main class of enzymes involved in nucleic acid degradation during plant programmed cell death; plant S1-like nucleases are the main class of enzymes involved in nucleic acid degradation during plant programmed cell death
physiological function
any mononucleotide produced by Sma nuc during hydrolysis of DNA or RNA may regulate the enzyme activity affecting the RNase activity without pronounced influence on the activity towards DNA. The type of carbohydrate residue in mononucleotides does not affect the regulation. In contrast, the effects depend on the type of bases in nucleotides
additional information
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treatment of enriched DNA with the mung bean nuclease, an endonuclease specific to single-stranded DNA or RNA, can dramatically reduce genomic DNA carry over of single-stranded template genomic DNA from microdroplet-PCR and increase on-target efficiency of the resultant library. Nuclease treatment of enrichment products shall be incorporated in the workflow of targeted sequencing using microdroplet-PCR for enrichment
additional information
specific site(s) for the nucleotide(s) binding in Sma nuc endonuclease
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
5'-CCTGGCAGTT + H2O
?
-
synthetic labeled deoxydecanucleotide, cleavage of 5'-Ap*G bond and with lower activity of Gp*T, Cp*A, and Gp*G bonds
-
-
?
B-Z-hybrid form DNA + H2O
?
-
hybrid B-Z form of herring testis DNA
-
-
?
lambda DNA + H2O
?
-
-
size of linear DNA fragments decreases with prolonged incubation time
-
?
pUC18 DNA + H2O
?
-
covalently closed circular plasmid DNA
substrate converted into relaxed circular form and than to the linear form
-
?
pUC19 DNA + H2O
?
-
relaxation of the supercoiled DNA and cutting of the open circular DNA to a linear form
-
-
?
DNA + H2O
5'-phosphonucleotides + 5'-phosphomononucleotides
Azotobacter agilis
-
-
-
-
?
DNA + H2O
5'-phosphonucleotides + 5'-phosphomononucleotides
-
heat denatured
-
-
?
DNA + H2O
5'-phosphonucleotides + 5'-phosphomononucleotides
-
native double-stranded
-
-
?
DNA + H2O
5'-phosphonucleotides + 5'-phosphomononucleotides
-
partially degraded DNA
-
-
?
DNA + H2O
5'-phosphonucleotides + 5'-phosphomononucleotides
-
hydrolysis rate about 3 times more slowly than compared to RNA
-
-
?
DNA + H2O
5'-phosphonucleotides + 5'-phosphomononucleotides
-
single-stranded DNA
-
-
?
DNA + H2O
5'-phosphonucleotides + 5'-phosphomononucleotides
-
heat denatured
-
-
?
DNA + H2O
5'-phosphonucleotides + 5'-phosphomononucleotides
-
native double-stranded
-
-
?
DNA + H2O
5'-phosphonucleotides + 5'-phosphomononucleotides
-
cleaves supercoiled DNA only at specific sites
-
-
?
DNA + H2O
5'-phosphonucleotides + 5'-phosphomononucleotides
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single-stranded DNA
-
-
?
DNA + H2O
5'-phosphonucleotides + 5'-phosphomononucleotides
-
cleaves supercoiled DNA only at specific sites
-
-
?
DNA + H2O
5'-phosphonucleotides + 5'-phosphomononucleotides
-
-
-
-
?
DNA + H2O
5'-phosphonucleotides + 5'-phosphomononucleotides
-
DNA is slightly preferred as a substrate than RNA
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-
?
DNA + H2O
5'-phosphonucleotides + 5'-phosphomononucleotides
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cleaves supercoiled DNA only at specific sites
-
-
?
DNA + H2O
5'-phosphonucleotides + 5'-phosphomononucleotides
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cleaves supercoiled DNA only at specific sites
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-
?
DNA + H2O
5'-phosphonucleotides + 5'-phosphomononucleotides
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native double-stranded
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-
?
