ATP-dependent DNA ligase [Stenotrophomonas maltophilia]
Protein Classification
ATP-dependent DNA ligase( domain architecture ID 11483682)
ATP-dependent DNA ligase catalyzes the joining of breaks in the phosphodiester backbone of duplex DNA
List of domain hits
| Name | Accession | Description | Interval | E-value | ||||||||
| PRK09247 | PRK09247 | ATP-dependent DNA ligase; Validated |
1-535 | 0e+00 | ||||||||
ATP-dependent DNA ligase; Validated : Pssm-ID: 236428 [Multi-domain] Cd Length: 539 Bit Score: 785.96 E-value: 0e+00
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| Name | Accession | Description | Interval | E-value | ||||||||
| PRK09247 | PRK09247 | ATP-dependent DNA ligase; Validated |
1-535 | 0e+00 | ||||||||
ATP-dependent DNA ligase; Validated Pssm-ID: 236428 [Multi-domain] Cd Length: 539 Bit Score: 785.96 E-value: 0e+00
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| DNA_lig_bact | TIGR04120 | DNA ligase, ATP-dependent, PP_1105 family; This model describes a family of ATP-dependent DNA ... |
2-533 | 0e+00 | ||||||||
DNA ligase, ATP-dependent, PP_1105 family; This model describes a family of ATP-dependent DNA ligases present in about 12 % of prokaryotic genomes. It occurs as part of a four-gene system with an exonuclease, a helicase and a phosphoesterase, with all four genes clustered or at least the first two and last two paired. This family resembles DNA ligase I (see TIGR00574 and pfam01068), and its presumed function may be in DNA repair, replication, or recombination. Pssm-ID: 274993 [Multi-domain] Cd Length: 526 Bit Score: 577.73 E-value: 0e+00
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| CDC9 | COG1793 | ATP-dependent DNA ligase [Replication, recombination and repair]; |
208-535 | 2.06e-114 | ||||||||
ATP-dependent DNA ligase [Replication, recombination and repair]; Pssm-ID: 441398 [Multi-domain] Cd Length: 435 Bit Score: 345.75 E-value: 2.06e-114
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| Adenylation_DNA_ligase_Bac1 | cd07897 | Adenylation domain of putative bacterial ATP-dependent DNA ligases; Bacterial DNA ligases are ... |
204-413 | 3.51e-102 | ||||||||
Adenylation domain of putative bacterial ATP-dependent DNA ligases; Bacterial DNA ligases are divided into two broad classes: NAD-dependent and ATP-dependent. All bacterial species have a NAD-dependent DNA ligase (LigA). Some bacterial genomes contain multiple genes for DNA ligases that are predicted to use ATP as their cofactor, including Mycobacterium tuberculosis LigB, LigC, and LigD. This group is composed of predicted bacterial ATP-dependent DNA ligases. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three-step reaction mechanism. The adenylation and C-terminal oligonucleotide/oligosaccharide binding (OB)-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family, including this group. The adenylation domain binds ATP and contains many of the active site residues. Pssm-ID: 185708 [Multi-domain] Cd Length: 207 Bit Score: 306.01 E-value: 3.51e-102
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| DNA_ligase_A_M | pfam01068 | ATP dependent DNA ligase domain; This domain belongs to a more diverse superfamily, including ... |
229-409 | 3.14e-39 | ||||||||
ATP dependent DNA ligase domain; This domain belongs to a more diverse superfamily, including pfam01331 and pfam01653. Pssm-ID: 426028 [Multi-domain] Cd Length: 203 Bit Score: 141.65 E-value: 3.14e-39
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| Name | Accession | Description | Interval | E-value | |||||||||
| PRK09247 | PRK09247 | ATP-dependent DNA ligase; Validated |
1-535 | 0e+00 | |||||||||
ATP-dependent DNA ligase; Validated Pssm-ID: 236428 [Multi-domain] Cd Length: 539 Bit Score: 785.96 E-value: 0e+00
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| DNA_lig_bact | TIGR04120 | DNA ligase, ATP-dependent, PP_1105 family; This model describes a family of ATP-dependent DNA ... |
2-533 | 0e+00 | |||||||||
