restriction endonuclease [Akkermansia muciniphila]
Protein Classification
List of domain hits
| Name | Accession | Description | Interval | E-value | ||||
| PLDc_SF super family | cl15239 | Catalytic domain of phospholipase D superfamily proteins; Catalytic domain of phospholipase D ... |
2-162 | 1.57e-93 | ||||
Catalytic domain of phospholipase D superfamily proteins; Catalytic domain of phospholipase D (PLD) superfamily proteins. The PLD superfamily is composed of a large and diverse group of proteins including plant, mammalian and bacterial PLDs, bacterial cardiolipin (CL) synthases, bacterial phosphatidylserine synthases (PSS), eukaryotic phosphatidylglycerophosphate (PGP) synthase, eukaryotic tyrosyl-DNA phosphodiesterase 1 (Tdp1), and some bacterial endonucleases (Nuc and BfiI), among others. PLD enzymes hydrolyze phospholipid phosphodiester bonds to yield phosphatidic acid and a free polar head group. They can also catalyze the transphosphatidylation of phospholipids to acceptor alcohols. The majority of members in this superfamily contain a short conserved sequence motif (H-x-K-x(4)-D, where x represents any amino acid residue), called the HKD signature motif. There are varying expanded forms of this motif in different family members. Some members contain variant HKD motifs. Most PLD enzymes are monomeric proteins with two HKD motif-containing domains. Two HKD motifs from two domains form a single active site. Some PLD enzymes have only one copy of the HKD motif per subunit but form a functionally active dimer, which has a single active site at the dimer interface containing the two HKD motifs from both subunits. Different PLD enzymes may have evolved through domain fusion of a common catalytic core with separate substrate recognition domains. Despite their various catalytic functions and a very broad range of substrate specificities, the diverse group of PLD enzymes can bind to a phosphodiester moiety. Most of them are active as bi-lobed monomers or dimers, and may possess similar core structures for catalytic activity. They are generally thought to utilize a common two-step ping-pong catalytic mechanism, involving an enzyme-substrate intermediate, to cleave phosphodiester bonds. The two histidine residues from the two HKD motifs play key roles in the catalysis. Upon substrate binding, a histidine from one HKD motif could function as the nucleophile, attacking the phosphodiester bond to create a covalent phosphohistidine intermediate, while the other histidine residue from the second HKD motif could serve as a general acid, stabilizing the leaving group. The actual alignment was detected with superfamily member cd09175: Pssm-ID: 472788 Cd Length: 161 Bit Score: 275.93 E-value: 1.57e-93
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| BfiI_C_EcoRII_N_B3 super family | cl15242 | DNA binding domains of BfiI, EcoRII and plant B3 proteins; This family contains the N-terminal ... |
201-355 | 7.00e-79 | ||||
DNA binding domains of BfiI, EcoRII and plant B3 proteins; This family contains the N-terminal DNA binding domain of type IIE restriction endonuclease EcoRII-like proteins, the C-terminal DNA binding domain of type IIS restriction endonuclease BfiI-like proteins and plant-specific B3 proteins. Type II restriction endonucleases are components of restriction modification (RM) systems that protect bacteria and archaea against invading foreign DNA. They usually function as homodimers or homotetramers that cleave DNA at defined sites of 4 to 8 bp in length, and they require Mg2+, not ATP or GTP, for catalysis. EcoRII is specific for the 5'-CCWGG sequence (W stands for A or T). EcoRII consists of 2 domains, the C-terminal catalytic/dimerization domain (EcoRII-C), and the N-terminal effector DNA binding domain (EcoRII-N). BfiI is unique in cleaving DNA at fixed positions downstream of an asymmetric sequence in the absence of Mg2+. BfiI consists of two discrete domains with distinct functions: an N-terminal catalytic domain with non-specific nuclease activity and dimerization function that is more closely related to Nuc, an EDTA-resistant nuclease from the phospholipase D (PLD) superfamily; and a C-terminal domain that specifically recognizes its target sequences, 5'-ACTGGG-3'. B3 proteins are a family of plant-specific transcription factors, involved in a great variety of processes, including seed development and auxin response. The actual alignment was detected with superfamily member cd10018: Pssm-ID: 449517 Cd Length: 157 Bit Score: 238.60 E-value: 7.00e-79
