The name of this superfamily has been modified since the most recent official CATH+ release (v4_2_0). At the point of the last release, this superfamily was named:

"
Nucleic acid-binding proteins
".

Functional Families

Overview of the Structural Clusters (SC) and Functional Families within this CATH Superfamily. Clusters with a representative structure are represented by a filled circle.
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FunFam 53268: Ligase III, DNA, ATP-dependent

Please note: GO annotations are assigned to the full protein sequence rather than individual protein domains. Since a given protein can contain multiple domains, it is possible that some of the annotations below come from additional domains that occur in the same protein, but have been classified elsewhere in CATH.

There are 8 GO terms relating to "molecular function"

The search results have been sorted with the annotations that are found most frequently at the top of the list. The results can be filtered by typing text into the search box at the top of the table.
GO Term Annotations Evidence
DNA ligase activity GO:0003909
Catalysis of the formation of a phosphodiester bond between the 3'-hydroxyl group at the end of one DNA chain and the 5'-phosphate group at the end of another. This reaction requires an energy source such as ATP or NAD+.
3 A0A096MKE9 (/IDA) P49916 (/IDA) Q5U2M4 (/IDA)
Protein binding GO:0005515
Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
2 P49916 (/IPI) P97386 (/IPI)
DNA ligase activity GO:0003909
Catalysis of the formation of a phosphodiester bond between the 3'-hydroxyl group at the end of one DNA chain and the 5'-phosphate group at the end of another. This reaction requires an energy source such as ATP or NAD+.
1 P97386 (/ISO)
DNA ligase activity GO:0003909
Catalysis of the formation of a phosphodiester bond between the 3'-hydroxyl group at the end of one DNA chain and the 5'-phosphate group at the end of another. This reaction requires an energy source such as ATP or NAD+.
1 P49916 (/TAS)
DNA ligase (ATP) activity GO:0003910
Catalysis of the reaction: ATP + deoxyribonucleotide(n) + deoxyribonucleotide(m) = AMP + diphosphate + deoxyribonucleotide(n+m).
1 P49916 (/IDA)
DNA ligase (ATP) activity GO:0003910
Catalysis of the reaction: ATP + deoxyribonucleotide(n) + deoxyribonucleotide(m) = AMP + diphosphate + deoxyribonucleotide(n+m).
1 P49916 (/IMP)
DNA ligase (ATP) activity GO:0003910
Catalysis of the reaction: ATP + deoxyribonucleotide(n) + deoxyribonucleotide(m) = AMP + diphosphate + deoxyribonucleotide(n+m).
1 P97386 (/ISO)
Ligase activity GO:0016874
Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
1 Q5ZLW6 (/TAS)

There are 25 GO terms relating to "biological process"

