5'-3' exonuclease H3TH domain-containing protein [Duganella sp. CF517]
Protein Classification
5'-3' exonuclease( domain architecture ID 11415718)
5'-3' exonuclease removes the RNA primers at the 5' ends of newly synthesized DNA so that the polymerase activity can fill in the resulting gaps
List of domain hits
| Name | Accession | Description | Interval | E-value | |||||
| ExoIX | COG0258 | 5'-3' exonuclease Xni/ExoIX (flap endonuclease) [Replication, recombination and repair]; |
1-255 | 4.42e-77 | |||||
5'-3' exonuclease Xni/ExoIX (flap endonuclease) [Replication, recombination and repair]; : Pssm-ID: 440028 [Multi-domain] Cd Length: 286 Bit Score: 234.92 E-value: 4.42e-77
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| Name | Accession | Description | Interval | E-value | |||||
| ExoIX | COG0258 | 5'-3' exonuclease Xni/ExoIX (flap endonuclease) [Replication, recombination and repair]; |
1-255 | 4.42e-77 | |||||
5'-3' exonuclease Xni/ExoIX (flap endonuclease) [Replication, recombination and repair]; Pssm-ID: 440028 [Multi-domain] Cd Length: 286 Bit Score: 234.92 E-value: 4.42e-77
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| PRK09482 | PRK09482 | flap endonuclease-like protein; Provisional |
1-247 | 9.77e-71 | |||||
flap endonuclease-like protein; Provisional Pssm-ID: 181896 [Multi-domain] Cd Length: 256 Bit Score: 217.47 E-value: 9.77e-71
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| 53EXOc | smart00475 | 5'-3' exonuclease; |
2-255 | 7.50e-66 | |||||
5'-3' exonuclease; Pssm-ID: 214682 [Multi-domain] Cd Length: 259 Bit Score: 205.14 E-value: 7.50e-66
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| PIN_53EXO | cd09859 | FEN-like PIN domains of PIN domain of the 5'-3' exonuclease of Thermus aquaticus DNA ... |
7-162 | 2.57e-41 | |||||
FEN-like PIN domains of PIN domain of the 5'-3' exonuclease of Thermus aquaticus DNA polymerase I (Taq) and homologs; The 5'-3' exonuclease (53EXO) PIN (PilT N terminus) domain of multi-domain DNA polymerase I and single domain protein homologs are included in this family. Taq contains a polymerase domain for synthesizing a new DNA strand and a 53EXO PIN domain for cleaving RNA primers or damaged DNA strands. Taq's 53EXO PIN domain recognizes and endonucleolytically cleaves a structure-specific DNA substrate that has a bifurcated downstream duplex and an upstream template-primer duplex that overlaps the downstream duplex by 1 bp. The 53EXO PIN domain cleaves the unpaired 5'-arm of the overlap flap DNA substrate. 5'-3' exonucleases are members of the structure-specific, 5' nuclease family (FEN-like) that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. Canonical members of the FEN-like family possess a PIN domain with a two-helical structure insert (also known as the helical arch, helical clamp or I domain) of variable length (approximately 16 to 800 residues), and at the C-terminus of the PIN domain a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included in this model) and the helical arch/clamp region are involved in DNA binding. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. Pssm-ID: 350209 Cd Length: 160 Bit Score: 139.04 E-value: 2.57e-41
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| 5_3_exonuc_N | pfam02739 | 5'-3' exonuclease, N-terminal resolvase-like domain; |
3-165 | 1.21e-36 | |||||
5'-3' exonuclease, N-terminal resolvase-like domain; Pssm-ID: 460672 Cd Length: 163 Bit Score: 127.13 E-value: 1.21e-36
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| Name | Accession | Description | Interval | E-value | |||||
| ExoIX | COG0258 | 5'-3' exonuclease Xni/ExoIX (flap endonuclease) [Replication, recombination and repair]; |
1-255 | 4.42e-77 | |||||
5'-3' exonuclease Xni/ExoIX (flap endonuclease) [Replication, recombination and repair]; Pssm-ID: 440028 [Multi-domain] Cd Length: 286 Bit Score: 234.92 E-value: 4.42e-77
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| PRK09482 | PRK09482 | flap endonuclease-like protein; Provisional |
1-247 | 9.77e-71 | |||||
flap endonuclease-like protein; Provisional Pssm-ID: 181896 [Multi-domain] Cd Length: 256 Bit Score: 217.47 E-value: 9.77e-71