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| Name | Accession | Description | Interval | E-value | ||||
| PLDc_Bfil | cd09175 | Catalytic domain of type IIs restriction endonuclease BfiI and similar proteins; Catalytic ... |
2-162 | 1.57e-93 | ||||
Catalytic domain of type IIs restriction endonuclease BfiI and similar proteins; Catalytic domain of a novel type IIs restriction endonuclease BfiI and similar proteins. Type II restriction endonucleases are components of restriction modification (RM) systems that protect bacteria and archaea against invading foreign DNA. They usually function as homodimers or homotetramers that cleave DNA at defined sites of 4 to 8 bp in length, and they require Mg2+, not ATP or GTP, for catalysis. Unlike all other restriction enzymes known to date, BfiI is unique in cleaving DNA at fixed positions downstream of an asymmetric sequence in the absence of Mg2+. BfiI consists of two discrete domains with distinct functions: an N-terminal catalytic domain with non-specific nuclease activity and dimerization function that is more closely related to Nuc, an EDTA-resistant nuclease from the phospholipase D (PLD) superfamily; and a C-terminal domain that specifically recognizes its target sequences, 5'-ACTGGG-3'. BfiI presumably evolved through domain fusion of a DNA recognition domain to the catalytic Nuc-like domain from the PLD superfamily. Most PLD enzymes have two copies of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) in a single polypeptide chain and both are required for catalytic activity. However, BfiI contains only one HKD motif per protein chain and forms a functionally active homodimer which has two DNA-binding surfaces located at the C-terminal domains but only one active site, located at the dimer interface between the two N-terminal catalytic domains that contain the two HKD motifs from both subunits. BfiI utilizes a single active site to cut both DNA strands, which represents a novel mechanism for the scission of double-stranded DNA. It uses a histidine residue from the HKD motif in one subunit as the nucleophile for the cleavage of the target phosphodiester bond in both of the anti-parallel DNA strands, while the symmetrically-related histidine residue from the HKD motif of the opposite subunit acts as the proton donor/acceptor during both strand-scission events. Pssm-ID: 197272 Cd Length: 161 Bit Score: 275.93 E-value: 1.57e-93
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| BfiI_C | cd10018 | C-terminal domain of type IIs restriction endonuclease BfiI and similar proteins; C-terminal ... |
201-355 | 7.00e-79 | ||||
C-terminal domain of type IIs restriction endonuclease BfiI and similar proteins; C-terminal domain of a novel type IIs restriction endonuclease BfiI and similar proteins. Type II restriction endonucleases are components of restriction modification (RM) systems that protect bacteria and archaea against invading foreign DNA. They usually function as homodimers or homotetramers that cleave DNA at defined sites of 4 to 8 bp in length, and they require Mg2+, not ATP or GTP, for catalysis. Unlike all other restriction enzymes known to date, BfiI is unique in cleaving DNA at fixed positions downstream of an asymmetric sequence in the absence of Mg2+. BfiI consists of two discrete domains with distinct functions: an N-terminal catalytic domain with non-specific nuclease activity and dimerization function that is more closely related to Nuc, an EDTA-resistant nuclease from the phospholipase D (PLD) superfamily; and a C-terminal domain that specifically recognizes its target sequences, 5'-ACTGGG-3'. BfiI presumably evolved through domain fusion of a DNA recognition domain to the catalytic Nuc-like domain from the PLD superfamily. BfiI forms a functionally active homodimer which has two DNA-binding surfaces located at the C-terminal domains but only one active site, located at the dimer interface between the two N-terminal catalytic domains. Pssm-ID: 197384 Cd Length: 157 Bit Score: 238.60 E-value: 7.00e-79
