Any feedback?
Information on EC 3.1.12.1 - 5' to 3' exodeoxyribonuclease (nucleoside 3'-phosphate-forming)
for references in articles please use BRENDA:EC3.1.12.1Please wait a moment until all data is loaded. This message will disappear when all data is loaded.
EC Tree
3.1.12.1 5' to 3' exodeoxyribonuclease (nucleoside 3'-phosphate-forming)Specify your search results
Word Map
The enzyme appears in viruses and cellular organisms
Reaction Schemes
exonucleolytic cleavage in the 5'- to 3'-direction to yield nucleoside 3'-phosphates
Synonyms
sso0001, cas4 nuclease, pcal_0546, type i-c cas4, cas4-1, cas4-2, 
more
topPlease wait a moment until the data is sorted. This message will disappear when the data is sorted.
SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
5' to 3' single stranded DNA exonuclease
BH0340
Cas4
Cas4 nuclease
Cas4-1
Cas4-2
CRISPR adaptation factor
CRISPR-associated exonuclease Cas4
DUF83Pc
DUF83Ss
Pcal_0546
SSO0001
type I-C Cas4
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
exonucleolytic cleavage in the 5'- to 3'-direction to yield nucleoside 3'-phosphates
-
-
-
-
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
single-stranded oligodeoxyribonucleotide + H2O
nucleoside 3'-phosphate + ?
-
-
-
?
single-stranded oligodeoxyribonucleotide + H2O
nucleoside 3'-phosphate + ?
cleavage of a 15T DNA oligonucleotide is observed in the presence of either magnesium or manganese, yielding a cluster of products of around 15 nt in size. A 20U RNA oligonucleotide is cleaved in the presence of manganese but not magnesium.
-
-
?
single-stranded oligodeoxyribonucleotide + H2O
nucleoside 3'-phosphate + ?
-
-
-
?
single-stranded oligodeoxyribonucleotide + H2O
nucleoside 3'-phosphate + ?
cleavage of a 15T DNA oligonucleotide is observed in the presence of either magnesium or manganese, yielding a cluster of products of around 15 nt in size. A 20U RNA oligonucleotide is cleaved in the presence of manganese but not magnesium.
-
-
?
ssDNA + H2O
nucleoside 3'-phosphate + ?
short oligonucleotides (17 nt) are cleaved faster than longer substrates (62 nt). Lack of significant sequence preference toward the substrates containing the Sulfolobus solfataricus protospacer adjacent motif (PAMs) in DNA binding and cleavage reactions in vitro. The rates of cleavage of ssRNA and dsDNA with blunt ends by the enzyme are approximately 20 times and 200 times lower, respectively compared to ssDNA
-
-
?
ssDNA + H2O
nucleoside 3'-phosphate + ?
the enzyme is specific for ssDNA
-
-
?
ssDNA + H2O
nucleoside 3'-phosphate + ?
short oligonucleotides (17 nt) are cleaved faster than longer substrates (62 nt). Lack of significant sequence preference toward the substrates containing the Sulfolobus solfataricus protospacer adjacent motif (PAMs) in DNA binding and cleavage reactions in vitro. The rates of cleavage of ssRNA and dsDNA with blunt ends by the enzyme are approximately 20 times and 200 times lower, respectively compared to ssDNA
-
-
?
ssDNA + H2O
nucleoside 3'-phosphate + ?
the enzyme is specific for ssDNA
-
-
?
additional information
?
-
Cas4 proteins contain a RecB-like nuclease domain and exhibit in vitro exonuclease activities
-
-
?
additional information
?
-
Halalkalibacterium halodurans
Cas4 is a Cas1-Cas2-dependent endonuclease that cleaves 3' overhangs of prespacers. Cas4 cleavage is sequence and site-specific and depends on the presence of a protospacer adjacent motif (PAM). Cas4 enhances prespacer processing. Mechanism and structural and mechanistic model, overview
-
-
?
additional information
?
-
Halalkalibacterium halodurans
Cas4 proteins contain a RecB-like nuclease domain and exhibit in vitro exonuclease activities. In the presence of Cas1 and Cas2, Cas4 of Bacillus halodurans endonucleolytically cuts long 3' overhangs of prespacers at the PAM site
-
-
?
additional information
?
-
Halalkalibacterium halodurans
in the presence of Cas1 and Cas2, Cas4 processes double-stranded substrates with long 3' overhangs through site-specific endonucleolytic cleavage. Cas4 recognizes PAM sequences within the prespacer and prevents integration of unprocessed prespacers, ensuring that only functional spacers will be integrated into the CRISPR array. Assays with dsDNA substrates containing blunt ends or a 24-bp duplex flanked by 15-nt 3' or 5' overhangs result in cleavage of the 3'-overhanging substrates at 65°C, but no cleavage of 5'-overhanging or blunt-end substrates by the enzyme under similar conditions. Exonucleolytic cleavage of the blunt-end substrate is observed using free Cas4, but only at very high concentrations. Sequence-specific integration and asymmetric prespacer processing by the adaptation complex
-
-
?
additional information
?
-
Halalkalibacterium halodurans ATCC BAA-125
Cas4 is a Cas1-Cas2-dependent endonuclease that cleaves 3' overhangs of prespacers. Cas4 cleavage is sequence and site-specific and depends on the presence of a protospacer adjacent motif (PAM). Cas4 enhances prespacer processing. Mechanism and structural and mechanistic model, overview
-
-
?
additional information
?
