Eukaryotic DNA Ligases: Structural and Functional Insights

Ellenberger, Tom; Tomkinson, Alan E.

doi:10.1146/annurev.biochem.77.061306.123941

Cited by 298 publications

(355 citation statements)

References 157 publications

(298 reference statements)

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“…This indicates that the catalytic events that are affected by PCNA binding to DNAligI are the binding of the nicked DNA and turnover event. Taken all together, the dispensability of PIP box for PCNA interaction and the observed conformational change in the yeast PCNA–DNAlig complex, we think that our data support a similar mechanism to the one proposed by Ellenberger and Tomkinson′s groups 9, 15, 16, 35 (Fig 8B). In this mechanism, in the absence of PCNA, DNAligI has to carry large structural changes previous to the nick‐sealing reaction followed by product release associated with return to the initial structural stage.…”

Section: Discussionsupporting

confidence: 89%

Proliferating cell nuclear antigen restores the enzymatic activity of a DNA ligase I deficient in DNA binding

Trasviña-Arenas¹,

Cardona-Félix²,

Azuara-Licéaga

et al. 2017

FEBS Open Bio

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Proliferating cell nuclear antigen (PCNA) coordinates multienzymatic reactions by interacting with a variety of protein partners. Family I DNA ligases are multidomain proteins involved in sealing of DNA nicks during Okazaki fragment maturation and DNA repair. The interaction of DNA ligases with the interdomain connector loop (IDCL) of PCNA through its PCNA‐interacting peptide (PIP box) is well studied but the role of the interacting surface between both proteins is not well characterized. In this work, we used a minimal DNA ligase I and two N‐terminal deletions to establish that DNA binding and nick‐sealing stimulation of DNA ligase I by PCNA are not solely dependent on the PIP box–IDCL interaction. We found that a truncated DNA ligase I with a deleted PIP box is stimulated by PCNA. Furthermore, the activity of a DNA ligase defective in DNA binding is rescued upon PCNA addition. As the rate constants for single‐turnover ligation for the full‐length and truncated DNA ligases are not affected by PCNA, our data suggest that PCNA stimulation is achieved by increasing the affinity for nicked DNA substrate and not by increasing catalytic efficiency. Surprisingly C‐terminal mutants of PCNA are not able to stimulate nick‐sealing activity of Entamoeba histolytica DNA ligase I. Our data support the notion that the C‐terminal region of PCNA may be involved in promoting an allosteric transition in E. histolytica DNA ligase I from a spread‐shaped to a ring‐shaped structure. This study suggests that the ring‐shaped PCNA is a binding platform able to stabilize coevolved protein–protein interactions, in this case an interaction with DNA ligase I.

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Section: Discussionsupporting

confidence: 89%

Proliferating cell nuclear antigen restores the enzymatic activity of a DNA ligase I deficient in DNA binding

Trasviña-Arenas¹,

Cardona-Félix²,

Azuara-Licéaga

et al. 2017

FEBS Open Bio

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“…D NA ligase plays essential roles in various DNA transactions, such as joining Okazaki fragments in DNA replication and nick-sealing at the final step of several DNA repair pathways, including nucleotide excision repair, base excision repair, and mismatch repair (1,2). The enzyme catalyzes phosphodiester bond formation at the nicks generated within dsDNA, through the well-conserved 3-step reaction using either NAD ϩ or ATP as a cofactor (3).…”

mentioning

confidence: 99%

Mechanism of replication machinery assembly as revealed by the DNA ligase–PCNA–DNA complex architecture