DNA ligase, ATP-dependent, PP_1105 family; This model describes a family of ATP-dependent DNA ligases present in about 12 % of prokaryotic genomes. It occurs as part of a four-gene system with an exonuclease, a helicase and a phosphoesterase, with all four genes clustered or at least the first two and last two paired. This family resembles DNA ligase I (see TIGR00574 and pfam01068), and its presumed function may be in DNA repair, replication, or recombination. Pssm-ID: 274993 [Multi-domain] Cd Length: 526 Bit Score: 577.73 E-value: 0e+00
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| CDC9 | COG1793 | ATP-dependent DNA ligase [Replication, recombination and repair]; |
208-535 | 2.06e-114 | |||||||||
ATP-dependent DNA ligase [Replication, recombination and repair]; Pssm-ID: 441398 [Multi-domain] Cd Length: 435 Bit Score: 345.75 E-value: 2.06e-114
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| Adenylation_DNA_ligase_Bac1 | cd07897 | Adenylation domain of putative bacterial ATP-dependent DNA ligases; Bacterial DNA ligases are ... |
204-413 | 3.51e-102 | |||||||||
Adenylation domain of putative bacterial ATP-dependent DNA ligases; Bacterial DNA ligases are divided into two broad classes: NAD-dependent and ATP-dependent. All bacterial species have a NAD-dependent DNA ligase (LigA). Some bacterial genomes contain multiple genes for DNA ligases that are predicted to use ATP as their cofactor, including Mycobacterium tuberculosis LigB, LigC, and LigD. This group is composed of predicted bacterial ATP-dependent DNA ligases. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three-step reaction mechanism. The adenylation and C-terminal oligonucleotide/oligosaccharide binding (OB)-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family, including this group. The adenylation domain binds ATP and contains many of the active site residues. Pssm-ID: 185708 [Multi-domain] Cd Length: 207 Bit Score: 306.01 E-value: 3.51e-102
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| Adenylation_DNA_ligase | cd07898 | Adenylation domain of ATP-dependent DNA Ligases; ATP-dependent polynucleotide ligases catalyze ... |
208-411 | 3.36e-59 | |||||||||
Adenylation domain of ATP-dependent DNA Ligases; ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriophages, eukarya, archaea and bacteria. Some organisms express a variety of different ligases which appear to be targeted to specific functions. ATP-dependent DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains including a DNA-binding domain, an adenylation (nucleotidyltransferase (NTase)) domain, and an oligonucleotide/oligosaccharide binding (OB)-fold domain. The adenylation domain binds ATP and contains many of the active-site residues. The adenylation and C-terminal OB-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The catalytic core unit contains six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases. Pssm-ID: 185709 [Multi-domain] Cd Length: 201 Bit Score: 194.86 E-value: 3.36e-59
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| OBF_DNA_ligase_Arch_LigB | cd07972 | The Oligonucleotide/oligosaccharide binding (OB)-fold domain of archaeal and bacterial ... |
414-532 | 1.97e-55 | |||||||||
The Oligonucleotide/oligosaccharide binding (OB)-fold domain of archaeal and bacterial ATP-dependent DNA ligases is a DNA-binding module that is part of the catalytic core unit; ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriohages, eukarya, archaea and bacteria. Bacterial DNA ligases are divided into two broad classes: NAD-dependent and ATP-dependent. All bacterial species have a NAD-dependent DNA ligase (LigA). Some bacterial genomes contain multiple genes for DNA ligases that are predicted to use ATP as their cofactor, including Mycobacterium tuberculosis LigB, LigC, and LigD. This group is composed of Pyrococcus furiosus DNA ligase, Mycobacterium tuberculosis LigB, and similar archaeal and bacterial proteins. ATP dependent DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains including a DNA-binding domain, an adenylation (nucleotidyltransferase (NTase)) domain, and an oligonucleotide/oligosaccharide binding (OB)-fold domain. The adenylation and C-terminal OB-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The catalytic core unit contains six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases. The OB-fold domain contacts the nicked DNA substrate and is required for the ATP-dependent DNA ligase nucleotidylation step. The RxDK motif (motif VI), which is essential for ATP hydrolysis, is located in the OB-fold domain. Pssm-ID: 153441 [Multi-domain] Cd Length: 122 Bit Score: 181.98 E-value: 1.97e-55