DNA + H2O
5'-phosphonucleotides + 5'-phosphomononucleotides
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single-stranded DNA
-
-
?
DNA + H2O
?
-
tritium labeled DNA from Escherichia coli, fragmented by limited sonication
random DNA cleavage with respect to all possible phosphodiester bonds
-
?
DNA + H2O
?
dsDNA to ssDNA preference ratio for Par_DSN-t4 is equal to 10, corresponding ratio for intact Par_DSN is equal to 1000
-
-
?
DNA + H2O
?
protein and DNA are held together by a mix of salt-bridges, water-mediated and direct hydrogen bond interactions between the protein and DNA backbone, almost no DNA bases are directly involved in the contacts
-
-
?
dsDNA + H2O
?
-
primarily responsible for internucleosomal DNA cleavage during the terminal stages of apoptosis, preference for cleaving the internucleosomal linker regions in chromatin
fragments possessing ends with 5-phosphate and 3-hydroxyl groups, exclusively double strand breaks (primarily blunt ends)
-
?
dsDNA + H2O
?
-
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DNA fragments carrying phosphate groups at 5' ends and hydroxyl group at the 3' ends
-
?
dsDNA + H2O
?
-
physiological function currently unknown
DNA fragments carrying phosphate groups at 5' ends and hydroxyl group at the 3' ends, random DNA cleavage with respect to all possible phosphodiester bonds
-
?
RNA + H2O
5'-phosphooligonucleotides + 5'-phosphomononucleotides
Azotobacter agilis
-
polyuridylic acid
-
-
?
RNA + H2O
5'-phosphooligonucleotides + 5'-phosphomononucleotides
Azotobacter agilis
-
polycytidylic acid
-
-
?
RNA + H2O
5'-phosphooligonucleotides + 5'-phosphomononucleotides
Azotobacter agilis
-
e.g.: polyadenylic acid
-
-
?
RNA + H2O
5'-phosphooligonucleotides + 5'-phosphomononucleotides
Azotobacter agilis
-
not polyguanylic acid
-
-
?
RNA + H2O
5'-phosphooligonucleotides + 5'-phosphomononucleotides
-
polyguanylic acid
-
-
?
RNA + H2O
5'-phosphooligonucleotides + 5'-phosphomononucleotides
-
rRNA
-
-
?
RNA + H2O
5'-phosphooligonucleotides + 5'-phosphomononucleotides
-
-
-
-
?
RNA + H2O
5'-phosphooligonucleotides + 5'-phosphomononucleotides
-
-
-
-
?
RNA + H2O
5'-phosphooligonucleotides + 5'-phosphomononucleotides
-
-
-
-
?
RNA + H2O
5'-phosphooligonucleotides + 5'-phosphomononucleotides
-
polyuridylic acid
-
-
?
RNA + H2O
5'-phosphooligonucleotides + 5'-phosphomononucleotides
-
polycytidylic acid
-
-
?
RNA + H2O
5'-phosphooligonucleotides + 5'-phosphomononucleotides
-
e.g.: polyadenylic acid
-
-
?
RNA + H2O
5'-phosphooligonucleotides + 5'-phosphomononucleotides
-
highest activity against poly(U)
-
-
?
additional information
?
-
isozyme ENDO2 digests ssDNA over dsDNA, it achieves strong DNase activity under two completely different conditions, but it exerts its nuclease activity towards dsDNA only in acidic buffer as a Ca2+/Zn2+-dependent enzyme
-
-
-
additional information
?
-
isozyme ENDO2 digests ssDNA over dsDNA, it achieves strong DNase activity under two completely different conditions, but it exerts its nuclease activity towards dsDNA only in acidic buffer as a Ca2+/Zn2+-dependent enzyme
-
-
-
additional information
?
-
isozyme ENDO2 digests ssDNA over dsDNA, it achieves strong DNase activity under two completely different conditions, but it exerts its nuclease activity towards dsDNA only in acidic buffer as a Ca2+/Zn2+-dependent enzyme
-
-
-
additional information
?