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| BfiI_DBD | pfam18243 | Metal-independent restriction enzyme BfiI DNA binding domain; This domain is found in the ... |
195-355 | 1.98e-74 | ||||
Metal-independent restriction enzyme BfiI DNA binding domain; This domain is found in the metal-independent restriction enzyme BfiI present in Bacillus firmus. This domain is found in the C-terminal of the protein and is responsible for DNA binding. The domain exhibits a beta-barrel-like structure similar to the effector DNA-binding domain of the Mg2+ dependent restriction enzyme EcoRII and to the B3-like DNA-binding domain of plant transcription factors. Pssm-ID: 436364 Cd Length: 165 Bit Score: 227.59 E-value: 1.98e-74
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| DISARM_DrmC_I | NF038319 | DISARM system phospholipase D-like protein DrmC; DrmC, a phospholipase D (PLD) ... |
103-148 | 6.13e-04 | ||||
DISARM system phospholipase D-like protein DrmC; DrmC, a phospholipase D (PLD) domain-containing protein, is a component of DISARM (Defence Island System Associated with Restriction Modification). This HMM represents most but not all DrmC of class I DISARM systems, which contain a DNA adenine N6 methyltransferase. DrmC appears to be an auxiliary rather than core component of DISARM, required for resistance to some phage but not others. Pssm-ID: 468473 [Multi-domain] Cd Length: 234 Bit Score: 40.63 E-value: 6.13e-04
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| PLDc_2 | pfam13091 | PLD-like domain; |
85-145 | 6.96e-04 | ||||
PLD-like domain; Pssm-ID: 463784 [Multi-domain] Cd Length: 132 Bit Score: 39.20 E-value: 6.96e-04
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| Name | Accession | Description | Interval | E-value | ||||
| PLDc_Bfil | cd09175 | Catalytic domain of type IIs restriction endonuclease BfiI and similar proteins; Catalytic ... |
2-162 | 1.57e-93 | ||||
Catalytic domain of type IIs restriction endonuclease BfiI and similar proteins; Catalytic domain of a novel type IIs restriction endonuclease BfiI and similar proteins. Type II restriction endonucleases are components of restriction modification (RM) systems that protect bacteria and archaea against invading foreign DNA. They usually function as homodimers or homotetramers that cleave DNA at defined sites of 4 to 8 bp in length, and they require Mg2+, not ATP or GTP, for catalysis. Unlike all other restriction enzymes known to date, BfiI is unique in cleaving DNA at fixed positions downstream of an asymmetric sequence in the absence of Mg2+. BfiI consists of two discrete domains with distinct functions: an N-terminal catalytic domain with non-specific nuclease activity and dimerization function that is more closely related to Nuc, an EDTA-resistant nuclease from the phospholipase D (PLD) superfamily; and a C-terminal domain that specifically recognizes its target sequences, 5'-ACTGGG-3'. BfiI presumably evolved through domain fusion of a DNA recognition domain to the catalytic Nuc-like domain from the PLD superfamily. Most PLD enzymes have two copies of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) in a single polypeptide chain and both are required for catalytic activity. However, BfiI contains only one HKD motif per protein chain and forms a functionally active homodimer which has two DNA-binding surfaces located at the C-terminal domains but only one active site, located at the dimer interface between the two N-terminal catalytic domains that contain the two HKD motifs from both subunits. BfiI utilizes a single active site to cut both DNA strands, which represents a novel mechanism for the scission of double-stranded DNA. It uses a histidine residue from the HKD motif in one subunit as the nucleophile for the cleavage of the target phosphodiester bond in both of the anti-parallel DNA strands, while the symmetrically-related histidine residue from the HKD motif of the opposite subunit acts as the proton donor/acceptor during both strand-scission events. Pssm-ID: 197272 Cd Length: 161 Bit Score: 275.93 E-value: 1.57e-93
