Structure and function of mammalian DNA ligases

Tomkinson, Alan E.; Mackey, Zachary B.

doi:10.1016/s0921-8777(97)00050-5

Cited by 185 publications

(131 citation statements)

References 54 publications

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“…It was also reported that mitochondrial DNA polymerase gamma (Polg) and mtDNA ligase (Lig IIIb), which are involved in mtDNA replication are also functional in mitochondrial BER [154,155]. Lig IIIb is a splice variant of the nuclear Lig IIIa, whereas Polg is unique for the mitochondria [156]. Similarly, splice variants of nuclear OGG1 and NTH1 have been characterized in mitochondria [69,157].…”

Section: Ber In Mitochondriamentioning

confidence: 99%

Early steps in the DNA base excision/single-strand interruption repair pathway in mammalian cells

2008

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Base excision repair (BER) is an evolutionarily conserved process for maintaining genomic integrity by eliminating several dozen damaged (oxidized or alkylated) or inappropriate bases that are generated endogenously or induced by genotoxicants, predominantly, reactive oxygen species (ROS). BER involves 4-5 steps starting with base excision by a DNA glycosylase, followed by a common pathway usually involving an AP-endonuclease (APE) to generate 3′ OH terminus at the damage site, followed by repair synthesis with a DNA polymerase and nick sealing by a DNA ligase. This pathway is also responsible for repairing DNA single-strand breaks with blocked termini directly generated by ROS. Nearly all glycosylases, far fewer than their substrate lesions particularly for oxidized bases, have broad and overlapping substrate range, and could serve as back-up enzymes in vivo. In contrast, mammalian cells encode only one APE, APE1, unlike two APEs in lower organisms. In spite of overall similarity, BER with distinct subpathways in the mammals is more complex than in E. coli. The glycosylases form complexes with downstream proteins to carry out efficient repair via distinct subpathways one of which, responsible for repair of strand breaks with 3′ phosphate termini generated by the NEIL family glycosylases or by ROS, requires the phosphatase activity of polynucleotide kinase instead of APE1. Different complexes may utilize distinct DNA polymerases and ligases. Mammalian glycosylases have nonconserved extensions at one of the termini, dispensable for enzymatic activity but needed for interaction with other BER and non-BER proteins for complex formation and organelle targeting. The mammalian enzymes are sometimes covalently modified which may affect activity and complex formation. The focus of this review is on the early steps in mammalian BER for oxidized damage.

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Section: Ber In Mitochondriamentioning

confidence: 99%

Early steps in the DNA base excision/single-strand interruption repair pathway in mammalian cells

2008

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“…1) (16,17) and have similar core structures, including a highly divergent DNAbinding domain (DBD) and a well conserved catalytic core (CC) made up of the nucleotidyltransferase (NTase) and oligonucleotide/oligosaccharide-binding domains (OBD) (18,19). Together, the DBD and CC enable mammalian ligases to fully encircle a DNA substrate, stabilizing a highly distorted, partially underwound structure that positions the DNA termini within the active site (18).…”

mentioning

confidence: 99%

Two DNA-binding and Nick Recognition Modules in Human DNA Ligase III

Cotner-Gohara

Kim

Tomkinson

et al. 2008

Journal of Biological Chemistry

100

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“…Lig4 contains one ATP-dependent DNA ligase domain at the N-terminal region (28) and two BRCA1 C terminus (BRCT) domains at the C-terminal region (29). The BRCT domain is often implicated in protein-protein interactions and is found predominantly in proteins involved in cell cycle checkpoint functions responsive to DNA damage.…”

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confidence: 99%

Phosphorylation and Regulation of DNA Ligase IV Stability by DNA-dependent Protein Kinase

Wang

Nnakwe

Lane

et al. 2004

Journal of Biological Chemistry

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DNA ligase IV (Lig4), x-ray cross-complementation group 4 (XRCC4), and DNA-dependent protein kinase (DNA-PK) are essential mammalian nonhomologous end joining proteins used for V(D)J recombination and DNA repair. Previously a Lig4 peptide was reported to be an in vitro substrate for DNA-PK, but the phosphorylation state of Lig4 protein in vivo is not known. In this study, we report that a full-length Lig4 construct was expressed as a phosphoprotein in the cell. Also the fulllength Lig4 protein, in complex with XRCC4, was an in vitro substrate for DNA-PK. Using tandem mass spectrometry, we identified a DNA-PK phosphorylation site at Thr-650 in human Lig4 and a potential second phosphorylation site at Ser-668 or Ser-672. Phosphorylation of Lig4 per se was not required for Lig4 DNA end joining activity. Substitution of these amino acids with alanine, individually or in combination, led to changes in Lig4 protein stability of mouse Lig4. The phosphomimetic mutation S650D returned Lig4 stability to that of the wild-type protein. Furthermore DNA-PK was found to negatively regulate Lig4 protein stability. Our results suggest that Lig4 stability is regulated by multiple factors, including interaction with XRCC4, phosphorylation status, and possibly Lig4 conformation.Nonhomologous end joining (NHEJ) 1 is an efficient mechanism used by mammalian cells to repair DNA double strand breaks (1, 2) and is also required for the process of V(D)J recombination, the rearrangement of immunoglobulin and Tcell receptor genes essential for the generation of a diverse immune response (3). XRCC4 and DNA ligase IV (Lig4), which form a ligation complex in the cell (4, 5), are two critical proteins involved in these two processes (6 -8).The five most well studied proteins that are required for both NHEJ and V(D)J recombination in mammalian cells are Ku70, Ku80, DNA-dependent protein kinase catalytic subunit (DNAPKcs), XRCC4, and Lig4. The heterodimeric Ku protein, comprising subunits Ku70 and Ku80, binds strongly to doublestranded DNA ends (9). When bound to DNA, Ku recruits DNA-PKcs and activates its kinase activity (10, 11). The XRCC4⅐Lig4 protein complex is recruited to the DNA ends to complete ligation (4,5,12). An additional protein, Artemis, which has nuclease activity and can open DNA hairpin intermediates with DNA-PKcs during V(D)J recombination (13), has also been shown to be involved in both NHEJ and V(D)J recombination (14, 15).Mice lacking NHEJ components have abnormal lymphocyte development due to defective V(D)J recombination (16). Mice deficient in Ku70, Ku80, XRCC4, or Lig4 also exhibit growth defects, premature senescence, and hypersensitivity to ionizing irradiation. Deficiency of XRCC4 or Lig4 is most severe, resulting in significant neuronal apoptosis and embryonic lethality (7,8,17). Embryonic fibroblast cells that are deficient for either DNA-PKcs or Artemis also exhibit cell type-specific ionizing irradiation hypersensitivity (16). Defects in the NHEJ factors have also been implicated in the generation of chromosome i...

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Structure and function of mammalian DNA ligases

Cited by 185 publications

References 54 publications

Early steps in the DNA base excision/single-strand interruption repair pathway in mammalian cells

Early steps in the DNA base excision/single-strand interruption repair pathway in mammalian cells

Two DNA-binding and Nick Recognition Modules in Human DNA Ligase III

Phosphorylation and Regulation of DNA Ligase IV Stability by DNA-dependent Protein Kinase

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