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Information on EC 3.1.30.2 - Serratia marcescens nuclease and Organism(s) Serratia marcescens and UniProt Accession P13717
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3.1.30.2 Serratia marcescens nucleaseSpecify your search results
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- 3.1.30.2
- strand
-
single-stranded
- nick
- chromatin
-
exonuclease
- phage
- nucleases
- rnase
- bacteriophage
-
endonucleolytic
- mismatch
-
palindromic
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structure-specific
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internucleosomal
-
homing
- glycosylase
-
methylase
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phosphodiester
- fork
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restriction-modification
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interspaced
-
supercoiled
-
crispr
- heteroduplexes
-
abasic
- deoxyribonuclease
-
retrotransposons
- xeroderma
- aif
-
caspase-independent
- dsdna
- pigmentosum
- ape1
-
endoribonuclease
-
holliday
-
end-joining
-
nucleolytic
- colicins
- ecorv
-
retrotransposition
-
interstrand
-
okazaki
- mre11
-
superhelical
- pvuii
- haeiii
-
overhang
-
cap-dependent
-
sgrnas
- resolvase
- molecular biology
The taxonomic range for the selected organisms is: Serratia marcescens
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota
Reaction Schemes
endonucleolytic cleavage to 5'-phosphomononucleotide and 5'-phosphooligonucleotide end-products
Synonyms
endonuclease, dna fragmentation factor, caspase-activated dnase, nuclease a, endonuclease 1, endo1, endo2, serratia marcescens nuclease, serratia marcescens endonuclease, dff40/cad endonuclease, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
NucANLS
endonuclease (Serratia marcescens)
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nuclease, nucleate endo-
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nucleate endonuclease
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plant nuclease I
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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
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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
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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
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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
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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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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
RNA + H2O
?
in absence of Mg2+ the enzyme shows a preference for DNA as compared to RNA
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?
B-Z-hybrid form DNA + H2O
?
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hybrid B-Z form of herring testis DNA
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?
RNA + H2O
5'-phosphooligonucleotides + 5'-phosphomononucleotides
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?
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
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?
DNA + H2O
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in absence of Mg2+ the enzyme shows a preference for DNA as compared to RNA
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?
DNA + H2O
?
Serratia marcescens nuclease is highly effective on sputum
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?
DNA + H2O
5'-phosphonucleotides + 5'-phosphomononucleotides
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?
DNA + H2O
5'-phosphonucleotides + 5'-phosphomononucleotides
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DNA is slightly preferred as a substrate than RNA
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?
additional information
?
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the subunits of the dimer function independently as monomers, molecular dynamic simulations involving Mg2+, modelling of complex building with DNA
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?
additional information
?
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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
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?
additional information
?
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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
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?
NATURAL SUBSTRATE
NATURAL 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
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
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?
additional information
?
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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
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?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Ca2+
in the presence of Mg2+ the DNase activity of Serratia marcescens nuclease is higher than in the presence of Ca2+
Mg2+
NaCl
the enzyme is capable to hydrolyze DNA in the presence of 0.9% NaCl containing 0.002 M calcium cations
Mg2+
[Co(NH3)6]3+
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binding to the DNA substrate induces changes in the secondary structure of the enzyme, followed by a decrease of the enzyme activity
Mg2+
in the presence of 0.58 mM Mg2+, the digestive activity of the enzyme is approximately fourfold increased as compared with the activity in the absence of Mg2+ taken as 100%. Further fivefold increase in Mg2+ concentration causes near 1.5fold enhancement in the enzyme activity. Subsequent two- and fourfold increases in Mg2+ concentration have only a minor impact on the enzyme activity within the experimental error range. 6.0-11.6 mM of Mg2+ corresponding to 20-40 Mg2+ per 1 phosphate in RNA is optimal for the hydrolysis of RNA. Optimal Mg2+ amount is linked with the changing secondary structure of RNA substrates within A-helix. Addition of Mg2+ affects both the rates of products dissociations from the enzyme-substrate complexes and the enzyme associations with the substrates, that is supported by strong increase in the Kcat values and change in the Km values
Mg2+
in the presence of Mg2+ the DNase activity of Serratia marcescens nuclease is higher than in the presence of Ca2+
Mg2+
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coordinates 5 water molecules that participate in the enzyme-controlled reaction
Mg2+
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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
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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
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
additional information
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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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Mg2+
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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
Mg2+
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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
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
DNA
at the optimal Mg2+ amount, both the Km and the Kcat values are similar to both RNA and DNA substrates
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
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additional information
additional information
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Km is approximately related to the association constant of the enzyme and the substrate since cleavage of DNA is rate limiting
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additional information
RNA
at the optimal Mg2+ amount, both the Km and the Kcat values are similar to both RNA and DNA substrates
additional information
additional information
-
0.085-0.1 mM for different monomeric variants
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additional information
additional information
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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
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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additional information
additional information
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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
-
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
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
physiological function
additional information
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
specific site(s) for the nucleotide(s) binding in Sma nuc endonuclease
additional information
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specific site(s) for the nucleotide(s) binding in Sma nuc endonuclease
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable).