-
Halalkalibacterium halodurans ATCC BAA-125
in the presence of Cas1 and Cas2, Cas4 processes double-stranded substrates with long 3' overhangs through site-specific endonucleolytic cleavage. Cas4 recognizes PAM sequences within the prespacer and prevents integration of unprocessed prespacers, ensuring that only functional spacers will be integrated into the CRISPR array. Assays with dsDNA substrates containing blunt ends or a 24-bp duplex flanked by 15-nt 3' or 5' overhangs result in cleavage of the 3'-overhanging substrates at 65°C, but no cleavage of 5'-overhanging or blunt-end substrates by the enzyme under similar conditions. Exonucleolytic cleavage of the blunt-end substrate is observed using free Cas4, but only at very high concentrations. Sequence-specific integration and asymmetric prespacer processing by the adaptation complex
-
-
?
additional information
?
-
Halalkalibacterium halodurans C-125
Cas4 is a Cas1-Cas2-dependent endonuclease that cleaves 3' overhangs of prespacers. Cas4 cleavage is sequence and site-specific and depends on the presence of a protospacer adjacent motif (PAM). Cas4 enhances prespacer processing. Mechanism and structural and mechanistic model, overview
-
-
?
additional information
?
-
Halalkalibacterium halodurans C-125
in the presence of Cas1 and Cas2, Cas4 processes double-stranded substrates with long 3' overhangs through site-specific endonucleolytic cleavage. Cas4 recognizes PAM sequences within the prespacer and prevents integration of unprocessed prespacers, ensuring that only functional spacers will be integrated into the CRISPR array. Assays with dsDNA substrates containing blunt ends or a 24-bp duplex flanked by 15-nt 3' or 5' overhangs result in cleavage of the 3'-overhanging substrates at 65°C, but no cleavage of 5'-overhanging or blunt-end substrates by the enzyme under similar conditions. Exonucleolytic cleavage of the blunt-end substrate is observed using free Cas4, but only at very high concentrations. Sequence-specific integration and asymmetric prespacer processing by the adaptation complex
-
-
?
additional information
?
-
Halalkalibacterium halodurans DSM 18197
Cas4 is a Cas1-Cas2-dependent endonuclease that cleaves 3' overhangs of prespacers. Cas4 cleavage is sequence and site-specific and depends on the presence of a protospacer adjacent motif (PAM). Cas4 enhances prespacer processing. Mechanism and structural and mechanistic model, overview
-
-
?
additional information
?
-
Halalkalibacterium halodurans DSM 18197
in the presence of Cas1 and Cas2, Cas4 processes double-stranded substrates with long 3' overhangs through site-specific endonucleolytic cleavage. Cas4 recognizes PAM sequences within the prespacer and prevents integration of unprocessed prespacers, ensuring that only functional spacers will be integrated into the CRISPR array. Assays with dsDNA substrates containing blunt ends or a 24-bp duplex flanked by 15-nt 3' or 5' overhangs result in cleavage of the 3'-overhanging substrates at 65°C, but no cleavage of 5'-overhanging or blunt-end substrates by the enzyme under similar conditions. Exonucleolytic cleavage of the blunt-end substrate is observed using free Cas4, but only at very high concentrations. Sequence-specific integration and asymmetric prespacer processing by the adaptation complex
-
-
?
additional information
?
-
Halalkalibacterium halodurans FERM 7344
Cas4 is a Cas1-Cas2-dependent endonuclease that cleaves 3' overhangs of prespacers. Cas4 cleavage is sequence and site-specific and depends on the presence of a protospacer adjacent motif (PAM). Cas4 enhances prespacer processing. Mechanism and structural and mechanistic model, overview
-
-
?
additional information
?
-
Halalkalibacterium halodurans FERM 7344
in the presence of Cas1 and Cas2, Cas4 processes double-stranded substrates with long 3' overhangs through site-specific endonucleolytic cleavage. Cas4 recognizes PAM sequences within the prespacer and prevents integration of unprocessed prespacers, ensuring that only functional spacers will be integrated into the CRISPR array. Assays with dsDNA substrates containing blunt ends or a 24-bp duplex flanked by 15-nt 3' or 5' overhangs result in cleavage of the 3'-overhanging substrates at 65°C, but no cleavage of 5'-overhanging or blunt-end substrates by the enzyme under similar conditions. Exonucleolytic cleavage of the blunt-end substrate is observed using free Cas4, but only at very high concentrations. Sequence-specific integration and asymmetric prespacer processing by the adaptation complex
-
-
?
additional information
?
-
Halalkalibacterium halodurans JCM 9153
Cas4 is a Cas1-Cas2-dependent endonuclease that cleaves 3' overhangs of prespacers. Cas4 cleavage is sequence and site-specific and depends on the presence of a protospacer adjacent motif (PAM). Cas4 enhances prespacer processing. Mechanism and structural and mechanistic model, overview
-
-
?
additional information
?
-
Halalkalibacterium halodurans JCM 9153
in the presence of Cas1 and Cas2, Cas4 processes double-stranded substrates with long 3' overhangs through site-specific endonucleolytic cleavage. Cas4 recognizes PAM sequences within the prespacer and prevents integration of unprocessed prespacers, ensuring that only functional spacers will be integrated into the CRISPR array. Assays with dsDNA substrates containing blunt ends or a 24-bp duplex flanked by 15-nt 3' or 5' overhangs result in cleavage of the 3'-overhanging substrates at 65°C, but no cleavage of 5'-overhanging or blunt-end substrates by the enzyme under similar conditions. Exonucleolytic cleavage of the blunt-end substrate is observed using free Cas4, but only at very high concentrations. Sequence-specific integration and asymmetric prespacer processing by the adaptation complex
-
-
?
additional information
?
