DNA Ligase IV

A family of Proteins

DNA ligases are a large family of proteins involved in DNA replication, repair and recombination. All DNA ligases follow the same reaction mechanism, but can be subdivided into two groups based on cofactor preferences: NAD+-dependent DNA ligases (EC 6.5.1.2; IPR0001679) are found only in eubacteria, while ATP-dependent DNA ligases (EC 6.5.1.1; IPR000977) are found in eukaryotes, archaea, eubacteria and viruses. In eukaryotes, three related classes of ATP-dependent enzymes (DNA ligases I, III and IV) are found, which differ in their ability to ligate a variety of nucleic acid substrates, and which have specific functions within the cell. DNA ligase I, which is conserved in all eukaryotes, is required during DNA replication for the ligation of Okazaki fragments during lagging-strand synthesis, as well as for DNA repair. DNA ligase III, which is unique to vertebrates, occurs as two distinct isoforms that arise by alternative splicing, one of which interacts with the mammalian DNA repair factor XRCC1. DNA ligase III functions to correct defective DNA strand-break repair, as well as in sister chromatid exchange during meiotic recombination.

DNA ligases I, III and IV are related in sequence and structure, being descended from a common ancestor. A series of motifs occur in the sequence alignments of ATP-dependent DNA ligases, which have been used to help construct the signatures in InterPro that define the family.

P49917 Human DNA ligase IV entry from InterPro

InterPro domain architecture

InterPro entry	Method accession	Graphical match	Method name
IPR000977	PF01068		DNA_ligase_A_M
IPR000977	PF04675		DNA_ligase_A_N
IPR000977	PF04679		DNA_ligase_A_C
IPR000977	PS00333		DNA_LIGASE_A2
IPR000977	PS00697		DNA_LIGASE_A1
IPR000977	PS50160		DNA_LIGASE_A3
IPR000977	PS50161		DNA_LIGASE_A4
IPR000977	TIGR00574		dnl1
IPR001357	PF00533		BRCT
IPR001357	PS50172		BRCT
IPR001357	SM00292		BRCT
IPR008994	SSF50249		Nucleic_acid_OB
Classification	PDB chain/Domain ID	PDB chain/Structural Domains
1ik9	1ik9c

What InterPro Tells Us

From the graphical match table above, you can see that the signatures (method accession) are divided into three InterPro entries for human DNA ligase IV. These entries give information about the domain architecture of the protein, as well as its family relationships.

To look at the family relationships that involve DNA ligase IV, we need to look at the entries at the top of the table, IPR000977, which has 8 signatures representing the ATP-dependent DNA ligase family. These signatures are: PF01068, PF04675 and PF04679 from the PFAM database, which represent the ATP-dependent ligase domain, the N-terminal domain and the C-terminal region, respectively, and which together detect members of this family; PS00333, PS00697, PS50160 and PS50161 from the PROSITE database, which represent the conserved regions found in the ATP-dependent DNA ligase family; and TIGR00574 from the TIGRFAM database, which covers the entire core of the protein family.

The domain architecture of DNA ligase IV is represented in the ‘InterPro domain architecture’ (IDA) diagram at the top of the page, as well as in the graphical match table. The IDA diagram describes two main domain types: a DNA ligase domain and (two) BRCT domains. The DNA ligase domain is the central core of the enzyme that is common to the ATP-dependent DNA ligase family, namely the N-terminal non-catalytic region and the catalytic region together. The two BRCT domains are found only in some DNA ligases, including DNA ligase IV, but are not common to the entire family. A comparison of IDA with the known domain architecture of DNA ligase IV is shown below:

The Graphical match table includes the signatures describing some of these domains. Three signatures represent IPR001357, the C-terminal BRCT domain: PF00533 from the PFAM database, PS50172 from the PROSITE database, and SM00292 from the SMART database. IPR008994 is the nucleic acid-binding OB-fold that forms part of the catalytic domain, and which is characteristic of many nucleic-acid-binding protein; it is represented by one signature, SSF50249 from the SUPERFAMILY database.

The remaining entry in the table is from the structural database PDB, and displays the region of the protein that has structural information (the name, 1ik9c, refers to PDB entry 1ik9, chain C). The region is very small, and corresponds to the insert region between the two BRCT domains, as depicted in the red-boxed region in the diagram above. This region is structurally important, because it is the site of binding to the XRCC4 protein, which undergoes conformational changes that are required for the NHEJ process.

What the Structure Tell Us

There are structures of DNA ligase IV and other DNA ligases in the Protein Data Bank (PDB); in particular the insert region between the two BRCT domains mentioned above. A detailed description and visualisation of the structural features of DNA ligase IV can be found at the PDB 'Molecule of the Month' .

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