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| 53EXOc | smart00475 | 5'-3' exonuclease; |
2-255 | 7.50e-66 | |||||
5'-3' exonuclease; Pssm-ID: 214682 [Multi-domain] Cd Length: 259 Bit Score: 205.14 E-value: 7.50e-66
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| PRK05755 | PRK05755 | DNA polymerase I; Provisional |
1-255 | 1.22e-61 | |||||
DNA polymerase I; Provisional Pssm-ID: 235591 [Multi-domain] Cd Length: 880 Bit Score: 207.64 E-value: 1.22e-61
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| PRK14976 | PRK14976 | 5'-3' exonuclease; Provisional |
1-244 | 2.14e-41 | |||||
5'-3' exonuclease; Provisional Pssm-ID: 237877 [Multi-domain] Cd Length: 281 Bit Score: 143.16 E-value: 2.14e-41
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| PIN_53EXO | cd09859 | FEN-like PIN domains of PIN domain of the 5'-3' exonuclease of Thermus aquaticus DNA ... |
7-162 | 2.57e-41 | |||||
FEN-like PIN domains of PIN domain of the 5'-3' exonuclease of Thermus aquaticus DNA polymerase I (Taq) and homologs; The 5'-3' exonuclease (53EXO) PIN (PilT N terminus) domain of multi-domain DNA polymerase I and single domain protein homologs are included in this family. Taq contains a polymerase domain for synthesizing a new DNA strand and a 53EXO PIN domain for cleaving RNA primers or damaged DNA strands. Taq's 53EXO PIN domain recognizes and endonucleolytically cleaves a structure-specific DNA substrate that has a bifurcated downstream duplex and an upstream template-primer duplex that overlaps the downstream duplex by 1 bp. The 53EXO PIN domain cleaves the unpaired 5'-arm of the overlap flap DNA substrate. 5'-3' exonucleases are members of the structure-specific, 5' nuclease family (FEN-like) that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. Canonical members of the FEN-like family possess a PIN domain with a two-helical structure insert (also known as the helical arch, helical clamp or I domain) of variable length (approximately 16 to 800 residues), and at the C-terminus of the PIN domain a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included in this model) and the helical arch/clamp region are involved in DNA binding. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. Pssm-ID: 350209 Cd Length: 160 Bit Score: 139.04 E-value: 2.57e-41
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| 5_3_exonuc_N | pfam02739 | 5'-3' exonuclease, N-terminal resolvase-like domain; |
3-165 | 1.21e-36 | |||||
5'-3' exonuclease, N-terminal resolvase-like domain; Pssm-ID: 460672 Cd Length: 163 Bit Score: 127.13 E-value: 1.21e-36
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| 5_3_exonuc | pfam01367 | 5'-3' exonuclease, C-terminal SAM fold; |
166-255 | 3.65e-32 | |||||
5'-3' exonuclease, C-terminal SAM fold; Pssm-ID: 460176 [Multi-domain] Cd Length: 93 Bit Score: 113.23 E-value: 3.65e-32
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| H3TH_53EXO | cd09898 | H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; H3TH ... |
169-240 | 3.97e-29 | |||||
H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; H3TH (helix-3-turn-helix) domains of the 5'-3' exonuclease (53EXO) of mutli-domain DNA polymerase I and single domain protein homologs are included in this family. Taq DNA polymerase I contains a polymerase domain for synthesizing a new DNA strand and a 53EXO domain for cleaving RNA primers or damaged DNA strands. Taq's 53EXO recognizes and endonucleolytically cleaves a structure-specific DNA substrate that has a bifurcated downstream duplex and an upstream template-primer duplex that overlaps the downstream duplex by 1 bp. The 53EXO cleaves the unpaired 5'-arm of the overlap flap DNA substrate. 