-
Cas4-1 trims and orients a duplexed DNA oligonucleotide pre-spacer. Nuclease activities of Cas4 proteins are essential to define PAM, length, and orientation of new spacers
-
-
?
additional information
?
-
Cas4-1 trims and orients a duplexed DNA oligonucleotide pre-spacer. Nuclease activities of Cas4 proteins are essential to define PAM, length, and orientation of new spacers
-
-
?
additional information
?
-
-
Cas4-1 trims and orients a duplexed DNA oligonucleotide pre-spacer. Nuclease activities of Cas4 proteins are essential to define PAM, length, and orientation of new spacers
-
-
?
additional information
?
-
Cas4 proteins contain a RecB-like nuclease domain and exhibit in vitro exonuclease activities
-
-
?
additional information
?
-
Cas4 proteins contain a RecB-like nuclease domain and exhibit in vitro exonuclease activities
-
-
?
additional information
?
-
Cas4-1 trims and orients a duplexed DNA oligonucleotide pre-spacer. Nuclease
-
-
?
additional information
?
-
Cas4-1 trims and orients a duplexed DNA oligonucleotide pre-spacer. Nuclease
-
-
?
additional information
?
-
-
Cas4-1 trims and orients a duplexed DNA oligonucleotide pre-spacer. Nuclease
-
-
?
additional information
?
-
Cas4-2 trims and orients a duplexed DNA oligonucleotide pre-spacer
-
-
?
additional information
?
-
Cas4-2 trims and orients a duplexed DNA oligonucleotide pre-spacer
-
-
?
additional information
?
-
-
Cas4-2 trims and orients a duplexed DNA oligonucleotide pre-spacer
-
-
?
additional information
?
-
the enzyme also exhibits ATP-independent DNA unwinding activity
-
-
?
additional information
?
-
-
the enzyme also exhibits ATP-independent DNA unwinding activity
-
-
?
additional information
?
-
the enzyme also exhibits ATP-independent DNA unwinding activity
-
-
?
additional information
?
-
Cas4 proteins contain a RecB-like nuclease domain and exhibit in vitro exonuclease activities
-
-
?
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
additional information
?
-
Halalkalibacterium halodurans
Cas4 is a Cas1-Cas2-dependent endonuclease that cleaves 3' overhangs of prespacers. Cas4 cleavage is sequence and site-specific and depends on the presence of a protospacer adjacent motif (PAM). Cas4 enhances prespacer processing. Mechanism and structural and mechanistic model, overview
-
-
?
additional information
?
-
Halalkalibacterium halodurans ATCC BAA-125
Cas4 is a Cas1-Cas2-dependent endonuclease that cleaves 3' overhangs of prespacers. Cas4 cleavage is sequence and site-specific and depends on the presence of a protospacer adjacent motif (PAM). Cas4 enhances prespacer processing. Mechanism and structural and mechanistic model, overview
-
-
?
additional information
?
-
Halalkalibacterium halodurans C-125
Cas4 is a Cas1-Cas2-dependent endonuclease that cleaves 3' overhangs of prespacers. Cas4 cleavage is sequence and site-specific and depends on the presence of a protospacer adjacent motif (PAM). Cas4 enhances prespacer processing. Mechanism and structural and mechanistic model, overview
-
-
?
additional information
?
-
Halalkalibacterium halodurans DSM 18197
Cas4 is a Cas1-Cas2-dependent endonuclease that cleaves 3' overhangs of prespacers. Cas4 cleavage is sequence and site-specific and depends on the presence of a protospacer adjacent motif (PAM). Cas4 enhances prespacer processing. Mechanism and structural and mechanistic model, overview
-
-
?
additional information
?
-
Halalkalibacterium halodurans FERM 7344
Cas4 is a Cas1-Cas2-dependent endonuclease that cleaves 3' overhangs of prespacers. Cas4 cleavage is sequence and site-specific and depends on the presence of a protospacer adjacent motif (PAM). Cas4 enhances prespacer processing. Mechanism and structural and mechanistic model, overview
-
-
?
additional information
?
-
Halalkalibacterium halodurans JCM 9153
Cas4 is a Cas1-Cas2-dependent endonuclease that cleaves 3' overhangs of prespacers. Cas4 cleavage is sequence and site-specific and depends on the presence of a protospacer adjacent motif (PAM). Cas4 enhances prespacer processing. Mechanism and structural and mechanistic model, overview
-
-
?
additional information
?
-
Cas4-1 trims and orients a duplexed DNA oligonucleotide pre-spacer. Nuclease activities of Cas4 proteins are essential to define PAM, length, and orientation of new spacers
-
-
?
additional information
?
-
Cas4-1 trims and orients a duplexed DNA oligonucleotide pre-spacer. Nuclease activities of Cas4 proteins are essential to define PAM, length, and orientation of new spacers
-
-
?
additional information
?
-
-
Cas4-1 trims and orients a duplexed DNA oligonucleotide pre-spacer. Nuclease activities of Cas4 proteins are essential to define PAM, length, and orientation of new spacers
-
-
?