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| BfiI_C | cd10018 | C-terminal domain of type IIs restriction endonuclease BfiI and similar proteins; C-terminal ... |
201-355 | 7.00e-79 | ||||
C-terminal domain of type IIs restriction endonuclease BfiI and similar proteins; C-terminal domain of a novel type IIs restriction endonuclease BfiI and similar proteins. Type II restriction endonucleases are components of restriction modification (RM) systems that protect bacteria and archaea against invading foreign DNA. They usually function as homodimers or homotetramers that cleave DNA at defined sites of 4 to 8 bp in length, and they require Mg2+, not ATP or GTP, for catalysis. Unlike all other restriction enzymes known to date, BfiI is unique in cleaving DNA at fixed positions downstream of an asymmetric sequence in the absence of Mg2+. BfiI consists of two discrete domains with distinct functions: an N-terminal catalytic domain with non-specific nuclease activity and dimerization function that is more closely related to Nuc, an EDTA-resistant nuclease from the phospholipase D (PLD) superfamily; and a C-terminal domain that specifically recognizes its target sequences, 5'-ACTGGG-3'. BfiI presumably evolved through domain fusion of a DNA recognition domain to the catalytic Nuc-like domain from the PLD superfamily. BfiI forms a functionally active homodimer which has two DNA-binding surfaces located at the C-terminal domains but only one active site, located at the dimer interface between the two N-terminal catalytic domains. Pssm-ID: 197384 Cd Length: 157 Bit Score: 238.60 E-value: 7.00e-79
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| BfiI_DBD | pfam18243 | Metal-independent restriction enzyme BfiI DNA binding domain; This domain is found in the ... |
195-355 | 1.98e-74 | ||||
Metal-independent restriction enzyme BfiI DNA binding domain; This domain is found in the metal-independent restriction enzyme BfiI present in Bacillus firmus. This domain is found in the C-terminal of the protein and is responsible for DNA binding. The domain exhibits a beta-barrel-like structure similar to the effector DNA-binding domain of the Mg2+ dependent restriction enzyme EcoRII and to the B3-like DNA-binding domain of plant transcription factors. Pssm-ID: 436364 Cd Length: 165 Bit Score: 227.59 E-value: 1.98e-74
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| BfiI_C_EcoRII_N_B3 | cd10015 | DNA binding domains of BfiI, EcoRII and plant B3 proteins; This family contains the N-terminal ... |
201-318 | 1.34e-22 | ||||
DNA binding domains of BfiI, EcoRII and plant B3 proteins; This family contains the N-terminal DNA binding domain of type IIE restriction endonuclease EcoRII-like proteins, the C-terminal DNA binding domain of type IIS restriction endonuclease BfiI-like proteins and plant-specific B3 proteins. Type II restriction endonucleases are components of restriction modification (RM) systems that protect bacteria and archaea against invading foreign DNA. They usually function as homodimers or homotetramers that cleave DNA at defined sites of 4 to 8 bp in length, and they require Mg2+, not ATP or GTP, for catalysis. EcoRII is specific for the 5'-CCWGG sequence (W stands for A or T). EcoRII consists of 2 domains, the C-terminal catalytic/dimerization domain (EcoRII-C), and the N-terminal effector DNA binding domain (EcoRII-N). BfiI is unique in cleaving DNA at fixed positions downstream of an asymmetric sequence in the absence of Mg2+. BfiI consists of two discrete domains with distinct functions: an N-terminal catalytic domain with non-specific nuclease activity and dimerization function that is more closely related to Nuc, an EDTA-resistant nuclease from the phospholipase D (PLD) superfamily; and a C-terminal domain that specifically recognizes its target sequences, 5'-ACTGGG-3'. B3 proteins are a family of plant-specific transcription factors, involved in a great variety of processes, including seed development and auxin response. Pssm-ID: 197381 Cd Length: 109 Bit Score: 91.16 E-value: 1.34e-22