5'-3' exonucleases are members of the structure-specific, 5' nuclease family that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. These nucleases contain a PIN (PilT N terminus) domain with a helical arch/clamp region/I domain (not included here) and inserted within the PIN domain is an atypical helix-hairpin-helix-2 (HhH2)-like region. This atypical HhH2 region, the H3TH domain, has an extended loop with at least three turns between the first two helices, and only three of the four helices appear to be conserved. Both the H3TH domain and the helical arch/clamp region are involved in DNA binding. Studies suggest that a glycine-rich loop in the H3TH domain contacts the phosphate backbone of the template strand in the downstream DNA duplex. The nucleases within this family have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (i. e., Mg2+ or Mn2+ or Zn2+) required for nuclease activity. The first metal binding site is composed entirely of Asp/Glu residues from the PIN domain, whereas, the second metal binding site is composed generally of two Asp residues from the PIN domain and two Asp residues from the H3TH domain. Together with the helical arch and network of amino acids interacting with metal binding ions, the H3TH region defines a positively charged active-site DNA-binding groove in structure-specific 5' nucleases. Pssm-ID: 188618 [Multi-domain] Cd Length: 73 Bit Score: 104.79 E-value: 3.97e-29
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| H3TH_StructSpec-5'-nucleases | cd00080 | H3TH domains of structure-specific 5' nucleases (or flap endonuclease-1-like) involved in DNA ... |
169-239 | 7.38e-15 | |||||
H3TH domains of structure-specific 5' nucleases (or flap endonuclease-1-like) involved in DNA replication, repair, and recombination; The 5' nucleases of this superfamily are capable of both 5'-3' exonucleolytic activity and cleaving bifurcated or branched DNA, in an endonucleolytic, structure-specific manner, and are involved in DNA replication, repair, and recombination. The superfamily includes the H3TH (helix-3-turn-helix) domains of Flap Endonuclease-1 (FEN1), Exonuclease-1 (EXO1), Mkt1, Gap Endonuclease 1 (GEN1) and Xeroderma pigmentosum complementation group G (XPG) nuclease. Also included are the H3TH domains of the 5'-3' exonucleases of DNA polymerase I and single domain protein homologs, as well as, the bacteriophage T4 RNase H, T5-5'nuclease, and other homologs. These nucleases contain a PIN (PilT N terminus) domain with a helical arch/clamp region/I domain (not included here) and inserted within the C-terminal region of the PIN domain is an atypical helix-hairpin-helix-2 (HhH2)-like region. This atypical HhH2 region, the H3TH domain, has an extended loop with at least three turns between the first two helices, and only three of the four helices appear to be conserved. Both the H3TH domain and the helical arch/clamp region are involved in DNA binding. Studies suggest that a glycine-rich loop in the H3TH domain contacts the phosphate backbone of the template strand in the downstream DNA duplex. Typically, the nucleases within this superfamily have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (i. e., Mg2+, Mn2+, Zn2+, or Co2+) required for nuclease activity. The first metal binding site is composed entirely of Asp/Glu residues from the PIN domain, whereas, the second metal binding site is composed generally of two Asp residues from the PIN domain and one or two Asp residues from the H3TH domain. Together with the helical arch and network of amino acids interacting with metal binding ions, the H3TH region defines a positively charged active-site DNA-binding groove in structure-specific 5' nucleases. Pssm-ID: 188616 [Multi-domain] Cd Length: 71 Bit Score: 67.40 E-value: 7.38e-15
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| HhH2 | smart00279 | Helix-hairpin-helix class 2 (Pol1 family) motifs; |
168-203 | 2.84e-11 | |||||
Helix-hairpin-helix class 2 (Pol1 family) motifs; Pssm-ID: 197623 [Multi-domain] Cd Length: 36 Bit Score: 56.69 E-value: 2.84e-11
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| PIN_T4-like | cd09860 | FEN-like PIN domains of bacteriophage T3, T4 RNase H, T5-5'nuclease, and homologs; PIN (PilT N ... |
4-135 | 1.88e-09 | |||||