-
isozyme ENDO2 digests ssDNA over dsDNA, it achieves strong DNase activity under two completely different conditions, but it exerts its nuclease activity towards dsDNA only in acidic buffer as a Ca2+/Zn2+-dependent enzyme
-
-
-
additional information
?
-
isozyme ENDO4 shows quite strong DNase activity, but relatively weak RNase activity
-
-
-
additional information
?
-
isozyme ENDO4 shows quite strong DNase activity, but relatively weak RNase activity
-
-
-
additional information
?
-
isozyme ENDO4 shows quite strong DNase activity, but relatively weak RNase activity
-
-
-
additional information
?
-
isozyme ENDO4 shows quite strong DNase activity, but relatively weak RNase activity
-
-
-
additional information
?
-
no activity by isozyme ENDO5 on ssDNA or dsDNA
-
-
-
additional information
?
-
no activity by isozyme ENDO5 on ssDNA or dsDNA
-
-
-
additional information
?
-
no activity by isozyme ENDO5 on ssDNA or dsDNA
-
-
-
additional information
?
-
no activity by isozyme ENDO5 on ssDNA or dsDNA
-
-
-
additional information
?
-
the isozyme ENDO1 is defined as bifunctional enzymes due to its ability to digest both DNA and RNA substrates, showing a quite strong DNase activity and weak RNase activity, it digests ssDNA over dsDNA
-
-
-
additional information
?
-
the isozyme ENDO1 is defined as bifunctional enzymes due to its ability to digest both DNA and RNA substrates, showing a quite strong DNase activity and weak RNase activity, it digests ssDNA over dsDNA
-
-
-
additional information
?
-
the isozyme ENDO1 is defined as bifunctional enzymes due to its ability to digest both DNA and RNA substrates, showing a quite strong DNase activity and weak RNase activity, it digests ssDNA over dsDNA
-
-
-
additional information
?
-
the isozyme ENDO1 is defined as bifunctional enzymes due to its ability to digest both DNA and RNA substrates, showing a quite strong DNase activity and weak RNase activity, it digests ssDNA over dsDNA
-
-
-
additional information
?
-
Azotobacter agilis
-
hydrolysis of shorter chains much slower than of longer chains
-
-
-
additional information
?
-
-
enzyme also shows 3'-nucleotidase activity
-
-
-
additional information
?
-
-
single-stranded DNA, single-stranded RNA, double-stranded RNA nor RNA-DNA heteroduplexes are not substrates for the enzyme
-
-
-
additional information
?
-
-
inactive towards 3'-phosphoester linkage of nucleoside cyclic 2',3'- and 3',5'-monophosphates
-
-
-
additional information
?
-
-
3'-nucleotidase activity is greater for purine than for pyrimidine ribonucleotides
-
-
-
additional information
?
-
-
little activity towards ribonucleoside 2'- and 5'-monophosphates and deoxyribonucleoside 3'- and 5'-monophosphates
-
-
-
additional information
?
-
-
poly(dC)poly(dG) is not substrate for the enzyme
-
-
-
additional information
?
-
-
recombinant protein is active on plasmid DNA, circular recessed and flap M13 substrate with short protruding single strand
-
-
-
additional information
?
-
-
linear flap structures with tails of more than 20 nucleotides and shorter duplex regions are not hydrolyzed
-
-
-
additional information
?
-
-
the subunits of the dimer function independently as monomers, molecular dynamic simulations involving Mg2+, modelling of complex building with DNA
-
-
-
additional information
?
-
-
the enzyme potently degrades both DNA and RNA and is a nuclease with broad specificity, but it shows some sensitivity to the secondary structure of the substrate
-
-
-
additional information
?
-
-
substrate is highly polymerized herring testis DNA of the random nucleotide sequence. Hydrolysis of the B-form and hybrid B-Z form DNA by the enzyme. The hybrid B-Z form is formed upon addition of MgSO4 and Co(NH3)6Cl3
-
-
-
additional information
?