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| ligB | PRK03180 | ATP-dependent DNA ligase; Reviewed |
125-535 | 1.61e-53 | |||||||||
ATP-dependent DNA ligase; Reviewed Pssm-ID: 235108 [Multi-domain] Cd Length: 508 Bit Score: 189.02 E-value: 1.61e-53
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| Adenylation_DNA_ligase_LigD_LigC | cd07906 | Adenylation domain of Mycobacterium tuberculosis LigD and LigC-like ATP-dependent DNA ligases; ... |
228-409 | 4.68e-46 | |||||||||
Adenylation domain of Mycobacterium tuberculosis LigD and LigC-like ATP-dependent DNA ligases; Bacterial DNA ligases are divided into two broad classes: NAD-dependent and ATP-dependent. All bacterial species have a NAD-dependent DNA ligase (LigA). Some bacterial genomes contain multiple genes for DNA ligases that are predicted to use ATP as their cofactor, including Mycobacterium tuberculosis LigB, LigC, and LigD. This group is composed of ATP-dependent DNA ligases similar to Mycobacterium tuberculosis LigC. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. Members of this group contain adenylation and C-terminal oligonucleotide/oligosaccharide binding (OB)-fold domains, comprising a catalytic core unit that is common to all members of the ATP-dependent DNA ligase family. The adenylation domain binds ATP and contains many of the active-site residues. The common catalytic core unit comprises six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases. LigD consists of a central ATP-dependent DNA ligase catalytic core unit fused to a C-terminal polymerase domain and an N-terminal 3'-phosphoesterase (PE) module. LigD catalyzes the end-healing and end-sealing steps during non-homologous end joining. Pssm-ID: 185715 [Multi-domain] Cd Length: 190 Bit Score: 159.63 E-value: 4.68e-46
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| dnl1 | TIGR00574 | DNA ligase I, ATP-dependent (dnl1); All proteins in this family with known functions are ... |
146-527 | 6.68e-40 | |||||||||
DNA ligase I, ATP-dependent (dnl1); All proteins in this family with known functions are ATP-dependent DNA ligases. Functions include DNA repair, DNA replication, and DNA recombination (or any process requiring ligation of two single-stranded DNA sections). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair] Pssm-ID: 273147 [Multi-domain] Cd Length: 514 Bit Score: 151.70 E-value: 6.68e-40
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| DNA_ligase_A_M | pfam01068 | ATP dependent DNA ligase domain; This domain belongs to a more diverse superfamily, including ... |
229-409 | 3.14e-39 | |||||||||
ATP dependent DNA ligase domain; This domain belongs to a more diverse superfamily, including pfam01331 and pfam01653. Pssm-ID: 426028 [Multi-domain] Cd Length: 203 Bit Score: 141.65 E-value: 3.14e-39
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| Adenylation_DNA_ligase_Arch_LigB | cd07901 | Adenylation domain of archaeal and bacterial LigB-like DNA ligases; ATP-dependent ... |
232-409 | 1.15e-36 | |||||||||
Adenylation domain of archaeal and bacterial LigB-like DNA ligases; ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriophages, eukarya, archaea and bacteria. Bacterial DNA ligases are divided into two broad classes: NAD-dependent and ATP-dependent. All bacterial species have a NAD-dependent DNA ligase (LigA). Some bacterial genomes contain multiple genes for DNA ligases that are predicted to use ATP as their cofactor, including Mycobacterium tuberculosis LigB, LigC, and LigD. This group is composed of archaeal DNA ligases and bacterial proteins similar to Mycobacterium tuberculosis LigB. Members of this group contain adenylation and C-terminal oligonucleotide/oligosaccharide binding (OB)-fold domains, comprising a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The adenylation domain binds ATP and contains many of the active-site residues. The common catalytic core unit comprises six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases. Pssm-ID: 185711 [Multi-domain] Cd Length: 207 Bit Score: 134.97 E-value: 1.15e-36
