BRENDA home
History
Enzyme Nomenclature
Information on EC 3.1.21.8 - T4 deoxyribonuclease II
for references in articles please use BRENDA:EC3.1.21.8Please wait a moment until all data is loaded. This message will disappear when all data is loaded.
EC Tree
3.1.21.8 T4 deoxyribonuclease IISpecify your search results
Word Map
- 3.1.21.8
- bacteriophage
- nick
- strands
- phage
- endonucleases
-
single-stranded
-
coliphage
- dctpase
- dcmp
- i-tevi
-
exonuclease
-
hydroxymethylase
-
cytosine-containing
- cytosine
-
scissile
The enzyme appears in viruses and cellular organisms
Reaction Schemes
endonucleolytic nicking and cleavage of cytosine-containing double-stranded DNA
topPlease wait a moment until the data is sorted. This message will disappear when the data is sorted.
SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
EndoII
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
endonucleolytic nicking and cleavage of cytosine-containing double-stranded DNA
-
-
-
-
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
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
DNA where cytosine is partially or completely replaced by hydroxymethylcytosine + H2O
?
DNA where cytosine is partially or completely replaced by hydroxymethylcytosine is degraded in vivo by T4 endonuclease II, EC 3.1.21.8, and endonuclease IV, EC 3.1.21.9
-
-
?
plasmid pBR322 + H2O
?
-
double-stranded restriction cleavage at 12 sites in pBR322 commence before 10-min postinfection with T4 at 37°C and proceeds more slowly in the presence of competing phage DNA than in its absence, utilizing the same sites in both cases. In a 200-base pair segment of the plasmid, single-stranded nicks also are frequent. The plasmid sites are cleaved with a speed that varies with the site, yielding frequencies of cleavage at different sites varying between 10 and 90%, at 50-min postinfection. All sites contain good matches to a consensus, 5'-GRCCGCNTYGC-3', most frequently cleaved around the variable central base pair, generating fragments with blunt ends or 1-2-base 5' overhangs. A larger consensus sequence, 5'-CGRCCGCNTTGSYNGC-3', has been identified. DNA sequence elements 3' to the cut site appear important for rapid cleavage
-
?
DNA + H2O
?
the phage T4 enzyme is involved in degradation of host DNA
-
-
?
DNA + H2O
?
the phage T4 enzyme is involved in degradation of host DNA. The enzyme primarily catalyses nicking of the bottom strand of double stranded DNA between the first and second base pair to the right of a top-strand CCGC motif. Double-stranded breaks are produced 5fold to 10fold less frequently. It does not cleave the T4 native DNA, which contains 5-hydroxymethylcytosine instead of cytosine
-
-
?
additional information
?
-
EndoII nicks both strands simultaneously at an in vivo-favoured site but not at an in vitro-favoured site. The right-side conserved sequence element at in vivo-favoured sites is important for simultaneous nicking of both strands, generating double-strand cleavage. EndoII nicks the lower strand about 1.5fold faster than the upper strand. In addition, the upper and lower strands are nicked independently of each other, seldom resulting in double-strand cleavage
-
-
?
additional information
?
-
-
EndoII nicks both strands simultaneously at an in vivo-favoured site but not at an in vitro-favoured site. The right-side conserved sequence element at in vivo-favoured sites is important for simultaneous nicking of both strands, generating double-strand cleavage. EndoII nicks the lower strand about 1.5fold faster than the upper strand. In addition, the upper and lower strands are nicked independently of each other, seldom resulting in double-strand cleavage
-
-
?
additional information
?
-
identification of seven major endonuclease II-dependent restriction sites in the T4 genome, in addition, abundant sites are cleaved in 55% of all molecules. Sites I, 11, and I11 share the sequence 5''CCGNNTTGGC-3' and are cleaved inabout 25% for I and III and 65% for II of all molecules, predominantly staggered around the first or second of the central unspecified base pairs to yield fragments with one 5' base. The less frequently cleaved sites I and I11 deviate from site I1 in predicted helical structure when viewed from the consensus strand, and in sequence when viewed from the opposite strand
-
-
?
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
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
?
the phage T4 enzyme is involved in degradation of host DNA
-
-
?
DNA where cytosine is partially or completely replaced by hydroxymethylcytosine + H2O
?
DNA where cytosine is partially or completely replaced by hydroxymethylcytosine is degraded in vivo by T4 endonuclease II, EC 3.1.21.8, and endonuclease IV, EC 3.1.21.9
-
-
?
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Mg2+
Mn2+
compared to Mg2+, relative nicking activity is 0.4 with top strand, 0.8 with bottom strand
Ni2+
compared to Mg2+, relative nicking activity is 0.1 with top strand, 0.1 with bottom strand
additional information
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
endonuclease IV activity is almost completely inhibited in the presence of very small amounts of hydroxymethylcytosine in the DNA
-
additional information
-
endonuclease IV activity is almost completely inhibited in the presence of very small amounts of hydroxymethylcytosine in the DNA
-
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
DISEASE
TITLE OF PUBLICATION
LINK TO PUBMED
Infections
Host DNA degradation after infection of Escherichia coli with bacteriophage T4: dependence of the alternate pathway of degradation which occurs in the absence of both T4 endonuclease II and nuclear disruption on T4 endonuclease IV.
t4 deoxyribonuclease ii deficiency
Partial suppression of bacteriophage T4 ligase mutations by T4 endonuclease II deficiency: role of host ligase.