-
-
substrate specificity in descending order is ssDNA, dsDNA, RNA
-
-
-
additional information
?
-
-
substrate specificity, no activity with dinucleoside monophosphates, overview
-
-
-
additional information
?
-
-
mung bean nuclease is an endonuclease specific to single-stranded DNA or RNA
-
-
-
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NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
DNA + H2O
?
Q8I9M9
dsDNA to ssDNA preference ratio for Par_DSN-t4 is equal to 10, corresponding ratio for intact Par_DSN is equal to 1000
-
-
?
DNA + H2O
?
P13717
protein and DNA are held together by a mix of salt-bridges, water-mediated and direct hydrogen bond interactions between the protein and DNA backbone, almost no DNA bases are directly involved in the contacts
-
-
?
dsDNA + H2O
?
-
primarily responsible for internucleosomal DNA cleavage during the terminal stages of apoptosis, preference for cleaving the internucleosomal linker regions in chromatin
fragments possessing ends with 5-phosphate and 3-hydroxyl groups, exclusively double strand breaks (primarily blunt ends)
-
?
dsDNA + H2O
?
-
-
DNA fragments carrying phosphate groups at 5' ends and hydroxyl group at the 3' ends
-
?
dsDNA + H2O
?
-
physiological function currently unknown
DNA fragments carrying phosphate groups at 5' ends and hydroxyl group at the 3' ends, random DNA cleavage with respect to all possible phosphodiester bonds
-
?
additional information
?
-
F4JJL0
isozyme ENDO2 digests ssDNA over dsDNA, it achieves strong DNase activity under two completely different conditions, but it exerts its nuclease activity towards dsDNA only in acidic buffer as a Ca2+/Zn2+-dependent enzyme
-
-
-
additional information
?
-
F4JJL3
isozyme ENDO2 digests ssDNA over dsDNA, it achieves strong DNase activity under two completely different conditions, but it exerts its nuclease activity towards dsDNA only in acidic buffer as a Ca2+/Zn2+-dependent enzyme
-
-
-
additional information
?
-
Q9C9G4
isozyme ENDO2 digests ssDNA over dsDNA, it achieves strong DNase activity under two completely different conditions, but it exerts its nuclease activity towards dsDNA only in acidic buffer as a Ca2+/Zn2+-dependent enzyme
-
-
-
additional information
?
-
Q9SXA6
isozyme ENDO2 digests ssDNA over dsDNA, it achieves strong DNase activity under two completely different conditions, but it exerts its nuclease activity towards dsDNA only in acidic buffer as a Ca2+/Zn2+-dependent enzyme
-
-
-
additional information
?
-
F4JJL0
isozyme ENDO4 shows quite strong DNase activity, but relatively weak RNase activity
-
-
-
additional information
?
-
F4JJL3
isozyme ENDO4 shows quite strong DNase activity, but relatively weak RNase activity
-
-
-
additional information
?
-
Q9C9G4
isozyme ENDO4 shows quite strong DNase activity, but relatively weak RNase activity
-
-
-
additional information
?
-
Q9SXA6
isozyme ENDO4 shows quite strong DNase activity, but relatively weak RNase activity
-
-
-
additional information
?
-
F4JJL0
no activity by isozyme ENDO5 on ssDNA or dsDNA
-
-
-
additional information
?
-
F4JJL3
no activity by isozyme ENDO5 on ssDNA or dsDNA
-
-
-
additional information
?
-
Q9C9G4
no activity by isozyme ENDO5 on ssDNA or dsDNA
-
-
-
additional information
?
-
Q9SXA6
no activity by isozyme ENDO5 on ssDNA or dsDNA
-
-
-
additional information
?
-
F4JJL0
the isozyme ENDO1 is defined as bifunctional enzymes due to its ability to digest both DNA and RNA substrates, showing a quite strong DNase activity and weak RNase activity, it digests ssDNA over dsDNA
-
-
-
additional information
?