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| PLDc_Bfil_DEXD_like | cd09117 | Catalytic domain of type II restriction endonucleases BfiI and NgoFVII, and uncharacterized ... |
27-140 | 8.84e-13 | ||||
Catalytic domain of type II restriction endonucleases BfiI and NgoFVII, and uncharacterized proteins with a DEAD domain; Catalytic domain of type II restriction endonucleases BfiI and NgoFVII, uncharacterized type III restriction endonuclease Res subunit, and uncharacterized DNA/RNA helicase superfamily II members. Proteins in this family are found mainly in prokaryotes. They contain one copy of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) in a single polypeptide chain, and have been classified as members of the phospholipase D (PLD, EC 3.1.4.4) superfamily. BfiI consists of two discrete domains with distinct functions: an N-terminal catalytic domain with non-specific nuclease activity and dimerization function that is more closely related to Nuc, an EDTA-resistant nuclease from the phospholipase D (PLD) superfamily; and a C-terminal domain that specifically recognizes its target sequences, 5'-ACTGGG-3'. BfiI forms a functionally active homodimer which has two DNA-binding surfaces located at the C-terminal domains but only one active site, located at the dimer interface between the two N-terminal catalytic domains that contain the two HKD motifs from both subunits. BfiI utilizes a single active site to cut both DNA strands, which represents a novel mechanism for the scission of double-stranded DNA. It uses a histidine residue from the HKD motif in one subunit as the nucleophile for the cleavage of the target phosphodiester bond in both of the anti-parallel DNA strands, while the symmetrically-related histidine residue from the HKD motif of the opposite subunit acts as the proton donor/acceptor during both strand-scission events. Pssm-ID: 197216 [Multi-domain] Cd Length: 117 Bit Score: 64.34 E-value: 8.84e-13
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| PLDc_SF | cd00138 | Catalytic domain of phospholipase D superfamily proteins; Catalytic domain of phospholipase D ... |
16-140 | 5.10e-06 | ||||
Catalytic domain of phospholipase D superfamily proteins; Catalytic domain of phospholipase D (PLD) superfamily proteins. The PLD superfamily is composed of a large and diverse group of proteins including plant, mammalian and bacterial PLDs, bacterial cardiolipin (CL) synthases, bacterial phosphatidylserine synthases (PSS), eukaryotic phosphatidylglycerophosphate (PGP) synthase, eukaryotic tyrosyl-DNA phosphodiesterase 1 (Tdp1), and some bacterial endonucleases (Nuc and BfiI), among others. PLD enzymes hydrolyze phospholipid phosphodiester bonds to yield phosphatidic acid and a free polar head group. They can also catalyze the transphosphatidylation of phospholipids to acceptor alcohols. The majority of members in this superfamily contain a short conserved sequence motif (H-x-K-x(4)-D, where x represents any amino acid residue), called the HKD signature motif. There are varying expanded forms of this motif in different family members. Some members contain variant HKD motifs. Most PLD enzymes are monomeric proteins with two HKD motif-containing domains. Two HKD motifs from two domains form a single active site. Some PLD enzymes have only one copy of the HKD motif per subunit but form a functionally active dimer, which has a single active site at the dimer interface containing the two HKD motifs from both subunits. Different PLD enzymes may have evolved through domain fusion of a common catalytic core with separate substrate recognition domains. Despite their various catalytic functions and a very broad range of substrate specificities, the diverse group of PLD enzymes can bind to a phosphodiester moiety. Most of them are active as bi-lobed monomers or dimers, and may possess similar core structures for catalytic activity. They are generally thought to utilize a common two-step ping-pong catalytic mechanism, involving an enzyme-substrate intermediate, to cleave phosphodiester bonds. The two histidine residues from the two HKD motifs play key roles in the catalysis. Upon substrate binding, a histidine from one HKD motif could function as the nucleophile, attacking the phosphodiester bond to create a covalent phosphohistidine intermediate, while the other histidine residue from the second HKD motif could serve as a general acid, stabilizing the leaving group. Pssm-ID: 197200 [Multi-domain] Cd Length: 119 Bit Score: 45.20 E-value: 5.10e-06