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| NHEJ_ligase_lig | TIGR02779 | DNA ligase D, ligase domain; DNA repair of double-stranded breaks by non-homologous end ... |
228-523 | 2.30e-36 | |||||||||
DNA ligase D, ligase domain; DNA repair of double-stranded breaks by non-homologous end joining (NHEJ) is accomplished by a two-protein system that is present in a minority of prokaryotes. One component is the Ku protein (see TIGR02772), which binds DNA ends. The other is a DNA ligase, a protein that is a multidomain polypeptide in most of those bacteria that have NHEJ, a permuted polypeptide in Mycobacterium tuberculosis and a few other species, and the product of tandem genes in some other bacteria. This model represents the ligase domain. Pssm-ID: 274295 [Multi-domain] Cd Length: 298 Bit Score: 137.05 E-value: 2.30e-36
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| PRK01109 | PRK01109 | ATP-dependent DNA ligase; Provisional |
5-525 | 3.14e-36 | |||||||||
ATP-dependent DNA ligase; Provisional Pssm-ID: 234900 [Multi-domain] Cd Length: 590 Bit Score: 142.42 E-value: 3.14e-36
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| Adenylation_DNA_ligase_LigC | cd07905 | Adenylation domain of Mycobacterium tuberculosis LigC-like ATP-dependent DNA ligases; ... |
215-409 | 3.29e-34 | |||||||||
Adenylation domain of Mycobacterium tuberculosis LigC-like ATP-dependent DNA ligases; Bacterial DNA ligases are divided into two broad classes: NAD-dependent and ATP-dependent. All bacterial species have a NAD-dependent DNA ligase (LigA). Some bacterial genomes contain multiple genes for DNA ligases that are predicted to use ATP as their cofactor, including Mycobacterium tuberculosis LigB, LigC, and LigD. This group is composed of ATP-dependent DNA ligases similar to Mycobacterium tuberculosis LigC. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. Members of this group contain adenylation and C-terminal oligonucleotide/oligosaccharide binding (OB)-fold domains, comprising a catalytic core unit that is common to all members of the ATP-dependent DNA ligase family. The adenylation domain binds ATP and contains many of the active-site residues. The common catalytic core unit comprises six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases. Pssm-ID: 185714 [Multi-domain] Cd Length: 194 Bit Score: 127.75 E-value: 3.29e-34
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| PRK09632 | PRK09632 | ATP-dependent DNA ligase; Reviewed |
198-523 | 2.10e-32 | |||||||||
ATP-dependent DNA ligase; Reviewed Pssm-ID: 236599 [Multi-domain] Cd Length: 764 Bit Score: 132.05 E-value: 2.10e-32
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| NHEJ_ligase_prk | TIGR02776 | DNA ligase D; Members of this protein family are DNA ligases involved in the repair of DNA ... |
254-523 | 1.02e-25 | |||||||||
DNA ligase D; Members of this protein family are DNA ligases involved in the repair of DNA double-stranded breaks by non-homologous end joining (NHEJ). The system of the bacterial Ku protein (TIGR02772) plus this DNA ligase is seen in about 20 % of bacterial genomes to date and at least one archaeon (Archeoglobus fulgidus). This model describes a central and a C-terminal domain. These two domains may be permuted, as in genus Mycobacterium, or divided into tandem ORFs, and therefore not be identified by this model. An additional N-terminal 3'-phosphoesterase (PE) domain present in some but not all examples of this ligase is not included in the seed alignment for this model; it only represents the central ATP-dependent ligase domain and the C-terminal polymerase domain. Most examples of genes for this ligase are adjacent to the gene for Ku. [DNA metabolism, DNA replication, recombination, and repair] Pssm-ID: 274293 [Multi-domain] Cd Length: 552 Bit Score: 110.87 E-value: 1.02e-25
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| ligD | PRK05972 | ATP-dependent DNA ligase; Reviewed |
212-409 | 4.88e-24 | |||||||||
ATP-dependent DNA ligase; Reviewed Pssm-ID: 235658 [Multi-domain] Cd Length: 860 Bit Score: 106.53 E-value: 4.88e-24
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| ligB | PRK07636 | ATP-dependent DNA ligase; Reviewed |
228-407 | 7.81e-24 | |||||||||