-
F4JJL3
the isozyme ENDO1 is defined as bifunctional enzymes due to its ability to digest both DNA and RNA substrates, showing a quite strong DNase activity and weak RNase activity, it digests ssDNA over dsDNA
-
-
-
additional information
?
-
Q9C9G4
the isozyme ENDO1 is defined as bifunctional enzymes due to its ability to digest both DNA and RNA substrates, showing a quite strong DNase activity and weak RNase activity, it digests ssDNA over dsDNA
-
-
-
additional information
?
-
Q9SXA6
the isozyme ENDO1 is defined as bifunctional enzymes due to its ability to digest both DNA and RNA substrates, showing a quite strong DNase activity and weak RNase activity, it digests ssDNA over dsDNA
-
-
-
additional information
?
-
-
single-stranded DNA, single-stranded RNA, double-stranded RNA nor RNA-DNA heteroduplexes are not substrates for the enzyme
-
-
-
additional information
?
-
-
recombinant protein is active on plasmid DNA, circular recessed and flap M13 substrate with short protruding single strand
-
-
-
additional information
?
-
-
the enzyme potently degrades both DNA and RNA and is a nuclease with broad specificity, but it shows some sensitivity to the secondary structure of the substrate
-
-
-
additional information
?
-
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substrate specificity in descending order is ssDNA, dsDNA, RNA
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-
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additional information
?
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mung bean nuclease is an endonuclease specific to single-stranded DNA or RNA
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-
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Ca2+
activates at pH 8.0; activates at pH 8.0; activates at pH 8.0, preferred divalent cation
Mg2+
Mn2+
Zn2+
[Co(NH3)6]3+
-
binding to the DNA substrate induces changes in the secondary structure of the enzyme, followed by a decrease of the enzyme activity
additional information
Mg2+
Azotobacter agilis
-
increases hydrolysis rate of EDTA-dialyzed RNA, no effect on hydrolysis of undialyzed RNA, inhibition at high concentrations
Mg2+
-
coordinates 5 water molecules that participate in the enzyme-controlled reaction
Mg2+
-
molecular dynamic simulations, interaction with enzyme monomer-DNA complex via 6 ligands, which are changing during the reaction simulation, e.g. Asn119 loses its coordination while Glu127 becomes a ligand, overview
Mn2+
activates; activates; activates, highly activating divalent cation
Zn2+
dependent on; dependent on, Zn2+-dependent activity of the enzyme can be strongly enhanced by the Ca2+
Zn2+
-
the enzyme is a zinc metalloprotein, three zinc ions interact with the DNA substrate and have different roles in catalysis, e.g. stabilization of the transition state and as reaction nucleophile, binding structures and kinetics, overview
additional information
although ENDO1 nuclease digests ssDNA in the presence of both Ca2+ and Mn2+ ions, its ability to digest dsDNA can be stimulated only by Mn2+ ions. The enzyme activity is not affected by Mg2+ or Fe2+; metal ion effect is dependent on pH. The enzyme activity is not affected by Mg2+ or Fe2+; the enzyme activity is not affected by Mg2+ or Fe2+; the enzyme activity is not affected by Mg2+ or Fe2+
additional information
although ENDO1 nuclease digests ssDNA in the presence of both Ca2+ and Mn2+ ions, its ability to digest dsDNA can be stimulated only by Mn2+ ions. The enzyme activity is not affected by Mg2+ or Fe2+; metal ion effect is dependent on pH. The enzyme activity is not affected by Mg2+ or Fe2+; the enzyme activity is not affected by Mg2+ or Fe2+; the enzyme activity is not affected by Mg2+ or Fe2+
additional information
although ENDO1 nuclease digests ssDNA in the presence of both Ca2+ and Mn2+ ions, its ability to digest dsDNA can be stimulated only by Mn2+ ions. The enzyme activity is not affected by Mg2+ or Fe2+; metal ion effect is dependent on pH. The enzyme activity is not affected by Mg2+ or Fe2+; the enzyme activity is not affected by Mg2+ or Fe2+; the enzyme activity is not affected by Mg2+ or Fe2+
additional information
although ENDO1 nuclease digests ssDNA in the presence of both Ca2+ and Mn2+ ions, its ability to digest dsDNA can be stimulated only by Mn2+ ions. The enzyme activity is not affected by Mg2+ or Fe2+; metal ion effect is dependent on pH. The enzyme activity is not affected by Mg2+ or Fe2+; the enzyme activity is not affected by Mg2+ or Fe2+; the enzyme activity is not affected by Mg2+ or Fe2+
