BRENDA - Enzyme Database
show all sequences of 3.4.21.B30

Dimer exchange and cleavage specificity of the DNA damage response protein UmuD

Ollivierre, J.N.; Sikora, J.L.; Beuning, P.J.; Biochim. Biophys. Acta 1834, 611-620 (2013)

Data extracted from this reference:

Engineering
Protein Variants
Commentary
Organism
C24A
site-directed mutagenesis, that removes the cleavage site Cys residue of UmuD, the mutation does not substantially affect UmuD function, cleavage site variant
Escherichia coli
C25D
site-directed mutagenesis, that removes the cleavage site Cys residue of UmuD, the mutation does not substantially affect UmuD function, cleavage site variant. For cleavage to occur, UmuD UmuD G25D dimer must first exchange in the presence of RecA:ssDNA, and any cleavage detected results from cleavage in trans. Cleavage is less efficient in this context, indicating that the decreased rate of cleavage in the trans dimers results from the time required for dimer exchange to first take place before cleavage can occur
Escherichia coli
G92C
site-directed mutagenesis of of UmuD'
Escherichia coli
N41D
site-directed mutagenesis, the monomeric UmuD N41D variant can only cleave in the cis conformation
Escherichia coli
S60A
site-directed mutagenesis, a non-cleavable mutant of UmuD and UmuD', inactive active site mutant. For cleavage to occur, UmuD S60A dimer must first exchange in the presence of RecA:ssDNA, and any cleavage detected results from cleavage in trans. Cleavage is less efficient in this context, indicating that the decreased rate of cleavage in the trans dimers results from the time required for dimer exchange to first take place before cleavage can occur
Escherichia coli
Natural Substrates/ Products (Substrates)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
ID
UmuD2 + H2O
Escherichia coli
slow auto-cleavage of UmuD2 to UmuD'2
UmuD2' + ?
-
-
?
UmuD2 + H2O
Escherichia coli AB1157
slow auto-cleavage of UmuD2 to UmuD'2
UmuD2' + ?
-
-
?
Organism
Organism
UniProt
Commentary
Textmining
Escherichia coli
-
gene umuD
-
Escherichia coli AB1157
-
gene umuD
-
Posttranslational Modification
Posttranslational Modification
Commentary
Organism
proteolytic modification
slow auto-cleavage of UmuD2 to UmuD'2, the heterodimer efficiently cleaves to form UmuD'2
Escherichia coli
Substrates and Products (Substrate)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
Substrate Product ID
UmuD2 + H2O
slow auto-cleavage of UmuD2 to UmuD'2
731345
Escherichia coli
UmuD2' + ?
-
-
-
?
UmuD2 + H2O
slow auto-cleavage of UmuD2 to UmuD'2. The wild-type UmuD homodimer cleaves in both cis and trans conformations
731345
Escherichia coli
UmuD2' + ?
-
-
-
?
UmuD2 + H2O
slow auto-cleavage of UmuD2 to UmuD'2
731345
Escherichia coli AB1157
UmuD2' + ?
-
-
-
?
UmuD2 + H2O
slow auto-cleavage of UmuD2 to UmuD'2. The wild-type UmuD homodimer cleaves in both cis and trans conformations
731345
Escherichia coli AB1157
UmuD2' + ?
-
-
-
?
