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Information on EC 3.1.99.B1 - flap endonuclease-1 and Organism(s) Pyrococcus horikoshii and UniProt Accession O50123

for references in articles please use BRENDA:EC3.1.99.B1
preliminary BRENDA-supplied EC number
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EC Tree
     3 Hydrolases
         3.1 Acting on ester bonds
            
                3.1.99.B1 flap endonuclease-1
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This record set is specific for:
Pyrococcus horikoshii
UNIPROT: O50123
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Word Map
The taxonomic range for the selected organisms is: Pyrococcus horikoshii
The expected taxonomic range for this enzyme is: Archaea, Eukaryota
Reaction Schemes
endonucleases that remove 5' DNA sequences from a DNA structure called a DNA flap. The DNA flap structure occurs in double-stranded DNA containing a single-stranded break where the 5' portion of the downstream strand is too long and overlaps the 3' end of the upstream strand. Flap endonucleases cleave the downstream strand of the overlap flap structure precisely after the first base-paired nucleotide, creating a ligatable nick.
endonucleases that remove 5' DNA sequences from a DNA structure called a DNA flap. The DNA flap structure occurs in double-stranded DNA containing a single-stranded break where the 5' portion of the downstream strand is too long and overlaps the 3' end of the upstream strand. Flap endonucleases cleave the downstream strand of the overlap flap structure precisely after the first base-paired nucleotide, creating a ligatable nick
Synonyms
flap endonuclease 1, flap endonuclease, flap endonuclease-1, hfen1, t5fen, fen1 endonuclease, t5 flap endonuclease, affen, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
flap endonuclease-1
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SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
DNA + H2O
?
show the reaction diagram
the aromatic residues Tyr33 and Phe79, and the aromatic cluster Phe278-Phe279 mainly contribute to the recognition of the substrates without the 3' projection of the upstream strand (the nick, 5'-recess-end, single-flap, and pseudo-Y substrates) for the both exo- and endo-activities, but play minor roles in recognizing the substrates with the 3' projection (the double flap substrate and the nick substrate with the 3' projection)
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-
?
additional information
?
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
KCl
60 mM, the activity increases 1.3-fold, 100 mM KCl result in significant inhibition of activity
Mg2+
addition of 1 mM MgCl2 increases the activity 1.4-fold. 10 mM MgCl2 results in greater than 90% inhibition
Mn2+
addition of 0.1 mM MgCl2 increases the activity 1.5-fold. 10 mM MnCl2 results in greater than 90% inhibition
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
Ca2+
10 mM CaCl2 results in greater than 90% inhibition
EDTA
5 mM, complete inhibition
KCl
60 mM, the activity increases 1.3-fold, 100 mM KCl result in significant inhibition of activity
Mg2+
addition of 1 mM MgCl2 increases the activity 1.4-fold. 10 mM MgCl2 results in greater than 90% inhibition
Mn2+
addition of 0.1 mM MgCl2 increases the activity 1.5-fold. 10 mM MnCl2 results in greater than 90% inhibition
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
additional information
additional information
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
additional information
additional information
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kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
additional information
additional information
-
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6 - 7
the activity of phFEN decreases immediately at pH values below 6.0 and over 7.0. The activity can not be detected at pH 5.0 and decreased to 24% at pH 9.4
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
pI VALUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
malfunction
the enzyme has important roles in DNA replication, repair, and recombination
metabolism
plays important roles with DNA polymerases in DNA replication, repair and recombination
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
41000
gel filtration
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
monomer
1 * 41000, SDS-PAGE
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
hanging-drop vapor diffusion, the crystal structure of flap endonuclease-1 from Pyrococcus horikoshii (phFEN-1) is determined to a resolution of 3.1 A
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
F278A
the substitution of the aromatic residues with alanine leads to a large reduction in kcat value, although the mutants retains Km-value similar to that of the wild-type enzyme
F278A/F279A
F278H/F279H
F278L/F279L
F278W/F279W
F278Y/F279Y
F279A
the substitution of the aromatic residues with alanine leads to a large reduction in kcat value, although the mutants retains Km-value similar to that of the wild-type enzyme
K193A