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
physiological function
the phage T4 enzyme is involved in degradation of host DNA
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
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). END2_BPT4
136
0
15802
Swiss-Prot
other Location (Reliability: 1)
A0A3G2KCD0_9CAUD
136
0
15884
TrEMBL
other Location (Reliability: 1)
A0A7T7K9A5_9CAUD
136
0
15786
TrEMBL
other Location (Reliability: 1)
A0A3G2KB65_9CAUD
136
0
15896
TrEMBL
other Location (Reliability: 2)
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
modeling based on strucuture of UvrC, PDB code 1YD0. Residues G49, R57, E118, and N130 in the putative catalytic surface are important for substrate recognition and binding. Residues G49 and R57 are essential for normal sequence recognition. and play a role in forming the DNA-binding surface and exposing the substrate scissile bond at the active site. Residues N130 and P127 likely contribute to positioning the catalytic domain correctly. Residue K76, part of a conserved NUMOD3 DNA-binding motif of homing endonucleases found to overlap the MR, affects both sequence recognition and catalysis
mutant E118A,crystallized in space group P21 with four monomers in the asymmetric unit. EndoII forms a striking X-shaped tetrameric structure composed as a dimer of dimers, with a protruding hairpin domain providing most of the dimerization and tetramerization interfaces. A bound phosphate ion in one of the four active sites of EndoII likely mimics the scissile phosphate in a true substrate complex. A protruding loop containing a nuclease-associated modular domain 3 element is likely to be involved in substrate binding, as well as residues forming a separate nucleic acid binding surface adjacent to the active site. The substrate would bind to a primary EndoII dimer diagonally over the active sites, requiring significant distortion of the enzyme or the substrate DNA, or both, for simultaneous nicking of both DNA strands. EndoII may bind its substrate inefficiently across the two sites in the dimer, offering a plausible explanation for the catalytic preponderance of single-strand nicks
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
A83L
similar to wild-type, cleavage activity is 20 to 70% of the nicking activity
E118A
G49A
I24A
similar to wild-type, cleavage activity is 20 to 70% of the nicking activity
K12A
similar to wild-type, cleavage activity is 20 to 70% of the nicking activity
L16A
similar to wild-type, cleavage activity is 20 to 70% of the nicking activity
R57A
S72A
similar to wild-type, cleavage activity is 20 to 70% of the nicking activity
V90A
similar to wild-type, cleavage activity is 20 to 70% of the nicking activity
E118A
mutation in a putatively catalytic residue. Mutant E118A is able to bind stably as monomer or dimer to a single substrate. In low-salt conditions, mutant is present as dimer in solution
G49A
in low-salt conditions, mutant is present as dimer in solution
R57A
in low-salt conditions, mutant is present as dimer in solution
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Carlson, K.; Lagerback, P.; Nystrom, A.C.
Bacteriophage T4 endonuclease II: concerted single-strand nicks yield double-strand cleavage
Mol. Microbiol.
52
1403-1411
2004
Escherichia virus T4 (P07059), Escherichia virus T4
brenda
Andersson, C.E.; Lagerbaeck, P.; Carlson, K.
Structure of bacteriophage T4 endonuclease II mutant E118A, a tetrameric GIY-YIG enzyme
J. Mol. Biol.
397
1003-1016
2010
Escherichia virus T4 (P07059), Escherichia virus T4
brenda
Carlson, K.; Kosturko, L.D.; Nystrom, A.C.
Sequence-specific cleavage by bacteriophage T4 endonuclease II in vitro
Mol. Microbiol.
31
1395-1405
1999
Escherichia virus T4 (P07059), Escherichia virus T4
brenda
Carlson, K.; Overvatn, A.
Bacteriophage T4 endonucleases II and IV, oppositely affected by dCMP hydroxymethylase activity, have different roles in the degradation and in the RNA polymerase-dependent replication of T4 cytosine-containing DNA
Genetics
114
669-685
1986
Escherichia virus T4 (P07059), Escherichia virus T4
brenda
Lagerbaeck, P.; Carlson, K.
Amino acid residues in the GIY-YIG endonuclease II of phage T4 affecting sequence recognition and binding as well as catalysis
J. Bacteriol.
190
5533-5544
2008
Escherichia virus T4 (P07059), Escherichia virus T4
brenda
Krabbe, M.; Carlson, K.
In vivo restriction. Sequence and structure of endonuclease II-dependent cleavage sites in bacteriophage T4 DNA
J. Biol. Chem.
266
23407-23415
1991
Escherichia virus T4 (P07059)
brenda
Carlson, K.; Krabbe, M.; Nystroem, A.C.; Kosturko, L.D.
DNA determinants of restriction. Bacteriophage T4 endonuclease II-dependent cleavage of plasmid DNA in vivo
J. Biol. Chem.
268
8908-8918
1993
Escherichia virus T4 (P07059)
brenda
Lagerbaeck, P.; Andersson, E.; Malmberg, C.; Carlson, K.
Bacteriophage T4 endonuclease II, a promiscuous GIY-YIG nuclease, binds as a tetramer to two DNA substrates
Nucleic Acids Res.
37
6174-6183
2009
Escherichia virus T4 (P07059), Escherichia virus T4
brenda
Select items on the left to see more content.
EXTERNAL LINKS (specific for EC-Number 3.1.21.8)
html completed
Use of this online version of BRENDA is free under the CC BY 4.0 license. See terms of use for full details.
About BRENDA
Help
Download
Contribution
member of
curated at
curated at
Server: brenda1 Ver: 9edf756-main (2022-05-17 10:30:03 +0200)