FEN-like PIN domains of bacteriophage T3, T4 RNase H, T5-5'nuclease, and homologs; PIN (PilT N terminus) domain of bacteriophage T5-5'nuclease (5'-3' exonuclease or T5FEN), bacteriophage T4 RNase H (T4FEN), bacteriophage T3 (T3 phage exodeoxyribonuclease) and other similar 5' nucleases are included in this family. T5-5'nuclease is a 5'-3'exodeoxyribonuclease that also exhibits endonucleolytic activity on flap structures (branched duplex DNA containing a free single-stranded 5'end). T4 RNase H, which removes the RNA primers that initiate lagging strand fragments, has 5'- 3'exonuclease activity on DNA/DNA and RNA/DNA duplexes and has endonuclease activity on flap or forked DNA structures. Bacteriophage T3 is believed to function in the removal of DNA-linked RNA primers and is essential for phage DNA replication and also necessary for host DNA degradation and phage genetic recombination. These nucleases are members of the structure-specific, 5' nuclease family (FEN-like) that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. Canonical members of the FEN-like family possess a PIN domain with a two-helical structure insert (also known as the helical arch, helical clamp or I domain) of variable length (approximately 16 to 800 residues), and at the C-terminus of the PIN domain a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included in this model) and the helical arch/clamp region are involved in DNA binding. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. In the T5-5'nuclease, structure-specific endonuclease activity requires binding of a single metal ion in the high-affinity, metal binding site 1, whereas exonuclease activity requires both, the high-affinity, metal binding site 1 and the low-affinity, metal binding site 2 to be occupied by a divalent cofactor. The T5-5'nuclease is reported to be able to bind several metal ions including, Mg2+, Mn2+, Zn2+ and Co2+, as co-factors. Pssm-ID: 350210 Cd Length: 158 Bit Score: 54.90 E-value: 1.88e-09
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| PIN_53EXO-like | cd00008 | FEN-like PIN domains of the 5'-3' exonucleases of DNA polymerase I, bacteriophage T4 RNase H ... |
7-154 | 2.80e-08 | |||||
FEN-like PIN domains of the 5'-3' exonucleases of DNA polymerase I, bacteriophage T4 RNase H and T5-5' nucleases, and homologs; PIN (PilT N terminus) domains of the 5'-3' exonucleases (53EXO) of multi-domain DNA polymerase I and single domain protein homologs, as well as, the PIN domains of bacteriophage T5-5'nuclease (T5FEN or 5'-3'exonuclease), bacteriophage T4 RNase H (T4FEN), bacteriophage T3 (T3 phage exodeoxyribonuclease) and other similar nucleases are included in this family. The 53EXO of DNA polymerase I recognizes and endonucleolytically cleaves a structure-specific DNA substrate that has a bifurcated downstream duplex and an upstream template-primer duplex that overlaps the downstream duplex by 1 bp. The T5-5'nuclease is a 5'-3'exodeoxyribonuclease that also exhibits endonucleolytic activity on flap structures (branched duplex DNA containing a free single-stranded 5'end). T4 RNase H, which removes the RNA primers that initiate lagging strand fragments, has 5'- 3'exonuclease activity on DNA/DNA and RNA/DNA duplexes and has endonuclease activity on flap or forked DNA structures. These nucleases are members of the structure-specific, 5' nuclease family (FEN-like) that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. Canonical members of the FEN-like family possess a PIN domain with a two-helical structure insert (also known as the helical arch, helical clamp or I domain) of variable length (approximately 16 to 800 residues), and at the C-terminus of the PIN domain a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included in this model) and the helical arch/clamp region are involved in DNA binding. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. Pssm-ID: 350199 Cd Length: 158 Bit Score: 51.88 E-value: 2.80e-08
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| PRK03980 | PRK03980 | flap endonuclease-1; Provisional |
163-215 | 4.52e-05 | |||||
flap endonuclease-1; Provisional Pssm-ID: 235185 [Multi-domain] Cd Length: 292 Bit Score: 43.66 E-value: 4.52e-05
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| H3TH_FEN1-XPG-like | cd09897 | H3TH domains of Flap endonuclease-1 (FEN1)-like structure specific 5' nucleases; The 5' ... |
169-210 | 8.98e-03 | |||||