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INHIBITORS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
dAMP
competitive inhibitor of partial type, dAMP forming a complex with Sma nuc does not completely prevent the RNA binding and reduces the enzyme affinity to RNA substrate in competition with RNA for the binding site
AMP
competitive inhibitor of partial type, AMP forming a complex with Sma nuc does not completely prevent the RNA binding and reduces the enzyme affinity to RNA substrate in competition with RNA for the binding site
EDTA
-
90% inhibition at 2.5 mM, inhibition fully reversible by addition of Mg2+
Mg2+
Azotobacter agilis
-
increases hydrolysis rate of EDTA-dialyzed RNA, no effect on hydrolysis of undialyzed RNA, inhibition at high concentrations
Mg2+
-
binding of Co(NH3)6 3+ to highly polymerized DNA caused correspondingly about 7fold decrease in Km and more than 600fold decrease in Kcat compared with that of Mg-DNA complex of B-form; binding of Mg2+ to highly polymerized DNA causes correspondingly about 80fold decrease in Km and more than 1600fold decrease in Kcat compared with that of Mg-DNA complex of B-form
Mn2+
-
inhibits hydrolysis of RNA, denatured DNA and 3'-AMP, not: native DNA
Zn2+
complete inhibition; complete inhibition
additional information
Azotobacter agilis
-
secondary interaction in long RNA chains inhibit the enzyme
-
additional information
-
DNA transition from the right handed B-form to the hybrid B-Z-form causes a decrease in Vmax, Km and Kcat of DNA cleavage with the nuclease
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
-
weak stimulation by addition of recombinant human PCNA
-
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
additional information
-
0.085-0.1 mM for different monomeric variants
-
additional information
additional information
-
Km is approximately related to the association constant of the enzyme and the substrate since cleavage of DNA is rate limiting
-
additional information
additional information
-
kinetics of the enzyme with differently structured DNA substrate and different metal ions, overview
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
additional information
inhibition kinetics of mononucleotides, hyperbolic inhibition of the enzyme, overview
-
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
additional information
G133V mutant, dsDNA, not detectable (inactive protein); G139V mutant, dsDNA, not detectable (inactive protein); H168A mutant, dsDNA, not detectable (inactive protein); H171A mutant, dsDNA, not detectable (inactive protein); H237A mutant, dsDNA, not detectable; K235A mutant, dsDNA, 110 Kunitz units; K235R mutant, dsDNA, 5980 Kunitz units; Par_DSN-t1 lacks DNAse activity; Par_DSN-t2 lacks DNase activity; Par_DSN-t3 lacks DNAse activity; Par_DSN-t4 has low specific activity (6 Kunitz-units compared to 6070 Kunitz units for intact Par_DSN), dsDNA; R121/122A mutant, dsDNA, not detectable (inactive protein); R121A mutant, dsDNA, 5960 Kunitz units; R121K mutant, dsDNA, 5990 Kunitz units; R122A mutant, dsDNA, 6030 Kunitz units; R122K mutant, dsDNA, 6050 Kunitz units; R184A mutant, dsDNA, 1810 Kunitz units; R184K mutant, dsDNA, 6100 Kunitz units; wild-type, dsDNA, 6070 Kunitz units
additional information
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cells transformed with plasmid pDS (carrying 2 copies of Serratia marcescens nuclease) are more effective in stopping cell division than those transformed with plasmid pSS (carrying 1 copy of Serratia marcescens nuclease), OD600 analysis, colony test on plates. Cells cotransformed grow more slowly before induction of Serratia marcescens nuclease, OD600 analysis, florescence, colony test on plates
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
5.5
additional information
additional information
isozyme ENDO5 is active in the neutral buffer and less efficiently in the acidic buffer; optimal activity at acidic pH; optimal activity at neutral pH; optimal activity at neutral pH
additional information
isozyme ENDO5 is active in the neutral buffer and less efficiently in the acidic buffer; optimal activity at acidic pH; optimal activity at neutral pH; optimal activity at neutral pH
additional information
isozyme ENDO5 is active in the neutral buffer and less efficiently in the acidic buffer; optimal activity at acidic pH; optimal activity at neutral pH; optimal activity at neutral pH