ATP-dependent DNA ligase; Reviewed Pssm-ID: 236070 [Multi-domain] Cd Length: 275 Bit Score: 100.99 E-value: 7.81e-24
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| ligD | PRK09633 | DNA ligase D; |
229-475 | 8.91e-24 | |||||||||
DNA ligase D; Pssm-ID: 182006 [Multi-domain] Cd Length: 610 Bit Score: 105.12 E-value: 8.91e-24
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| ligC | PRK08224 | ATP-dependent DNA ligase; Reviewed |
214-401 | 6.39e-22 | |||||||||
ATP-dependent DNA ligase; Reviewed Pssm-ID: 236191 [Multi-domain] Cd Length: 350 Bit Score: 97.27 E-value: 6.39e-22
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| Adenylation_DNA_ligase_IV | cd07903 | Adenylation domain of DNA Ligase IV; ATP-dependent polynucleotide ligases catalyze ... |
228-409 | 2.15e-19 | |||||||||
Adenylation domain of DNA Ligase IV; ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriophages, eukarya, archaea and bacteria. There are three classes of ATP-dependent DNA ligase in eukaryotic cells (I, III and IV). DNA ligase IV is required for DNA non-homologous end joining pathways, including recombination of the V(D)J immunoglobulin gene segments in cells of the mammalian immune system. DNA ligase IV is stabilized by forming a complex with XRCC4, a nuclear phosphoprotein, which is phosphorylated by DNA-dependent protein kinase. DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains. The adenylation and C-terminal oligonucleotide/oligosaccharide binding (OB)-fold domains comprise a catalytic core unit that is common to all members of the ATP-dependent DNA ligase family. The adenylation domain binds ATP and contains many of the active-site residues. The common catalytic unit comprises six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases. Pssm-ID: 185713 [Multi-domain] Cd Length: 225 Bit Score: 86.86 E-value: 2.15e-19
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| Adenylation_DNA_ligase_I_Euk | cd07900 | Adenylation domain of eukaryotic DNA Ligase I; ATP-dependent polynucleotide ligases catalyze ... |
212-411 | 2.33e-18 | |||||||||
Adenylation domain of eukaryotic DNA Ligase I; ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriophages, eukarya, archaea and bacteria. Some organisms express a variety of different ligases which appear to be targeted to specific functions. There are three classes of ATP-dependent DNA ligases in eukaryotic cells (I, III and IV). DNA ligase I is required for the ligation of Okazaki fragments during lagging-strand DNA synthesis and for base excision repair (BER). DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains. The adenylation and C-terminal oligonucleotide/oligosaccharide binding (OB)-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The adenylation domain binds ATP and contains many of the active-site residues. DNA ligase I is the main replicative ligase in eukaryotes. The common catalytic core unit comprises six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases. Pssm-ID: 185710 [Multi-domain] Cd Length: 219 Bit Score: 83.76 E-value: 2.33e-18
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| PLN03113 | PLN03113 | DNA ligase 1; Provisional |
233-530 | 7.20e-18 | |||||||||
DNA ligase 1; Provisional Pssm-ID: 215584 [Multi-domain] Cd Length: 744 Bit Score: 86.96 E-value: 7.20e-18
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| DNA_ligase_A_N | pfam04675 | DNA ligase N terminus; This region is found in many but not all ATP-dependent DNA ligase ... |
2-166 | 2.31e-16 | |||||||||
DNA ligase N terminus; This region is found in many but not all ATP-dependent DNA ligase enzymes (EC:6.5.1.1). It is thought to be involved in DNA binding and in catalysis. In human DNA ligase I, and in Saccharomyces cerevisiae, this region was necessary for catalysis, and separated from the amino terminus by targeting elements. In vaccinia virus this region was not essential for catalysis, but deletion decreases the affinity for nicked DNA and decreased the rate of strand joining at a step subsequent to enzyme-adenylate formation. Pssm-ID: 461387 [Multi-domain] Cd Length: 174 Bit Score: 76.84 E-value: 2.31e-16
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| DNA_ligase_A_C | pfam04679 | ATP dependent DNA ligase C terminal region; This region is found in many but not all ... |