H3TH domains of Flap endonuclease-1 (FEN1)-like structure specific 5' nucleases; The 5' nucleases within this family are capable of both 5'-3' exonucleolytic activity and cleaving bifurcated or branched DNA, in an endonucleolytic, structure-specific manner, and are involved in DNA replication, repair, and recombination. This family includes the H3TH (helix-3-turn-helix) domains of Flap Endonuclease-1 (FEN1), Exonuclease-1 (EXO1), Mkt1, Gap Endonuclease 1 (GEN1), Xeroderma pigmentosum complementation group G (XPG) nuclease, and other eukaryotic and archaeal homologs. These nucleases contain a PIN (PilT N terminus) domain with a helical arch/clamp region/I domain (not included here) and inserted within the PIN domain is an atypical helix-hairpin-helix-2 (HhH2)-like region. This atypical HhH2 region, the H3TH domain, has an extended loop with at least three turns between the first two helices, and only three of the four helices appear to be conserved. Both the H3TH domain and the helical arch/clamp region are involved in DNA binding. Studies suggest that a glycine-rich loop in the H3TH domain contacts the phosphate backbone of the template strand in the downstream DNA duplex. With the except of the Mkt1-like proteins, the nucleases within this family have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (i. e., Mg2+, Mn2+, Zn2+, or Co2+) required for nuclease activity. The first metal binding site is composed entirely of Asp/Glu residues from the PIN domain, whereas, the second metal binding site is composed generally of two Asp residues from the PIN domain and one Asp residue from the H3TH domain. Together with the helical arch and network of amino acids interacting with metal binding ions, the H3TH region defines a positively charged active-site DNA-binding groove in structure-specific 5' nucleases. Pssm-ID: 188617 [Multi-domain] Cd Length: 68 Bit Score: 34.11 E-value: 8.98e-03
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| H3TH_XPG-like | cd09900 | H3TH domains of Flap endonuclease-1 (FEN1)-like structure specific 5' nucleases: FEN1 ... |
169-206 | 9.75e-03 | |||||
H3TH domains of Flap endonuclease-1 (FEN1)-like structure specific 5' nucleases: FEN1 (archaeal), GEN1, YEN1, and XPG; The 5' nucleases within this family are capable of both 5'-3' exonucleolytic activity and cleaving bifurcated or branched DNA, in an endonucleolytic, structure-specific manner, and are involved in DNA replication, repair, and recombination. This family includes the H3TH (helix-3-turn-helix) domains of archaeal Flap Endonuclease-1 (FEN1), Gap Endonuclease 1 (GEN1), Yeast Endonuclease 1 (YEN1), Xeroderma pigmentosum complementation group G (XPG) nuclease, and other eukaryotic and archaeal homologs. These nucleases contain a PIN (PilT N terminus) domain with a helical arch/clamp region/I domain (not included here) and inserted within the PIN domain is an atypical helix-hairpin-helix-2 (HhH2)-like region. This atypical HhH2 region, the H3TH domain, has an extended loop with at least three turns between the first two helices, and only three of the four helices appear to be conserved. Both the H3TH domain and the helical arch/clamp region are involved in DNA binding. Studies suggest that a glycine-rich loop in the H3TH domain contacts the phosphate backbone of the template strand in the downstream DNA duplex. With the except of the Mkt1-like proteins, the nucleases within this family have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (i. e., Mg2+, Mn2+, Zn2+, or Co2+) required for nuclease activity. The first metal binding site is composed entirely of Asp/Glu residues from the PIN domain, whereas, the second metal binding site is composed generally of two Asp residues from the PIN domain and one Asp residue from the H3TH domain. Together with the helical arch and network of amino acids interacting with metal binding ions, the H3TH region defines a positively charged active-site DNA-binding groove in structure-specific 5' nucleases. Pssm-ID: 188620 [Multi-domain] Cd Length: 52 Bit Score: 33.61 E-value: 9.75e-03
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