KM-value is 4fold of the wild-type value, kcat is almost the same as for wild-type enzyme
K193A/R194A/K195A
K193E/R194E/K195E
the negatively charged triple mutant shows similar but more magnified effects on both parameters compared with the alanine triple mutant K193A/R194A/K195A
K195A
KM-value is 8fold of the wild-type value, kcat is almost the same as for wild-type enzyme
K199A
km and kcat values of the mutant enzyme differ little from the wild-type values
K243A
Km and kcat/Km values of the mutant enzyme do not change markedly compared with the wild-type values
K243E
Km and kcat/Km values of the mutant enzyme do not change markedly compared with the wild-type values
K248A
Km and kcat/Km values of the mutant enzyme do not change markedly compared with the wild-type values
K249A
Km and kcat/Km values of the mutant enzyme do not change markedly compared with the wild-type values
K263A
Km and kcat/Km values of the mutant enzyme do not change markedly compared with the wild-type values
K263E
Km and kcat/Km values of the mutant enzyme do not change markedly compared with the wild-type values
K51E/R53E
the double mutant retains 30% of the wild-type kcat/Km value
K87A
the kcat value of the mutant decreased 400fold, whereas the Km value is almost the same as that of wild-type enzyme
K87A/R88A/K89A
the Km-value is 5fold higher, the kcat is 184fold lower than that of the wild-type enzyme
K93A/R94A/R95A
Km-value and kcat-value is increased 17fold and decreased 96fold, respectively, compared with the wild-type values
L47F
Km-value is similat to the value of the wild-type
L47G
Km value of the mutant is increased 20fold
R118A/K119A
R194A
KM-value is 5fold of the wild-type value, kcat is almost the same as for wild-type enzyme
R40E/R42E
the Km of the mutynt is increased 105fold compared with wild-type. The kcat and kcat/Km values areo decreased 4- and 680fold, respectively
R40G
Km of the mutant increases 7fold, compared with that of the wild-type enzyme
R40G/R42G
R40Q
Km value of the single mutant enzyme increases 10fold
R42E
Km and kcat/Km values of the mutant are 19fold higher and 25fold lower than the values of wild-type enzyme, respectively
R42G
Km of the mutant increases 7fold, compared with that of the wild-type enzyme
R42Q
KM-value is almost the same as the value for wild-type enzyme
R88A
Km and kcat values of the mutant enzyme do not change markedly, compared with the wild-type values
R89A
Km and kcat values of the mutant enzyme do not change markedly, compared with the wild-type values
Y237A
Km and kcat/Km values of the mutant enzyme do not change markedly compared with the wild-type values
additional information
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
102
Tm-value is 102°C in 0.0085 and 0.0014 mM protein with 1 M NaCl concentrations. Values of Tm are not dependent on the protein concentration
95
at a final concentration of 0.3 mg/ml, the half-life is 2 h in the presence of 1 M NaCl and 20 min in 50 mM NaCl
additional information
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
4°C or 20°C, stable for over 3 months without loss of activity
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expression in Escherichia coli
expression of the mutant proteins in Escherichia coli BL21(DE3)
overexpressed in Escherichia coli
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Matsui, E.; Kawasaki, S.; Ishida, H.; Ishikawa, K.; Kosugi, Y.; Kikuchi, H.; Kawarabayashi, Y.; Matsui, I.
Thermostable flap endonuclease from the archaeon, Pyrococcus horikoshii, cleaves the replication fork-like structure endo/exonucleolytically
J. Biol. Chem.
274
18297-18309
1999
Pyrococcus horikoshii (O50123), Pyrococcus horikoshii
Manually annotated by BRENDA team
Matsui, E.; Musti, K.V.; Abe, J.; Yamasaki, K.; Matsui, I.; Harata, K.
Molecular structure and novel DNA binding sites located in loops of flap endonuclease-1 from Pyrococcus horikoshii
J. Biol. Chem.
277
37840-37847
2002
Pyrococcus horikoshii (O50123), Pyrococcus horikoshii
Manually annotated by BRENDA team
Matsui, E.; Abe, J.; Yokoyama, H.; Matsui, I.
Aromatic residues located close to the active center are essential for the catalytic reaction of flap endonuclease-1 from hyperthermophilic archaeon Pyrococcus horikoshii
J. Biol. Chem.
279
16687-16696
2004
Pyrococcus horikoshii (O50123), Pyrococcus horikoshii
Manually annotated by BRENDA team
Matsui, E.; Urushibata, Y.; Abe, J.; Matsui, I.
Serial intermediates with a 1 nt 3'-flap and 5' variable-length flaps are formed by cooperative functioning of Pyrococcus horikoshii FEN-1 with either B or D DNA polymerases
Extremophiles
18
415-427
2014
Pyrococcus horikoshii (O50123), Pyrococcus horikoshii, Pyrococcus horikoshii OT-3 (O50123)
Manually annotated by BRENDA team
Matsui, E.; Abe, J.; Yokoyama, H.; Matsui, I.
Aromatic residues located close to the active center are essential for the catalytic reaction of flap endonuclease-1 from hyperthermophilic archaeon Pyrococcus horikoshii
J. Biol. Chem.
279
16687-16696
2004
Pyrococcus horikoshii (O50123), Pyrococcus horikoshii, Pyrococcus horikoshii OT-3 (O50123)
Manually annotated by BRENDA team