429-519 | 1.33e-09 | |||||||||
ATP dependent DNA ligase C terminal region; This region is found in many but not all ATP-dependent DNA ligase enzymes (EC:6.5.1.1). It is thought to constitute part of the catalytic core of ATP dependent DNA ligase. Pssm-ID: 398383 [Multi-domain] Cd Length: 94 Bit Score: 55.29 E-value: 1.33e-09
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| Adenylation_DNA_ligase_III | cd07902 | Adenylation domain of DNA Ligase III; ATP-dependent polynucleotide ligases catalyze ... |
233-411 | 2.22e-09 | |||||||||
Adenylation domain of DNA Ligase III; ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three-step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriophages, eukarya, archaea and bacteria. There are three classes of ATP-dependent DNA ligases in eukaryotic cells (I, III and IV). DNA ligase III is not found in lower eukaryotes and is present both in the nucleus and mitochondria. It has several isoforms; two splice forms, III-alpha and III-beta, differ in their carboxy-terminal sequences. DNA ligase III-beta is believed to play a role in homologous recombination during meiotic prophase. DNA ligase III-alpha interacts with X-ray Cross Complementing factor 1 (XRCC1) and functions in single nucleotide Base Excision Repair (BER). The mitochondrial form of DNA ligase III originates from the nucleolus and is involved in the mitochondrial DNA repair pathway. This isoform is expressed by a second start site on the DNA ligase III gene. DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains. The adenylation and C-terminal oligonucleotide/oligosaccharide binding (OB)-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The adenylation domain binds ATP and contains many active site residues. The common catalytic core unit comprises six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases. Pssm-ID: 185712 [Multi-domain] Cd Length: 213 Bit Score: 57.73 E-value: 2.22e-09
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| OBF_DNA_ligase_III | cd07967 | The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase III ... |
414-528 | 2.26e-09 | |||||||||
The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase III is a DNA-binding module that is part of the catalytic core unit; ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriohages, eukarya, archaea and bacteria. There are three classes of ATP-dependent DNA ligases in eukaryotic cells (I, III and IV). DNA ligase III is not found in lower eukaryotes and is present both in the nucleus and mitochondria. It has several isoforms; two splice forms, III-alpha and III-beta, differ in their carboxy-terminal sequences. DNA ligase III-beta is believed to play a role in homologous recombination during meiotic prophase. DNA ligase III-alpha interacts with X-ray Cross Complementing factor 1 (XRCC1) and functions in single nucleotide Base Excision Repair (BER). The mitochondrial form of DNA ligase III originates from the nucleolus and is involved in the mitochondrial DNA repair pathway. This isoform is expressed by a second start site on the DNA ligase III gene. DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains. The adenylation and C-terminal oligouncleotide/oligosaccharide binding (OB)-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The catalytic core unit contains six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases. The OB-fold domain contacts the nicked DNA substrate and is required for the ATP-dependent DNA ligase nucleotidylation step. The RxDK motif (motif VI), which is essential for ATP hydrolysis, is located in the OB-fold domain. Pssm-ID: 153436 Cd Length: 139 Bit Score: 55.83 E-value: 2.26e-09
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| Adenylation_kDNA_ligase_like | cd07896 | Adenylation domain of kDNA ligases and similar proteins; The mitochondrial DNA of parasitic ... |
212-409 | 5.71e-09 | |||||||||