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
iron-sulfur centre
K+
nuclease activity of the enzyme is maximal in the presence of 20-200 mM KCl
Mg2+
Mn2+
additional information
iron-sulfur centre
near the active site, each enzyme protomer contains one [4Fe-4S] cluster, which is important for both maintaining the decameric state and nuclease activity
Mg2+
cleavage of a 15T DNA oligonucleotide by Sso0001 is observed in the presence of either magnesium or manganese, yielding a cluster of products of around 15 nt in size. A 20U RNA oligonucleotide is cleaved in the presence of manganese but not magnesium
Mg2+
nuclease activity of the enzyme is maximal in the presence of Mg2+ or Mn2+ (5 mM)
Mn2+
cleavage of a 15T DNA oligonucleotide by Sso0001 is observed in the presence of either magnesium or manganese, yielding a cluster of products of around 15 nt in size. A 20U RNA oligonucleotide is cleaved in the presence of manganese but not magnesium
Mn2+
nuclease activity of the enzyme is maximal in the presence of Mg2+ or Mn2+ (5 mM). Mn2+ is bound in the active site located inside the internal tunnel
additional information
Ca2+ does not support the nuclease activity
additional information
-
Ca2+ does not support the nuclease activity
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
evolution
malfunction
physiological function
additional information
evolution
a capsid protein, TTV1 nucleocapsid protein TP1, of a filamentous archaeal virus, Thermoproteus tenax virus 1 (TTV1), evolved relatively recently through exaptation from a CRISPR-associated Cas4 nuclease. The corresponding surface in Cas4 is shielded by the C-terminal domain, suggesting that removal of this domain is a prerequisite for the transformation of the ancestral TTV1 Cas4 into a nucleocapsid protein
evolution
Cas4 proteins exhibit low sequence similarity among themselves and are currently classified into 2 main classes: DUF83 and DUF911. The genome of Sulfolobus solfataricus encodes five Cas4 like protein comprising low sequence similarity (below 30%). Out of them, SSO0001, SSO1392, and SSO1449 belong to DUF83 class, and SSO1391 and SSO1451 belong to DUF911 class. SSO1391 has been reported to show broad range cleavage specificity for cleaving ssDNA in both the directions (5'-3') and (3'-5') (DUF911). By contrast, members of DUF83 class cleave the ssDNA substrate only in the direction 5'-3'. The overall three-dimensional structural fold of DUF83Ss and DUF83Pc appears to be conserved. The separation of Cas4 proteins of DUF83 class into 2 separate branches hints at the possibility of specific sites which guide the evolutionary divergence between Cas4 proteins of the 2 clades, prediction of discriminative motifs among the two subclasses of DUF83 Cas4 proteins through motif analysis, overview. Divergence type I analyses of two clusters and their intra molecular hydrogen bonding with other residues
evolution
Cas4 proteins exhibit low sequence similarity among themselves and are currently classified into 2 main classes: DUF83 and DUF911. The genome of Sulfolobus solfataricus encodes five Cas4 like protein comprising low sequence similarity (below 30%). Out of them, SSO0001, SSO1392, and SSO1449 belong to DUF83 class, and SSO1391 and SSO1451 belong to DUF911 class. SSO1391 has been reported to show broad range cleavage specificity for cleaving ssDNA in both the directions (5'-3') and (3'-5') (DUF911). By contrast, members of DUF83 class cleave the ssDNA substrate only in the direction 5'-3'. The overall three-dimensional structural fold of DUF83Ss and DUF83Pc appears to be conserved. The separation of Cas4 proteins of DUF83 class into 2 separate branches hints at the possibility of specific sites which guide the evolutionary divergence between Cas4 proteins of the 2 clades, prediction of discriminative motifs among the two subclasses of DUF83 Cas4 proteins through motif analysis, overview. Divergence type I analyses of two clusters and their intra molecular hydrogen bonding with other residues
evolution
the Pyrococcus furiosus genome harbors two distinct cas4 genes, one in a cas4-1/ cas1/cas2 operon and the other cas4-2 at a remote location not associated with CRISPR
evolution
-
Cas4 proteins exhibit low sequence similarity among themselves and are currently classified into 2 main classes: DUF83 and DUF911. The genome of Sulfolobus solfataricus encodes five Cas4 like protein comprising low sequence similarity (below 30%). Out of them, SSO0001, SSO1392, and SSO1449 belong to DUF83 class, and SSO1391 and SSO1451 belong to DUF911 class. SSO1391 has been reported to show broad range cleavage specificity for cleaving ssDNA in both the directions (5'-3') and (3'-5') (DUF911). By contrast, members of DUF83 class cleave the ssDNA substrate only in the direction 5'-3'. The overall three-dimensional structural fold of DUF83Ss and DUF83Pc appears to be conserved. The separation of Cas4 proteins of DUF83 class into 2 separate branches hints at the possibility of specific sites which guide the evolutionary divergence between Cas4 proteins of the 2 clades, prediction of discriminative motifs among the two subclasses of DUF83 Cas4 proteins through motif analysis, overview. Divergence type I analyses of two clusters and their intra molecular hydrogen bonding with other residues
-
evolution
-