Subunits
Subunits
Commentary
Organism
dimer
UmuD dimers exchange readily, and the subunits of UmuD2 and UmuD'2 exchange to form the UmuDD' heterodimer. The heterodimer is the preferred but not exclusive protein form, and both the heterodimer and homodimers exhibit slow exchange kinetics, which is further inhibited in the presence of interacting partner DinB
Escherichia coli
More
UmuD proteins are shown to adopt multiple conformations in solution. UmuD contains only one cysteine (residue 24) per monomer at the cleavage site, which is between residues C24 and G25, cleavage of UmuD to form UmuD? removes the N-terminal 24 amino acids, which includes residue C24
Escherichia coli
Synonyms
Synonyms
Commentary
Organism
DNA damage response protein
-
Escherichia coli
UmuD
-
Escherichia coli
UmuD2
-
Escherichia coli
Temperature Optimum [°C]
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
37
-
assay at
Escherichia coli
pH Optimum
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
7.5
-
assay at
Escherichia coli
Engineering (protein specific)
Protein Variants
Commentary
Organism
C24A
site-directed mutagenesis, that removes the cleavage site Cys residue of UmuD, the mutation does not substantially affect UmuD function, cleavage site variant
Escherichia coli
C25D
site-directed mutagenesis, that removes the cleavage site Cys residue of UmuD, the mutation does not substantially affect UmuD function, cleavage site variant. For cleavage to occur, UmuD UmuD G25D dimer must first exchange in the presence of RecA:ssDNA, and any cleavage detected results from cleavage in trans. Cleavage is less efficient in this context, indicating that the decreased rate of cleavage in the trans dimers results from the time required for dimer exchange to first take place before cleavage can occur
Escherichia coli
G92C
site-directed mutagenesis of of UmuD'
Escherichia coli
N41D
site-directed mutagenesis, the monomeric UmuD N41D variant can only cleave in the cis conformation
Escherichia coli
S60A
site-directed mutagenesis, a non-cleavable mutant of UmuD and UmuD', inactive active site mutant. For cleavage to occur, UmuD S60A dimer must first exchange in the presence of RecA:ssDNA, and any cleavage detected results from cleavage in trans. Cleavage is less efficient in this context, indicating that the decreased rate of cleavage in the trans dimers results from the time required for dimer exchange to first take place before cleavage can occur
Escherichia coli
Natural Substrates/ Products (Substrates) (protein specific)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
ID
UmuD2 + H2O
Escherichia coli
slow auto-cleavage of UmuD2 to UmuD'2
UmuD2' + ?
-
-
?
UmuD2 + H2O
Escherichia coli AB1157
slow auto-cleavage of UmuD2 to UmuD'2
UmuD2' + ?
-
-
?
Posttranslational Modification (protein specific)
Posttranslational Modification
Commentary
Organism
proteolytic modification
slow auto-cleavage of UmuD2 to UmuD'2, the heterodimer efficiently cleaves to form UmuD'2
Escherichia coli
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
ID
UmuD2 + H2O
slow auto-cleavage of UmuD2 to UmuD'2
731345
Escherichia coli
UmuD2' + ?
-
-
-
?
UmuD2 + H2O
slow auto-cleavage of UmuD2 to UmuD'2. The wild-type UmuD homodimer cleaves in both cis and trans conformations
731345
Escherichia coli
UmuD2' + ?
-
-
-
?
UmuD2 + H2O
slow auto-cleavage of UmuD2 to UmuD'2
731345
Escherichia coli AB1157
UmuD2' + ?
-
-
-
?
UmuD2 + H2O
slow auto-cleavage of UmuD2 to UmuD'2. The wild-type UmuD homodimer cleaves in both cis and trans conformations
731345
Escherichia coli AB1157
UmuD2' + ?
-
-
-
?
Subunits (protein specific)
Subunits
Commentary
Organism
dimer
UmuD dimers exchange readily, and the subunits of UmuD2 and UmuD'2 exchange to form the UmuDD' heterodimer. The heterodimer is the preferred but not exclusive protein form, and both the heterodimer and homodimers exhibit slow exchange kinetics, which is further inhibited in the presence of interacting partner DinB
Escherichia coli
More
UmuD proteins are shown to adopt multiple conformations in solution. UmuD contains only one cysteine (residue 24) per monomer at the cleavage site, which is between residues C24 and G25, cleavage of UmuD to form UmuD? removes the N-terminal 24 amino acids, which includes residue C24
Escherichia coli
Temperature Optimum [°C] (protein specific)
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
37
-
assay at
Escherichia coli
pH Optimum (protein specific)
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
7.5
-
assay at
Escherichia coli
Expression
Organism
Commentary
Expression
Escherichia coli
the enzyme is expressed shortly after the induction of the SOS response
up
General Information
General Information
Commentary
Organism
malfunction
for cleavage to occur, UmuD S60A and UmuD G25D mutant dimers must first exchange in the presence of RecA:ssDNA, and any cleavage detected results from cleavage in trans. Cleavage is less efficient in this context, indicating that the decreased rate of cleavage in the trans dimers results from the time required for dimer exchange to first take place before cleavage can occur
Escherichia coli
additional information
UmuD proteins are shown to adopt multiple conformations in solution, homology models of UmuD and the structure of UmuD', overview. The heterodimer is the predominant UmuD protein conformer