Adenylation domain of kDNA ligases and similar proteins; The mitochondrial DNA of parasitic protozoans is highly unusual. It is termed the kinetoplast DNA (kDNA) and consists of circular DNA molecules (maxicircles) and several thousand smaller circular molecules (minicircles). This group is composed of kDNA ligase, Chlorella virus DNA ligase, and similar proteins. kDNA ligase and Chlorella virus DNA ligase are the smallest known ATP-dependent ligases. They are involved in DNA replication or repair. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. They have a highly modular architecture consisting of a unique arrangement of two or more discrete domains. The adenylation and the C-terminal oligonucleotide/oligosaccharide binding (OB)-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family, including this group. The adenylation domain binds ATP and contains many of the active-site residues. Pssm-ID: 185707 [Multi-domain] Cd Length: 174 Bit Score: 55.65 E-value: 5.71e-09
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| Adenylation_DNA_ligase_like | cd06846 | Adenylation domain of proteins similar to ATP-dependent polynucleotide ligases; ATP-dependent ... |
209-409 | 5.95e-09 | |||||||||
Adenylation domain of proteins similar to ATP-dependent polynucleotide ligases; ATP-dependent polynucleotide ligases catalyze the phosphodiester bond formation of nicked nucleic acid substrates using ATP as a cofactor in a three step reaction mechanism. This family includes ATP-dependent DNA and RNA ligases. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent DNA ligases have a highly modular architecture, consisting of a unique arrangement of two or more discrete domains, including a DNA-binding domain, an adenylation or nucleotidyltransferase (NTase) domain, and an oligonucleotide/oligosaccharide binding (OB)-fold domain. The adenylation domain binds ATP and contains many active site residues. Together with the C-terminal OB-fold domain, it comprises a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The catalytic core contains six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases including eukaryotic GRP-dependent mRNA-capping enzymes. The catalytic core contains both the active site as well as many DNA-binding residues. The RNA circularization protein from archaea and bacteria contains the minimal catalytic unit, the adenylation domain, but does not contain an OB-fold domain. This family also includes the m3G-cap binding domain of snurportin, a nuclear import adaptor that binds m3G-capped spliceosomal U small nucleoproteins (snRNPs), but doesn't have enzymatic activity. Pssm-ID: 185704 [Multi-domain] Cd Length: 182 Bit Score: 55.50 E-value: 5.95e-09
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| OBF_DNA_ligase_I | cd07969 | The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase I is ... |
414-530 | 1.28e-06 | |||||||||
The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase I is a DNA-binding module that is part of the catalytic core unit; ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriohages, eukarya, archaea and bacteria. There are three classes of ATP-dependent DNA ligases in eukaryotic cells (I, III and IV). This group is composed of eukaryotic DNA ligase I, Sulfolobus solfataricus DNA ligase and similar proteins. DNA ligase I is required for the ligation of Okazaki fragments during lagging-strand DNA synthesis and for base excision repair (BER). ATP dependent DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains including a DNA-binding domain, an adenylation (nucleotidyltransferase (NTase)) domain, and an oligonucleotide/oligosaccharide binding (OB)-fold domain. The adenylation and C-terminal OB-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The catalytic core unit contains six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases. The OB-fold domain contacts the nicked DNA substrate and is required for the ATP-dependent DNA ligase nucleotidylation step. The RxDK motif (motif VI), which is essential for ATP hydrolysis, is located in the OB-fold domain. Pssm-ID: 153438 [Multi-domain] Cd Length: 144 Bit Score: 47.86 E-value: 1.28e-06
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| OBF_DNA_ligase | cd07893 | The Oligonucleotide/oligosaccharide binding (OB)-fold domain is a DNA-binding module that is ... |
414-524 | 1.48e-06 | |||||||||