additional information
isozyme ENDO5 is active in the neutral buffer and less efficiently in the acidic buffer; optimal activity at acidic pH; optimal activity at neutral pH; optimal activity at neutral pH
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pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
4.2 - 9
-
adenosine 3'-monophosphate, less than 20% of maximal activity above and below
5.2 - 7.2
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pH 5.2: about 15% of activity maximum, pH 7.2: about 70% of activity maximum
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
37
70
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TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
50 - 80
-
50°C: 50% nuclease B, 10% nuclease A of activity maximum, 80°C: 30% nuclease B, 60% nuclease A of activity maximum
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pI VALUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
expression of ENDO1 is associated with flower development, expression in stamen, sepal and petal
additional information
; high level of ENDO2 transcription is maintained specifically in chalazal endosperm from the preglobular to the linear cotyledon stage and rapidly decreases at later stages of seed development
additional information
in late endosperm the decrease in isozyme ENDO2 is accompanied by a significant increase in isozyme ENDO1 nucleases; in late endosperm the decrease in isozyme ENDO2 is accompanied by a significant increase in isozyme ENDO1 nucleases
additional information
in late endosperm the decrease in isozyme ENDO2 is accompanied by a significant increase in isozyme ENDO1 nucleases; in late endosperm the decrease in isozyme ENDO2 is accompanied by a significant increase in isozyme ENDO1 nucleases
additional information
in late endosperm the decrease in isozyme ENDO2 is accompanied by a significant increase in isozyme ENDO1 nucleases; in late endosperm the decrease in isozyme ENDO2 is accompanied by a significant increase in isozyme ENDO1 nucleases
additional information
in late endosperm the decrease in isozyme ENDO2 is accompanied by a significant increase in isozyme ENDO1 nucleases; in late endosperm the decrease in isozyme ENDO2 is accompanied by a significant increase in isozyme ENDO1 nucleases
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LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
-
N-terminal His-tagged protein mainly found in the culture supernatant
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PDB
SCOP
CATH
ORGANISM
UNIPROT
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
33000
35000
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SUBUNITS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
dimer
homodimer
-
each monomer consists of 245 amino acids, they function independently of each other, monomer and dimer can function with same specific activity. Dimer form has an electrostatic advantage over the monomer to associate with DNA, inner-sphere binding in the monomer, outer-sphere in the dimer, interface of the protein and DNA is full of charged side chains, such as Arg57, Arg87, Arg125, Arg196, and Mg2+. Interfacial region is highly hydrated with an average of 27 hydration sites in the monomer (water acts more to screen the electrostatic region between the monomer and DNA) and 31 sites in the dimer (water acts more as a glue to provide structural adaptability with the protein and DNA). Dynamics of H-bonds of water in this active centre only little difference is found (water in the working region in the dimer complex has larger fluctuations than in monomer). Dimerization leads to different contacts between DNA and protein residues, especially to Mg2+
monomer
additional information
-
the subunits of the dimer function independently as monomers, molecular dynamic simulations, modelling of complex building with DNA, hydration sites of the enzyme depending on solvent density, overview
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POSTTRANSLATIONAL MODIFICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
glycoprotein
-
about 8% carbohydrate, asparagin-linked high-mannose oligosaccharide
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Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
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pH STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
60
70
80
70
activity of Par_DSN-t4 completely disappears after incubation for 20 min, full-length Par_DSN retains 25% activity