The search results have been sorted with the annotations that are found most frequently at the top of the list. The results can be filtered by typing text into the search box at the top of the table.
GO Term Annotations Evidence
Base-excision repair, DNA ligation GO:0006288
The ligation by DNA ligase of DNA strands. Ligation occurs after polymerase action to fill the gap left by the action of endonucleases during base-excision repair.
3 A0A096MKE9 (/IDA) P49916 (/IDA) Q5U2M4 (/IDA)
Mitochondrial DNA repair GO:0043504
The process of restoring mitochondrial DNA after damage.
2 P49916 (/IMP) P97386 (/IMP)
Double-strand break repair via alternative nonhomologous end joining GO:0097681
An instance of double-strand break repair via nonhomologous end joining that is independent of factors important for V(D)J recombination (as opposed to classical nonhomologous end joining). It often results in a deletion with microhomology (i.e. 5-25bp homology) at the repair junction. Among different subclasses of nonhomologous end joining (NHEJ), alternative NHEJ appears to play a significant role in the etiology of mutations that arise during cancer development and treatment.
2 A0A0R4ITF1 (/IMP) P97386 (/IMP)
Double-strand break repair via homologous recombination GO:0000724
The error-free repair of a double-strand break in DNA in which the broken DNA molecule is repaired using homologous sequences. A strand in the broken DNA searches for a homologous region in an intact chromosome to serve as the template for DNA synthesis. The restoration of two intact DNA molecules results in the exchange, reciprocal or nonreciprocal, of genetic material between the intact DNA molecule and the broken DNA molecule.
1 P49916 (/TAS)
DNA ligation GO:0006266
The re-formation of a broken phosphodiester bond in the DNA backbone, carried out by DNA ligase.
1 P49916 (/IDA)
DNA ligation GO:0006266
The re-formation of a broken phosphodiester bond in the DNA backbone, carried out by DNA ligase.
1 P97386 (/ISO)
DNA repair GO:0006281
The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
1 Q5ZLW6 (/TAS)
Transcription-coupled nucleotide-excision repair GO:0006283
The nucleotide-excision repair process that carries out preferential repair of DNA lesions on the actively transcribed strand of the DNA duplex. In addition, the transcription-coupled nucleotide-excision repair pathway is required for the recognition and repair of a small subset of lesions that are not recognized by the global genome nucleotide excision repair pathway.
1 P49916 (/TAS)
Base-excision repair GO:0006284
In base excision repair, an altered base is removed by a DNA glycosylase enzyme, followed by excision of the resulting sugar phosphate. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase.
1 Q5ZLW6 (/TAS)
Base-excision repair, DNA ligation GO:0006288
The ligation by DNA ligase of DNA strands. Ligation occurs after polymerase action to fill the gap left by the action of endonucleases during base-excision repair.
1 P49916 (/IMP)
Base-excision repair, DNA ligation GO:0006288
The ligation by DNA ligase of DNA strands. Ligation occurs after polymerase action to fill the gap left by the action of endonucleases during base-excision repair.
1 P97386 (/ISO)
Base-excision repair, DNA ligation GO:0006288
The ligation by DNA ligase of DNA strands. Ligation occurs after polymerase action to fill the gap left by the action of endonucleases during base-excision repair.
1 P49916 (/TAS)
Nucleotide-excision repair, DNA gap filling GO:0006297
Repair of the gap in the DNA helix by DNA polymerase and DNA ligase after the portion of the strand containing the lesion has been removed by pyrimidine-dimer repair enzymes.
1 P49916 (/TAS)
Double-strand break repair GO:0006302
The repair of double-strand breaks in DNA via homologous and nonhomologous mechanisms to reform a continuous DNA helix.
1 P49916 (/IDA)
Double-strand break repair GO:0006302
The repair of double-strand breaks in DNA via homologous and nonhomologous mechanisms to reform a continuous DNA helix.
1 P97386 (/ISO)
Double-strand break repair via nonhomologous end joining GO:0006303
The repair of a double-strand break in DNA in which the two broken ends are rejoined with little or no sequence complementarity. Information at the DNA ends may be lost due to the modification of broken DNA ends. This term covers instances of separate pathways, called classical (or canonical) and alternative nonhomologous end joining (C-NHEJ and A-NHEJ). These in turn may further branch into sub-pathways, but evidence is still unclear.
1 P97386 (/IMP)
Mitochondrion organization GO:0007005
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a mitochondrion; includes mitochondrial morphogenesis and distribution, and replication of the mitochondrial genome as well as synthesis of new mitochondrial components.
1 P49916 (/IDA)
Mitochondrion organization GO:0007005
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a mitochondrion; includes mitochondrial morphogenesis and distribution, and replication of the mitochondrial genome as well as synthesis of new mitochondrial components.
1 P97386 (/IMP)
Mitochondrion organization GO:0007005
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a mitochondrion; includes mitochondrial morphogenesis and distribution, and replication of the mitochondrial genome as well as synthesis of new mitochondrial components.
1 P97386 (/ISO)
Mitochondrial DNA repair GO:0043504
The process of restoring mitochondrial DNA after damage.
1 P97386 (/ISO)
Negative regulation of DNA recombination GO:0045910
Any process that stops, prevents, or reduces the frequency, rate or extent of DNA recombination.
1 P97386 (/IMP)
Negative regulation of mitochondrial DNA replication GO:0090298
Any process that decreases the rate, frequency or extent of the process in which new strands of DNA are synthesized in the mitochondrion.
1 P49916 (/IMP)
Negative regulation of mitochondrial DNA replication GO:0090298
Any process that decreases the rate, frequency or extent of the process in which new strands of DNA are synthesized in the mitochondrion.
1 P97386 (/ISO)
Double-strand break repair via alternative nonhomologous end joining GO:0097681
An instance of double-strand break repair via nonhomologous end joining that is independent of factors important for V(D)J recombination (as opposed to classical nonhomologous end joining). It often results in a deletion with microhomology (i.e. 5-25bp homology) at the repair junction. Among different subclasses of nonhomologous end joining (NHEJ), alternative NHEJ appears to play a significant role in the etiology of mutations that arise during cancer development and treatment.
1 P49916 (/IGI)
Double-strand break repair via alternative nonhomologous end joining GO:0097681
An instance of double-strand break repair via nonhomologous end joining that is independent of factors important for V(D)J recombination (as opposed to classical nonhomologous end joining). It often results in a deletion with microhomology (i.e. 5-25bp homology) at the repair junction. Among different subclasses of nonhomologous end joining (NHEJ), alternative NHEJ appears to play a significant role in the etiology of mutations that arise during cancer development and treatment.
1 P97386 (/ISO)

There are 11 GO terms relating to "cellular component"

The search results have been sorted with the annotations that are found most frequently at the top of the list. The results can be filtered by typing text into the search box at the top of the table.
GO Term Annotations Evidence
Nucleus GO:0005634
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
3 A0A096MKE9 (/IDA) P49916 (/IDA) Q5U2M4 (/IDA)
Nucleoplasm GO:0005654
That part of the nuclear content other than the chromosomes or the nucleolus.
2 P49916 (/TAS) Q5ZLW6 (/TAS)
Condensed nuclear chromosome GO:0000794
A highly compacted molecule of DNA and associated proteins resulting in a cytologically distinct nuclear chromosome.
1 P97386 (/IDA)
Synaptonemal complex GO:0000795
A proteinaceous scaffold found between homologous chromosomes during meiosis. It consists of 2 lateral elements and a central element, all running parallel to each other. Transverse filaments connect the lateral elements to the central element.
1 P97386 (/IDA)
Nucleus GO:0005634
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
1 P97386 (/ISO)
Nucleoplasm GO:0005654
That part of the nuclear content other than the chromosomes or the nucleolus.
1 P49916 (/IDA)
Nucleoplasm GO:0005654
That part of the nuclear content other than the chromosomes or the nucleolus.
1 P97386 (/ISO)
Mitochondrion GO:0005739
A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
1 P49916 (/IDA)
Mitochondrion GO:0005739
A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
1 P97386 (/ISO)
DNA ligase III-XRCC1 complex GO:0070421
A protein complex that contains DNA ligase III and XRCC1, and is involved in base excision repair.
1 P49916 (/IDA)
DNA ligase III-XRCC1 complex GO:0070421
A protein complex that contains DNA ligase III and XRCC1, and is involved in base excision repair.
1 P97386 (/ISO)