Escherichia coli
physiological function
The umuD gene products perform distinct functions in preventing and facilitating mutagenesis. The full-length dimeric UmuD2 is the initial product that is expressed shortly after the induction of the SOS response and inhibits bacterial mutagenesis, allowing for error-free repair to occur. The slow auto-cleavage of UmuD2 to UmuD'2 promotes mutagenesis to ensure cell survival. The intracellular levels of UmuD2 and UmuD?2 are further regulated by degradation in vivo, returning the cell to a nonmutagenic state. Dynamic regulatory roles of the umuD gene, overview. UmuD lifecycle involves dimer exchange and cleavage in the regulation of the DNA damage respons
Escherichia coli
General Information (protein specific)
General Information
Commentary
Organism
malfunction
for cleavage to occur, UmuD S60A and UmuD G25D mutant dimers must first exchange in the presence of RecA:ssDNA, and any cleavage detected results from cleavage in trans. Cleavage is less efficient in this context, indicating that the decreased rate of cleavage in the trans dimers results from the time required for dimer exchange to first take place before cleavage can occur
Escherichia coli
additional information
UmuD proteins are shown to adopt multiple conformations in solution, homology models of UmuD and the structure of UmuD', overview. The heterodimer is the predominant UmuD protein conformer
Escherichia coli
physiological function
The umuD gene products perform distinct functions in preventing and facilitating mutagenesis. The full-length dimeric UmuD2 is the initial product that is expressed shortly after the induction of the SOS response and inhibits bacterial mutagenesis, allowing for error-free repair to occur. The slow auto-cleavage of UmuD2 to UmuD'2 promotes mutagenesis to ensure cell survival. The intracellular levels of UmuD2 and UmuD?2 are further regulated by degradation in vivo, returning the cell to a nonmutagenic state. Dynamic regulatory roles of the umuD gene, overview. UmuD lifecycle involves dimer exchange and cleavage in the regulation of the DNA damage respons
Escherichia coli
Expression (protein specific)
Organism
Commentary
Expression
Escherichia coli
the enzyme is expressed shortly after the induction of the SOS response
up
Other publictions for EC 3.4.21.B30
No.
1st author
Pub Med
title
organims
journal
volume
pages
year
Activating Compound
Application
Cloned(Commentary)
Crystallization (Commentary)
Engineering
General Stability
Inhibitors
KM Value [mM]
Localization
Metals/Ions
Molecular Weight [Da]
Natural Substrates/ Products (Substrates)
Organic Solvent Stability
Organism
Oxidation Stability
Posttranslational Modification
Purification (Commentary)
Reaction
Renatured (Commentary)
Source Tissue
Specific Activity [micromol/min/mg]
Storage Stability
Substrates and Products (Substrate)
Subunits
Synonyms
Temperature Optimum [°C]
Temperature Range [°C]
Temperature Stability [°C]
Turnover Number [1/s]
pH Optimum
pH Range
pH Stability
Cofactor
Ki Value [mM]
pI Value
IC50 Value
Activating Compound (protein specific)
Application (protein specific)
Cloned(Commentary) (protein specific)
Cofactor (protein specific)
Crystallization (Commentary) (protein specific)
Engineering (protein specific)
General Stability (protein specific)
IC50 Value (protein specific)
Inhibitors (protein specific)
Ki Value [mM] (protein specific)
KM Value [mM] (protein specific)
Localization (protein specific)
Metals/Ions (protein specific)
Molecular Weight [Da] (protein specific)
Natural Substrates/ Products (Substrates) (protein specific)
Organic Solvent Stability (protein specific)
Oxidation Stability (protein specific)
Posttranslational Modification (protein specific)
Purification (Commentary) (protein specific)
Renatured (Commentary) (protein specific)
Source Tissue (protein specific)
Specific Activity [micromol/min/mg] (protein specific)
Storage Stability (protein specific)
Substrates and Products (Substrate) (protein specific)
Subunits (protein specific)
Temperature Optimum [°C] (protein specific)
Temperature Range [°C] (protein specific)
Temperature Stability [°C] (protein specific)
Turnover Number [1/s] (protein specific)
pH Optimum (protein specific)
pH Range (protein specific)
pH Stability (protein specific)
pI Value (protein specific)
Expression
General Information
General Information (protein specific)
Expression (protein specific)
KCat/KM [mM/s]
KCat/KM [mM/s] (protein specific)
752775
Murison
Identification of the dimer e ...
Escherichia coli, Escherichia coli K12
Biochemistry
56
4773-4785
2017
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1
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755139
Murison
Altering the N-terminal arms ...
Escherichia coli, Escherichia coli K12
PLoS ONE
12
e0173388
2017
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754656
Diaz-Magana
A plasmid-encoded UmuD homolo ...
Pseudomonas aeruginosa
Microbiology
161
1516-1523
2015
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1
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1
1
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731145
Aranda
Role of Acinetobacter baumanni ...