The Oligonucleotide/oligosaccharide binding (OB)-fold domain is a DNA-binding module that is part of the catalytic core unit of ATP dependent DNA ligases; ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP dependent DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains including a DNA-binding domain, an adenylation (nucleotidyltransferase (NTase)) domain, and an oligonucleotide/oligosaccharide binding (OB)-fold domain. The adenylation and C-terminal OB-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The catalytic core unit contains six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases. The OB-fold domain contacts the nicked DNA substrate and is required for the ATP-dependent DNA ligase nucleotidylation step. The RxDK motif (motif VI), which is essential for ATP hydrolysis, is located in the OB-fold domain. Pssm-ID: 153435 [Multi-domain] Cd Length: 129 Bit Score: 47.34 E-value: 1.48e-06
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| Adenylation_DNA_ligase_Fungal | cd08039 | Adenylation domain of uncharacterized fungal ATP-dependent DNA ligase-like proteins; ... |
277-411 | 1.51e-06 | |||||||||
Adenylation domain of uncharacterized fungal ATP-dependent DNA ligase-like proteins; ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriophages, eukarya, archaea and bacteria. This group is composed of uncharacterized fungal proteins with similarity to ATP-dependent DNA ligases. ATP dependent DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains including a DNA-binding domain, an adenylation (nucleotidyltransferase (NTase)) domain, and an oligonucleotide/oligosaccharide binding (OB)-fold domain. The adenylation domain binds ATP and contains many of the active-site residues. The adenylation and C-terminal OB-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The catalytic core unit contains six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases. This model characterizes the adenylation domain of this group of uncharacterized fungal proteins. It is not known whether these proteins also contain an OB-fold domain. Pssm-ID: 185716 [Multi-domain] Cd Length: 235 Bit Score: 49.32 E-value: 1.51e-06
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| PHA00454 | PHA00454 | ATP-dependent DNA ligase |
235-409 | 5.11e-06 | |||||||||
ATP-dependent DNA ligase Pssm-ID: 222798 [Multi-domain] Cd Length: 315 Bit Score: 48.49 E-value: 5.11e-06
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| PRK09125 | PRK09125 | DNA ligase; Provisional |
226-400 | 5.23e-05 | |||||||||
DNA ligase; Provisional Pssm-ID: 181662 [Multi-domain] Cd Length: 282 Bit Score: 45.24 E-value: 5.23e-05
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| OBF_DNA_ligase_LigD | cd07971 | The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase LigD ... |
439-523 | 8.91e-03 | |||||||||
The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase LigD is a DNA-binding module that is part of the catalytic core unit; ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriohages, eukarya, archaea and bacteria. Bacterial DNA ligases are divided into two broad classes: NAD-dependent and ATP-dependent. All bacterial species have a NAD-dependent DNA ligase (LigA). Some bacterial genomes contain multiple genes for DNA ligases that are predicted to use ATP as their cofactor, including Mycobacterium tuberculosis LigB, LigC, and LigD. This group is composed of Mycobacterium tuberculosis LigD and similar bacterial proteins. LigD, or DNA ligase D, catalyzes the end-healing and end-sealing steps during nonhomologous end joining. ATP dependent DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains including a DNA-binding domain, an adenylation (nucleotidyltransferase (NTase)) domain, and an oligonucleotide/oligosaccharide binding (OB)-fold domain. The adenylation and C-terminal OB-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The catalytic core unit contains six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases. The OB-fold domain contacts the nicked DNA substrate and is required for the ATP-dependent DNA ligase nucleotidylation step. The RxDK motif (motif VI), which is essential for ATP hydrolysis, is located in the OB-fold domain. Pssm-ID: 153440 [Multi-domain] Cd Length: 115 Bit Score: 36.38 E-value: 8.91e-03
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