Cas4 proteins exhibit low sequence similarity among themselves and are currently classified into 2 main classes: DUF83 and DUF911. The genome of Sulfolobus solfataricus encodes five Cas4 like protein comprising low sequence similarity (below 30%). Out of them, SSO0001, SSO1392, and SSO1449 belong to DUF83 class, and SSO1391 and SSO1451 belong to DUF911 class. SSO1391 has been reported to show broad range cleavage specificity for cleaving ssDNA in both the directions (5'-3') and (3'-5') (DUF911). By contrast, members of DUF83 class cleave the ssDNA substrate only in the direction 5'-3'. The overall three-dimensional structural fold of DUF83Ss and DUF83Pc appears to be conserved. The separation of Cas4 proteins of DUF83 class into 2 separate branches hints at the possibility of specific sites which guide the evolutionary divergence between Cas4 proteins of the 2 clades, prediction of discriminative motifs among the two subclasses of DUF83 Cas4 proteins through motif analysis, overview. Divergence type I analyses of two clusters and their intra molecular hydrogen bonding with other residues
-
evolution
-
Cas4 proteins exhibit low sequence similarity among themselves and are currently classified into 2 main classes: DUF83 and DUF911. The genome of Sulfolobus solfataricus encodes five Cas4 like protein comprising low sequence similarity (below 30%). Out of them, SSO0001, SSO1392, and SSO1449 belong to DUF83 class, and SSO1391 and SSO1451 belong to DUF911 class. SSO1391 has been reported to show broad range cleavage specificity for cleaving ssDNA in both the directions (5'-3') and (3'-5') (DUF911). By contrast, members of DUF83 class cleave the ssDNA substrate only in the direction 5'-3'. The overall three-dimensional structural fold of DUF83Ss and DUF83Pc appears to be conserved. The separation of Cas4 proteins of DUF83 class into 2 separate branches hints at the possibility of specific sites which guide the evolutionary divergence between Cas4 proteins of the 2 clades, prediction of discriminative motifs among the two subclasses of DUF83 Cas4 proteins through motif analysis, overview. Divergence type I analyses of two clusters and their intra molecular hydrogen bonding with other residues
-
evolution
-
Cas4 proteins exhibit low sequence similarity among themselves and are currently classified into 2 main classes: DUF83 and DUF911. The genome of Sulfolobus solfataricus encodes five Cas4 like protein comprising low sequence similarity (below 30%). Out of them, SSO0001, SSO1392, and SSO1449 belong to DUF83 class, and SSO1391 and SSO1451 belong to DUF911 class. SSO1391 has been reported to show broad range cleavage specificity for cleaving ssDNA in both the directions (5'-3') and (3'-5') (DUF911). By contrast, members of DUF83 class cleave the ssDNA substrate only in the direction 5'-3'. The overall three-dimensional structural fold of DUF83Ss and DUF83Pc appears to be conserved. The separation of Cas4 proteins of DUF83 class into 2 separate branches hints at the possibility of specific sites which guide the evolutionary divergence between Cas4 proteins of the 2 clades, prediction of discriminative motifs among the two subclasses of DUF83 Cas4 proteins through motif analysis, overview. Divergence type I analyses of two clusters and their intra molecular hydrogen bonding with other residues
-
evolution
-
Cas4 proteins exhibit low sequence similarity among themselves and are currently classified into 2 main classes: DUF83 and DUF911. The genome of Sulfolobus solfataricus encodes five Cas4 like protein comprising low sequence similarity (below 30%). Out of them, SSO0001, SSO1392, and SSO1449 belong to DUF83 class, and SSO1391 and SSO1451 belong to DUF911 class. SSO1391 has been reported to show broad range cleavage specificity for cleaving ssDNA in both the directions (5'-3') and (3'-5') (DUF911). By contrast, members of DUF83 class cleave the ssDNA substrate only in the direction 5'-3'. The overall three-dimensional structural fold of DUF83Ss and DUF83Pc appears to be conserved. The separation of Cas4 proteins of DUF83 class into 2 separate branches hints at the possibility of specific sites which guide the evolutionary divergence between Cas4 proteins of the 2 clades, prediction of discriminative motifs among the two subclasses of DUF83 Cas4 proteins through motif analysis, overview. Divergence type I analyses of two clusters and their intra molecular hydrogen bonding with other residues
-
malfunction
in TTV1, the Cas4 gene has been split into two, with the N-terminal portion becoming TP1, and lost some of the catalytic amino acid residues, apparently resulting in the inactivation of the nuclease
malfunction
while cas4-2 deletion does not increase adaptation frequency overall, it dramatically increases incorporation of the duplexed DNA oligonucleotide. The plasmid-expressed wild-type Cas4-2 rescues spacer sizes and the downstream NW motif, but the nuclease-defective Cas4-2 does not
physiological function
a potential functional role of the enzyme and other Cas4 proteins in CRISPR (Clusters of Regularly interspaced Palindromic Repeats) immunity is based on the presence of 5' to 3' exonuclease and DNA unwinding activities, which produce 3'-ssDNA overhangs as potential intermediates in the process of new spacer addition. The toroidal structures of the enzyme can serve as sliding clamps for other Cas proteins
physiological function
the role of the enzyme in vivo may be to process viral DNA to generate new spacers with 3' ssDNA overhangs suitable for recombination or integration in a CRISPR (Clusters of Regularly interspaced Palindromic Repeats) locus mediated by the enzyme Cas1
physiological function
Halalkalibacterium halodurans
Bacillus halodurans type I-C Cas4 is required for efficient prespacer processing prior to Cas1-Cas2-mediated integration. Cas4, a core family of CRISPR-associated proteins, associates with the Cas1 spacer integrase and is required for efficient prespacer processing during CRISPR-Cas adaptation. Cas4 processing prevents non-functional spacers from being integrated into the CRISPR array, ensuring the fidelity of the adaptation process. Cas4 forms a tight heterohexameric complex with the Cas1 spacer integrase. Mechanism, overview. Cas4 is a Cas1-Cas2-dependent endonuclease that cleaves 3' overhangs of prespacers. Cas4 cleavage is sequence and site-specific and depends on the presence of a protospacer adjacent motif (PAM). Cas4 blocks premature integration of uncleaved prespacers, ensuring spacer fidelity