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable). PDB
SCOP
CATH
UNIPROT
ORGANISM
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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+
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
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
H89G
hydroxylamine reduces the growth of the recombinant strain Escherichia coli TGE900 pHisNucSma (H89G) compared to the control without hydroxylamine. Such a decrease in growth may be due to the restoration of the activity of the mutant enzyme, leading to the cleavage of nucleic acids in the cell
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
one-step protocol for chromatographic purification. The purification procedure provides substantial yields of homogenously pure and highly active enzyme
ion exchange chromatography on DEAE-cellulose DE-32 and DEAE-cellulose DE-52
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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
molecular dynamics simulations of model-built monomer-DNA complexes and dimer-DNA complexes
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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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
RENATURED/Commentary
ORGANISM
UNIPROT
LITERATURE
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Varlamov, V.P.; Lopatin, S.A.; Bannikova, G.E.; Andrushina, I.A.; Rogozhin, S.V.
Ligand-exchange chromatography of nucleases
J. Chromatogr.
364
215-223
1986
Serratia marcescens
Franke, I.; Meiss, G.; Blecher, D.; Gimadutdinow, O.; Urbanke, C.; Pingoud, A.
Genetic engineering, production and characterization of monomeric variants of the dimeric Serratia marcescens endonuclease
FEBS Lett.
425
517-522
1998
Serratia marcescens
Shlyapnikov, S.V.; Lunin, V.V.; Perbandt, M.; Polyakov, K.M.; Lunin, V.Y.; Levdikov, V.M.; Betzel, C.; Mikhailov, A.M.
Atomic structure of the Serratia marcescens endonuclease at 1.1 A resolution and the enzyme reaction mechanism
Acta Crystallogr. Sect. D
56
567-572
2000
Serratia marcescens
Friedhoff, P.; Gimadutdinow, O.; Rueter, T.; Wende, W.; Urbanke, C.; Thole, H.; Pingoud, A.
A procedure for renaturation and purification of the extracellular Serratia marcescens nuclease from genetically engineered Escherichia coli
Protein Expr. Purif.
5
37-43
1994
Serratia marcescens
Bannikova, G.E.; Blagova, E.V.; Dementiev, A.A.; Morgunova, E.Y.; Mikchailov, A.M.; Shlyapnikov, S.V.; Verlamov, V.P.; Vainstein, B.K.
Two isoforms of Serratia marcescens nuclease. Crystallization and preliminary X-ray investigation of the enzyme
Biochem. Int.
24
813-822
1991
Serratia marcescens
Filimonova, M.N.; Krause, K.L.; Benedik, M.J.
Kinetic studies of the Serratia marcescens extracellular nuclease isoforms
Biochem. Mol. Biol. Int.
33
1229-1236
1994
Serratia marcescens
Pedersen, J.; Filimonova, M.; Roepstorff, P.; Biedermann, K.
Characterization of Serratia marcescens nuclease isoforms by plasma desorption mass spectrometry
Biochim. Biophys. Acta
1202
13-21
1993
Serratia marcescens
Lunin, V.Y.; Blagova, E.V.; Levdikov, V.M.; Lunin, V.V.; Shlypnikov, S.V.; Perbandt, M.; Raishankar, K.S.; Betzel, H.; Mikhailov, A.M.