Acinetobacter baumannii, Acinetobacter baumannii ATCC 17978
Antimicrob. Agents Chemother.
58
1771-1773
2014
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1
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1
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731345
Ollivierre
Dimer exchange and cleavage sp ...
Escherichia coli, Escherichia coli AB1157
Biochim. Biophys. Acta
1834
611-620
2013
-
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5
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2
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9
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4
2
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1
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4
2
1
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1
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1
3
3
1
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732588
Chaurasiya
Polymerase manager protein Umu ...
Escherichia coli
Nucleic Acids Res.
41
8959-8968
2013
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-
1
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2
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2
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2
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1
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1
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2
2
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731823
Hare
The Acinetobacter regulatory U ...
Acinetobacter baylyi, Escherichia coli
FEMS Microbiol. Lett.
334
57-65
2012
2
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2
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5
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6
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6
6
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717851
Ollivierre
The dimeric SOS mutagenesis pr ...
Escherichia coli
J. Biol. Chem.
286
3607-3617
2011
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718102
Ollivierre
Electron spin labeling reveals ...
Escherichia coli
Mol. Biosyst.
7
3183-3186
2011
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3
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709122
Foti
UmuD2 inhibits a non-covalent ...
Escherichia coli
J. Biol. Chem.
285
23086-23095
2010
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709543
Fang
Conformational dynamics of the ...
Escherichia coli
J. Mol. Biol.
398
40-53
2010
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718023
Ollivierre
The roles of UmuD in regulatin ...
Escherichia coli
J. Nucleic Acids
2010
pii: 947680
2010
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705887
Jiang
The active form of DNA polymer ...
Escherichia coli
Nature
460
359-363
2009
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682581
Simon
Regulation of Escherichia coli ...
Escherichia coli
Proc. Natl. Acad. Sci. USA
105
1152-1157
2008
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681885
Godoy
UmuD and RecA directly modulat ...
Escherichia coli, Escherichia coli FC40
Mol. Cell
28
1058-1070
2007
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669529
Beuning Penny
A non-cleavable UmuD variant t ...
Escherichia coli
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A constitutively expressed, tr ...
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2006
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668385
Bridges
Error-prone repair and transle ...
Escherichia coli
DNA Repair
4
1047-1059
2005
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668384
Duzen Jill
Identification of specific ami ...
Escherichia coli
DNA Repair
3
301-312
2004
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668779
Paetzel
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UmuD and UmuD proteins ...
Escherichia coli, Pseudomonas syringae, Salmonella enterica subsp. enterica serovar Typhimurium
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668783
Paetzel
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UmuD and UmuD proteins ...
Escherichia coli
Handbook of Proteolytic Enzymes (Barrett, A. J. , Rawlings, N. D. , Woessner; J. F. , eds. )Academic Press
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1976-1981
2004
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653588
Neher
Distinct peptide signals in th ...
Escherichia coli
Proc. Natl. Acad. Sci. USA
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13219-13224
2003
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651685
Sutton
Genetic and biochemical charac ...
Escherichia coli
J. Bacteriol.
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650976
Gonzalez
Subunit-specific degradation o ...
Escherichia coli
EMBO J.
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Analysis of Escherichia coli R ...
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653620
Sutton
The Escherichia coli SOS mutag ...
Escherichia coli
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651420
Gonzalez
Lon-mediated proteolysis of th ...
Escherichia coli
Genes Dev.
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1998
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Konola
Differential cleavage of LexA ...
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McDonald
Regulation of UmuD cleavage: r ...
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Interactions of Escherichia co ...
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651629
Guzzo
Analysis of the region between ...
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651630
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Inhibition of RecA-mediated cl ...
Escherichia coli
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653917
Peat
The UmuD' protein filament and ...
Escherichia coli
Structure
4
1401-1412
1996
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651622
Lee
A monocysteine approach for pr ...
Escherichia coli
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1
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653236
Koch
Escherichia coli umuDC mutants ...
Escherichia coli
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653235
Woodgate
Levels of chromosomally encode ...
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651617
Thomas
Structural characterization of ...
Salmonella enterica subsp. enterica serovar Typhimurium, Salmonella enterica subsp. enterica serovar Typhimurium LT2
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653604
Battista
Dominant negative umuD mutatio ...
Escherichia coli
Proc. Natl. Acad. Sci. USA
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1990
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653602
Shinagawa
RecA protein-dependent cleavag ...
Escherichia coli
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1988
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