physiological function
the Cas4 proteins of the CRISPR-Cas systems are thought to be responsible for the adaptation step in the CRISPR (clustered regularly interspaced short palindromic repeats) mechanism
physiological function
the Cas4 proteins of the CRISPR-Cas systems are thought to be responsible for the adaptation step in the CRISPR (clustered regularly interspaced short palindromic repeats) mechanism
physiological function
the nucleocapsid protein (TP1) of Thermoproteus tenax virus 1 (TTV1) is a derivative of the Cas4 nuclease, a component of the CRISPR-Cas adaptive immunity system
physiological function
Halalkalibacterium halodurans
the widespread CRISPR-Cas systems provide adaptive immunity to help prokaryotes fend off invading viruses and mobile elements. CRISPR loci contain arrays of repeats separated by distinct spacers, and CRISPR RNA (crRNA) produced from each spacer guides Cas nuclease complexes to find sequence matches in the invader's genome. A short protospacer-adjacent motif (PAM) that flanks the DNA target licenses crRNA-guided invader destruction. CRISPR-Cas has the ability to generate immunological memory by acquiring new spacers from invaders' DNA in a process known as adaptation. To ensure successful defense, microbes must select PAM-flanking sequences, process them to appropriate sizes, and insert them into CRISPR in the right orientation. The core spacer integration machinery is encoded by cas1 and cas2, two genes universally present in all CRISPR systems
physiological function
the widespread CRISPR-Cas systems provide adaptive immunity to help prokaryotes fend off invading viruses and mobile elements. CRISPR loci contain arrays of repeats separated by distinct spacers, and CRISPR RNA (crRNA) produced from each spacer guides Cas nuclease complexes to find sequence matches in the invader's genome. A short protospacer-adjacent motif (PAM) that flanks the DNA target licenses crRNA-guided invader destruction. CRISPR-Cas has the ability to generate immunological memory by acquiring new spacers from invaders' DNA in a process known as adaptation. To ensure successful defense, microbes must select PAM-flanking sequences, process them to appropriate sizes, and insert them into CRISPR in the right orientation. The core spacer integration machinery is encoded by cas1 and cas2, two genes universally present in all CRISPR systems. Cas4 selects PAM-compliant spacers. Gene cas4-1 is genetically required to specify the 5' PAM for new spacers, whereas cas4-2 determines the weak NW motif
physiological function
the widespread CRISPR-Cas systems provide adaptive immunity to help prokaryotes fend off invading viruses and mobile elements. CRISPR loci contain arrays of repeats separated by distinct spacers, and CRISPR RNA (crRNA) produced from each spacer guides Cas nuclease complexes to find sequence matches in the invader's genome. A short protospacer-adjacent motif (PAM) that flanks the DNA target licenses crRNA-guided invader destruction. CRISPR-Cas has the ability to generate immunological memory by acquiring new spacers from invaders' DNA in a process known as adaptation. To ensure successful defense, microbes must select PAM-flanking sequences, process them to appropriate sizes, and insert them into CRISPR in the right orientation. The core spacer integration machinery is encoded by cas1 and cas2, two genes universally present in all CRISPR systems. For the type I-E CRISPR native to Escherichia coli, cas1 and cas2 are necessary and sufficient to drive adaptation
physiological function
the widespread CRISPR-Cas systems provide adaptive immunity to help prokaryotes fend off invading viruses and mobile elements. CRISPR loci contain arrays of repeats separated by distinct spacers, and CRISPR RNA (crRNA) produced from each spacer guides Cas nuclease complexes to find sequence matches in the invader's genome. A short protospacer-adjacent motif (PAM) that flanks the DNA target licenses crRNA-guided invader destruction. CRISPR-Cas has the ability to generate immunological memory by acquiring new spacers from invaders' DNA in a process known as adaptation. To ensure successful defense, microbes must select PAM-flanking sequences, process them to appropriate sizes, and insert them into CRISPR in the right orientation. The core spacer integration machinery is encoded by cas1 and cas2, two genes universally present in all CRISPR systems. Type I-D CRISPR of Synechocystis relies on its sole Cas4 to select PAM-compliant spacers, examining the strandedness of PAM recognition during acquisition
physiological function
two distinct Cas4 nucleases are essential for CRISPR DNA acquisition in Pyrococcus furiosus. Cas4-1 defines the 5' NGG PAM, and Cas4-2 defines the 3' NW motif. Cas4-1 and Cas4-2 nucleases trim opposite ends of prespacer DNA to the correct size. Both Cas4 proteins direct integration of DNA in the correct orientation for immunity. The concerted action of two different Cas4 nucleases is required for protospace adjacent motif (PAM) definition, prespacer processing, and integration of DNA fragments at the CRISPR array in a functional orientation. Pyrococcus furiosus actively takes up spacers into each CRISPR locus in a PAM-dependent manner. Adaptation occurs under normal growth conditions, and the frequency of adaptation can be increased by overexpression of Cas1, Cas2, and Cas4 proteins. Cas4-1 and Cas4-2 nuclease activity is essential for PAM recognition and spacer sizing