Extracellular endonuclease of Serratia marcescens. 1. Three-dimensional structure of crystalline protein at 1.7 A resolution
Mol. Biol.
33
180-187
1999
Serratia marcescens
-
Filimonova, M.; Gubskaya, V.; Nuretdinov, I.; Leshchinskaya, I.
Action of hexaamminecobalt on the activity of Serratia marcescens nuclease
BioMetals
16
447-453
2003
Serratia marcescens
Koziolkiewicz, M.; Owczarek, A.; Domanski, K.; Nowak, M.; Guga, P.; Stec, W.J.
Stereochemistry of cleavage of internucleotide bonds by Serratia marcescens endonuclease
Bioorg. Med. Chem.
9
2403-2409
2001
Serratia marcescens
Berkmen, M.; Benedik, M.J.
Multi-copy repression of Serratia marcescens nuclease expression by dinI
Curr. Microbiol.
44
44-48
2002
Serratia marcescens
Shlyapnikov, S.V.; Lunin, V.V.; Blagova, E.V.; Abaturov, L.V.; Perbandt, M.; Betzel, C.; Mikhailov, A.M.
A comparative structure-function analysis and molecular mechanism of action of endonucleases from Serratia marcescens and Physarum polycephalum
Russ. J. Bioorg. Chem.
28
20-27
2002
Serratia marcescens
-
Chen, C.; Beck, B.W.; Krause, K.; Pettitt, B.M.
Solvent participation in Serratia marcescens endonuclease complexes
Proteins
62
982-995
2006
Serratia marcescens
Li, Q.; Wu, Y.J.
A fluorescent, genetically engineered microorganism that degrades organophosphates and commits suicide when required
Appl. Microbiol. Biotechnol.
82
749-756
2009
Serratia marcescens
Chen, C.; Krause, K.; Pettitt, B.M.
Advantage of being a dimer for Serratia marcescens endonuclease
J. Phys. Chem. B
113
511-521
2009
Serratia marcescens (P13717), Serratia marcescens
Caballero, I.; Piedrahita, J.A.
Evaluation of the Serratia marcescens nuclease (NucA) as a transgenic cell ablation system in porcine
Anim. Biotechnol.
20
177-185
2009
Serratia marcescens (P13717), Serratia marcescens
Filimonova, M.; Gubskaya, V.; Nuretdinov, I.
Some features of hydrolysis of the hybrid B-Z-form dna by Serratia marcescens nuclease
OnLine J. Biol. Sci.
14
179-185
2014
Serratia marcescens
-
Romanova, J.; Filimonova, M.
The effects of addition of mononucleotides on Sma nuc endonuclease activity
ScientificWorldJournal
2012
454176
2012
Serratia marcescens (P13717), Serratia marcescens
Vafina, G.; Bulatov, E.; Zaynutdinova, E.; Filimonova, M.
A one-step protocol for chromatographic purification of non-recombinant exogenous bacterial enzyme nuclease of Serratia marcescens
BioNanoSci.
6
335-337
2016
Serratia marcescens (P13717)
-
Romanova, J.; Gubskaya, V.; Nuretdinov, I.; Zainutdinova, E.; Filimonova, M.
Analysis of the mechanism of Mg2+ action on the RNase activity of Serratia marcescens endonuclease
BioNanoSci.
7
276-283
2017
Serratia marcescens (P13717)
-
Vafina, G.; Zainutdinova, E.; Bulatov, E.; Filimonova, M.N.
Endonuclease from Gram-negative bacteria Serratia marcescens is as effective as pulmozyme in the hydrolysis of DNA in sputum
Front. Pharmacol.
9
114
2018
Serratia marcescens (P13717)
Khamidullina, R.; Fazleeva, I.; Trushin, M.; Gimadutdinov, O.
Reactivation of Serratia marcescens mutant endonuclease by hydroxilamine
J. Pharm. Sci. Res.
10
2341-2345
2018
Serratia marcescens (P13717)
-
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