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| PLDc_unchar4 | cd09132 | Putative catalytic domain of uncharacterized phospholipase D-like proteins; Putative catalytic ... |
103-140 | 2.98e-05 | ||||
Putative catalytic domain of uncharacterized phospholipase D-like proteins; Putative catalytic domain of uncharacterized phospholipase D (PLD, EC 3.1.4.4)-like proteins. Members of this subfamily contain one copy of HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) that characterizes the PLD superfamily. Pssm-ID: 197230 [Multi-domain] Cd Length: 122 Bit Score: 43.03 E-value: 2.98e-05
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| PLDc_unchar6 | cd09176 | Putative catalytic domain of uncharacterized hypothetical proteins with one or two copies of ... |
97-138 | 2.96e-04 | ||||
Putative catalytic domain of uncharacterized hypothetical proteins with one or two copies of the HKD motif; Putative catalytic domain of uncharacterized hypothetical proteins with similarity to phospholipase D (PLD, EC 3.1.4.4). PLD enzymes hydrolyze phospholipid phosphodiester bonds to yield phosphatidic acid and a free polar head group. They can also catalyze transphosphatidylation of phospholipids to acceptor alcohols. Members of this subfamily contain one or two copies of the HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) that characterizes the PLD superfamily. Pssm-ID: 197273 [Multi-domain] Cd Length: 114 Bit Score: 40.02 E-value: 2.96e-04
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| DISARM_DrmC_I | NF038319 | DISARM system phospholipase D-like protein DrmC; DrmC, a phospholipase D (PLD) ... |
103-148 | 6.13e-04 | ||||
DISARM system phospholipase D-like protein DrmC; DrmC, a phospholipase D (PLD) domain-containing protein, is a component of DISARM (Defence Island System Associated with Restriction Modification). This HMM represents most but not all DrmC of class I DISARM systems, which contain a DNA adenine N6 methyltransferase. DrmC appears to be an auxiliary rather than core component of DISARM, required for resistance to some phage but not others. Pssm-ID: 468473 [Multi-domain] Cd Length: 234 Bit Score: 40.63 E-value: 6.13e-04
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| PLDc_2 | pfam13091 | PLD-like domain; |
85-145 | 6.96e-04 | ||||
PLD-like domain; Pssm-ID: 463784 [Multi-domain] Cd Length: 132 Bit Score: 39.20 E-value: 6.96e-04
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| PLDc_N_Snf2_like | cd09178 | N-terminal putative catalytic domain of uncharacterized HKD family nucleases fused to putative ... |
99-135 | 4.93e-03 | ||||
N-terminal putative catalytic domain of uncharacterized HKD family nucleases fused to putative helicases from the Snf2-like family; N-terminal putative catalytic domain of uncharacterized archaeal and prokaryotic HKD family nucleases fused to putative helicases from the Snf2-like family, which belong to the DNA/RNA helicase superfamily II (SF2). Although Snf2-like family enzymes do not possess helicase activity, they contain a helicase-like region, where seven helicase-related sequence motifs are found, similar to those in DEAD/DEAH box helicases, which represent the biggest family within the SF2 superfamily. In addition to the helicase-like region, members of this family also contain an N-terminal putative catalytic domain with one copy of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue), and have been classified as members of the phospholipase D (PLD, EC 3.1.4.4) superfamily. Pssm-ID: 197275 [Multi-domain] Cd Length: 134 Bit Score: 36.76 E-value: 4.93e-03
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| Blast search parameters | ||||
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