physiological function
two distinct Cas4 nucleases are essential for CRISPR DNA acquisition in Pyrococcus furiosus. Cas4-1 defines the 5' NGG PAM, and Cas4-2 defines the 3' NW motif. Cas4-1 and Cas4-2 nucleases trim opposite ends of prespacer DNA to the correct size. Both Cas4 proteins direct integration of DNA in the correct orientation for immunity. The concerted action of two different Cas4 nucleases is required for protospacer adjacent motif (PAM) definition, prespacer processing, and integration of DNA fragments at the CRISPR array in a functional orientation. Pyrococcus furiosus actively takes up spacers into each CRISPR locus in a PAM-dependent manner. Adaptation occurs under normal growth conditions, and the frequency of adaptation can be increased by overexpression of Cas1, Cas2, and Cas4 proteins. Cas4-1 and Cas4-2 nuclease activity is essential for PAM recognition and spacer sizing
physiological function
-
a potential functional role of the enzyme and other Cas4 proteins in CRISPR (Clusters of Regularly interspaced Palindromic Repeats) immunity is based on the presence of 5' to 3' exonuclease and DNA unwinding activities, which produce 3'-ssDNA overhangs as potential intermediates in the process of new spacer addition. The toroidal structures of the enzyme can serve as sliding clamps for other Cas proteins
-
physiological function
-
the role of the enzyme in vivo may be to process viral DNA to generate new spacers with 3' ssDNA overhangs suitable for recombination or integration in a CRISPR (Clusters of Regularly interspaced Palindromic Repeats) locus mediated by the enzyme Cas1
-
physiological function
-
the Cas4 proteins of the CRISPR-Cas systems are thought to be responsible for the adaptation step in the CRISPR (clustered regularly interspaced short palindromic repeats) mechanism
-
physiological function
Halalkalibacterium halodurans ATCC BAA-125
-
Bacillus halodurans type I-C Cas4 is required for efficient prespacer processing prior to Cas1-Cas2-mediated integration. Cas4, a core family of CRISPR-associated proteins, associates with the Cas1 spacer integrase and is required for efficient prespacer processing during CRISPR-Cas adaptation. Cas4 processing prevents non-functional spacers from being integrated into the CRISPR array, ensuring the fidelity of the adaptation process. Cas4 forms a tight heterohexameric complex with the Cas1 spacer integrase. Mechanism, overview. Cas4 is a Cas1-Cas2-dependent endonuclease that cleaves 3' overhangs of prespacers. Cas4 cleavage is sequence and site-specific and depends on the presence of a protospacer adjacent motif (PAM). Cas4 blocks premature integration of uncleaved prespacers, ensuring spacer fidelity
-
physiological function
Halalkalibacterium halodurans JCM 9153
-
Bacillus halodurans type I-C Cas4 is required for efficient prespacer processing prior to Cas1-Cas2-mediated integration. Cas4, a core family of CRISPR-associated proteins, associates with the Cas1 spacer integrase and is required for efficient prespacer processing during CRISPR-Cas adaptation. Cas4 processing prevents non-functional spacers from being integrated into the CRISPR array, ensuring the fidelity of the adaptation process. Cas4 forms a tight heterohexameric complex with the Cas1 spacer integrase. Mechanism, overview. Cas4 is a Cas1-Cas2-dependent endonuclease that cleaves 3' overhangs of prespacers. Cas4 cleavage is sequence and site-specific and depends on the presence of a protospacer adjacent motif (PAM). Cas4 blocks premature integration of uncleaved prespacers, ensuring spacer fidelity
-
physiological function
Halalkalibacterium halodurans FERM 7344
-
Bacillus halodurans type I-C Cas4 is required for efficient prespacer processing prior to Cas1-Cas2-mediated integration. Cas4, a core family of CRISPR-associated proteins, associates with the Cas1 spacer integrase and is required for efficient prespacer processing during CRISPR-Cas adaptation. Cas4 processing prevents non-functional spacers from being integrated into the CRISPR array, ensuring the fidelity of the adaptation process. Cas4 forms a tight heterohexameric complex with the Cas1 spacer integrase. Mechanism, overview. Cas4 is a Cas1-Cas2-dependent endonuclease that cleaves 3' overhangs of prespacers. Cas4 cleavage is sequence and site-specific and depends on the presence of a protospacer adjacent motif (PAM). Cas4 blocks premature integration of uncleaved prespacers, ensuring spacer fidelity
-
physiological function
-
the Cas4 proteins of the CRISPR-Cas systems are thought to be responsible for the adaptation step in the CRISPR (clustered regularly interspaced short palindromic repeats) mechanism
-
physiological function
Halalkalibacterium halodurans C-125
-
Bacillus halodurans type I-C Cas4 is required for efficient prespacer processing prior to Cas1-Cas2-mediated integration. Cas4, a core family of CRISPR-associated proteins, associates with the Cas1 spacer integrase and is required for efficient prespacer processing during CRISPR-Cas adaptation. Cas4 processing prevents non-functional spacers from being integrated into the CRISPR array, ensuring the fidelity of the adaptation process. Cas4 forms a tight heterohexameric complex with the Cas1 spacer integrase. Mechanism, overview. Cas4 is a Cas1-Cas2-dependent endonuclease that cleaves 3' overhangs of prespacers. Cas4 cleavage is sequence and site-specific and depends on the presence of a protospacer adjacent motif (PAM). Cas4 blocks premature integration of uncleaved prespacers, ensuring spacer fidelity
-
physiological function
Halalkalibacterium halodurans DSM 18197
-