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GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
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STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
0°C, Tris-HCl buffer, pH 7.4, 10 mM EDTA, 10% glycerol, 15 days storage on ice, fully stable for at least 15 days
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Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
ion exchange chromatography on DEAE-cellulose DE-32 and DEAE-cellulose DE-52
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native enzyme 265fold to homogeneity from seedlings by ammonium sulfate fractionation, anion exchange chromatography and heparin affinity chromatography
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Par_DSN-t1 is insoluble and inactive after puriciation and renaturation
recombinant protein using His-tag
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Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
construct containing the NucA gene driven by the beta-actin promoter coupled with enhancer elements from the cytomegalovirus promoter and rabbit beta-globin gene and the blasticidin resistance gene driven by the phosphoglycerate kinase promoter are generated and electroporated into porcine fetal fibroblasts
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gene ENDO1, DNA and amino acid sequence determination and analysis, recombinant transient overexpression in Arabidosis thaliana leaf protoplasts; gene ENDO2, DNA and amino acid sequence determination and analysis, recombinant transient overexpression in Arabidosis thaliana leaf protoplasts; gene ENDO4, DNA and amino acid sequence determination and analysis, recombinant transient overexpression in Arabidosis thaliana leaf protoplasts; gene ENDO5, DNA and amino acid sequence determination and analysis, recombinant transient overexpression in Arabidosis thaliana leaf protoplasts
generation of plasmids pSS and pDS (for induction of suicide mechanism) consisting of kanamycin resistance, T7-promotor, Serratia marcescens nuclease (1 copy in pSS, 2 copies in pDS) minus its lead-peptide-coding nucleotide sequence. cotransformation with plasmid pL-EGFP-OPH (containing organophosphorus hydrolase and enhanced green fluorescent protein for degradation of organophosphates) of Escherichia coli strain BL21-AI(TM) to generate BL21AI-GOS (pDS)
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His-tag fusion protein expressed in Escherichia coli
molecular dynamics simulations of model-built monomer-DNA complexes and dimer-DNA complexes
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Par_DSN-t1: residues 192-379 of Par_DSN precursor (GenBank ID AAN86143) linked with a bacterial signal peptide and 6×His tag (sequence corresponds to the NUC domain). Par_DSN-t2: residues 149-406, corresponds to the NUC domain identified by multiple sequence alignment, is sensitive to proteinase K and is completely cleaved by this protease. Par_DSN-t3: residues 162-406, additionaly all unpaired Cys residues are deleted, Par_DSN-t3 is soluble, sensitive to proteinase K. Par_DSN-t4: residues 114-406, Par_DSN-t4 is degraded by proteinase K
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EXPRESSION
ORGANISM
UNIPROT
LITERATURE
both NucA with and without a nuclear localization signal prove to be effective in killing porcine fibroblasts compared to controls, gene expression analysis of surviving colonies indicates that survival is related to low or absent expression of the toxic genes
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ENGINEERING
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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Renatured/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
Par_DSN-t1 is insoluble and inactive after purification and renaturation. Par_DSN-t2, Par_DSN-t3, Par_DSN-t4 could be renaturated.
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APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
molecular biology
-
the enzyme is useful in DNA enrichment by PCR based applications for which removal of template DNA is beneficial before end repair, method overview. Mung bean nuclease treatment abolished the high molecular DNA smear in microdroplet-PCR captured DNA after end repair
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LINKS TO OTHER DATABASES (specific for EC-Number 3.1.30.2)
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