Bacillus halodurans type I-C Cas4 is required for efficient prespacer processing prior to Cas1-Cas2-mediated integration. Cas4, a core family of CRISPR-associated proteins, associates with the Cas1 spacer integrase and is required for efficient prespacer processing during CRISPR-Cas adaptation. Cas4 processing prevents non-functional spacers from being integrated into the CRISPR array, ensuring the fidelity of the adaptation process. Cas4 forms a tight heterohexameric complex with the Cas1 spacer integrase. Mechanism, overview. Cas4 is a Cas1-Cas2-dependent endonuclease that cleaves 3' overhangs of prespacers. Cas4 cleavage is sequence and site-specific and depends on the presence of a protospacer adjacent motif (PAM). Cas4 blocks premature integration of uncleaved prespacers, ensuring spacer fidelity
-
physiological function
-
the Cas4 proteins of the CRISPR-Cas systems are thought to be responsible for the adaptation step in the CRISPR (clustered regularly interspaced short palindromic repeats) mechanism
-
physiological function
-
the Cas4 proteins of the CRISPR-Cas systems are thought to be responsible for the adaptation step in the CRISPR (clustered regularly interspaced short palindromic repeats) mechanism
-
physiological function
-
the Cas4 proteins of the CRISPR-Cas systems are thought to be responsible for the adaptation step in the CRISPR (clustered regularly interspaced short palindromic repeats) mechanism
-
additional information
three-dimensional structure modelling
additional information
analysis of protospace adjacent motif (PAM) sequence recognition by the Cas4 isozymes, overview
additional information
analysis of protospace adjacent motif (PAM) sequence recognition by the Cas4 isozymes, overview
additional information
-
analysis of protospace adjacent motif (PAM) sequence recognition by the Cas4 isozymes, overview
additional information
Halalkalibacterium halodurans
Cas4 forms a tight complex with Cas1 in vitro, compatible with the fact that the cas4 gene is usually encoded next to or in fusion with cas1
Show AA Sequence and Transmembrane Helices (6985 entries)
Longer loading times are possible. Please use the AA Sequence and Transmembrane Helices Search for a specific query.
Longer loading times are possible. Please use the AA Sequence and Transmembrane Helices Search for a specific query.
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
PDB
SCOP
CATH
UNIPROT
ORGANISM
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
decamer
additional information
decamer
crystallized at room temperature using the sitting drop vapour diffusion method. The crystal structure reveals a decameric toroid with a large 55 A diameter central channel formed by five tightly packed dimers
decamer
-
crystallized at room temperature using the sitting drop vapour diffusion method. The crystal structure reveals a decameric toroid with a large 55 A diameter central channel formed by five tightly packed dimers
-
additional information
Halalkalibacterium halodurans
Cas4 forms a tight heterohexameric complex with the Cas1 spacer integrase containing two Cas1 dimers and two Cas4 subunits
additional information
Halalkalibacterium halodurans ATCC BAA-125
-
Cas4 forms a tight heterohexameric complex with the Cas1 spacer integrase containing two Cas1 dimers and two Cas4 subunits
-
additional information
Halalkalibacterium halodurans C-125
-
Cas4 forms a tight heterohexameric complex with the Cas1 spacer integrase containing two Cas1 dimers and two Cas4 subunits
-
additional information
Halalkalibacterium halodurans DSM 18197
-
Cas4 forms a tight heterohexameric complex with the Cas1 spacer integrase containing two Cas1 dimers and two Cas4 subunits
-
additional information
Halalkalibacterium halodurans FERM 7344
-
Cas4 forms a tight heterohexameric complex with the Cas1 spacer integrase containing two Cas1 dimers and two Cas4 subunits
-
additional information
Halalkalibacterium halodurans JCM 9153
-
Cas4 forms a tight heterohexameric complex with the Cas1 spacer integrase containing two Cas1 dimers and two Cas4 subunits
-
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
the crystal structure reveals a decameric toroid with a large 55 A diameter central channel formed by five tightly packed dimers
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
C188A
the mutant protein is inactive in both binding and cleavage of ssDNA. It forms various protein aggregates
C191A
the mutant protein is inactive in both binding and cleavage of ssDNA. It forms various protein aggregates
C32A
the mutant protein is inactive in both binding and cleavage of ssDNA. It forms various protein aggregates
D99A
C188A
-
the mutant protein is inactive in both binding and cleavage of ssDNA. It forms various protein aggregates
-
C191A
-
the mutant protein is inactive in both binding and cleavage of ssDNA. It forms various protein aggregates
-
C32A
-
the mutant protein is inactive in both binding and cleavage of ssDNA. It forms various protein aggregates
-
D99A
additional information
additional information
determining genetic requirement for in vivo adaptation by analyzing mutant strains lacking cas4-1 and cas4-2 individually or simultaneously, phenotypes. Adaptation is reduced, but not completely prevented, by deletion of either or both of the cas4 genes. Strikingly, longer spacers around 40-70 base pairs (bp) in length are acquired in the double deletion strain as opposed to only about 37 bp in wild-type
additional information
determining genetic requirement for in vivo adaptation by analyzing mutant strains lacking cas4-1 and cas4-2 individually or simultaneously, phenotypes. Adaptation is reduced, but not completely prevented, by deletion of either or both of the cas4 genes. Strikingly, longer spacers around 40-70 base pairs (bp) in length are acquired in the double deletion strain as opposed to only about 37 bp in wild-type
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.