Mayanagi

Kiyonari

Saito

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

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The 3D structure of the ternary complex, consisting of DNA ligase, the proliferating cell nuclear antigen (PCNA) clamp, and DNA, was investigated by single-particle analysis. This report presents the structural view, where the crescent-shaped DNA ligase with 3 distinct domains surrounds the central DNA duplex, encircled by the closed PCNA ring, thus forming a double-layer structure with dual contacts between the 2 proteins. The relative orientations of the DNA ligase domains, which remarkably differ from those of the known crystal structures, suggest that a large domain rearrangement occurs upon ternary complex formation. A second contact was found between the PCNA ring and the middle adenylation domain of the DNA ligase. Notably, the map revealed a substantial DNA tilt from the PCNA ring axis. This structure allows us to propose a switching mechanism for the replication factors operating on the PCNA ring.DNA replication ͉ electron microscopy ͉ single-particle analysis ͉ DNA sliding clamp ͉ protein-DNA complex D NA ligase plays essential roles in various DNA transactions, such as joining Okazaki fragments in DNA replication and nick-sealing at the final step of several DNA repair pathways, including nucleotide excision repair, base excision repair, and mismatch repair (1, 2). The enzyme catalyzes phosphodiester bond formation at the nicks generated within dsDNA, through the well-conserved 3-step reaction using either NAD ϩ or ATP as a cofactor (3). At the first step, the DNA ligase interacts with the nucleotide cofactor to form a covalent ligase-nucleoside monophosphate. At the second step, the bound AMP is transferred to the 5Ј terminus of the DNA, and finally, a phosphodiester bond is formed by a reaction between the 5Ј-DNAadenylate and the 3Ј-hydroxy group.To date, 3 crystal structures of ATP-dependent eukaryotictype DNA ligases have been reported. The structures of the 2 archaeal DNA ligases from Pyrococcus furiosus (PfuLig) and Sulfolobus solfataricus (SsoLig) were determined in the closed (4) and extended forms (5), respectively. The structure of the human DNA ligase 1 (hLigI) in complex with DNA (6) revealed that the enzyme entirely encircles the nicked DNA. All of these DNA ligases are in common composed of 3 domains, designated as the DNA binding domain (DBD), the adenylation domain (AdD), and the OB-fold domain (OBD), in the sequences from the N to C termini. Although the internal architectures of these domains are strikingly similar among the 3 DNA ligases, their relative domain orientations within each enzyme are quite different. Similar to many other replication factors, such as DNA polymerase and Flap endonuclease 1 (FEN1), DNA ligases exhibit the full activity by binding to proliferating cell nuclear antigen (PCNA). A small-angle X-ray scattering analysis revealed that the morphology of SsoLig in complex with PCNA coincides with the extended structure of SsoLig alone (5). However, the structure of the ternary Lig-PCNA-DNA complex remains unknown.PCNA interacts with various protein factors to contr...

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“…Vertebrates have three ATP-dependent ligases (I, III, and IV) (13). Lig4 appears to be dedicated to NHEJ as no other function has been described for Lig4 outside the NHEJ realm.…”

mentioning

confidence: 99%

“…Conceivably, joining of S region breaks in Lig4-deficient cells must depend on Lig1 and/or Lig3. Normally, Lig1 complexes with proliferating cell nuclear antigen and is recruited to the replication fork to join Okazaki fragments during DNA replication (13). Lig3 complexes with XRCC1 and was generally considered the ligase involved in single-strand break (SSB) repair pathways.…”

mentioning

confidence: 99%

“…It has been shown that cellular Lig3 activity is dependent on XRCC1 (14), which is a scaffold protein that interacts with many other DNA repair factors (e.g., Parp1, Pol β, APE1, PNKP, aprataxin, etc.) (13). Although the traditional view of Lig3 in nuclear DNA repair has been recently challenged (15,16), the importance of XRCC1 in SSB repair has been well established.…”

mentioning

confidence: 99%

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X-ray repair cross-complementing protein 1 (XRCC1) deficiency enhances class switch recombination and is permissive for alternative end joining

Han

Mao

2012

Proc. Natl. Acad. Sci. U.S.A.

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DNA double-strand breaks (DSBs) are essential intermediates in Ig gene rearrangements: V(D)J and class switch recombination (CSR). In contrast to V(D)J recombination, which is almost exclusively dependent on nonhomologous end joining (NHEJ), CSR can occur in NHEJ-deficient cells via a poorly understand backup pathway (or pathways) often termed alternative end joining (A-EJ). Recently, several components of the single-strand DNA break (SSB) repair machinery, including XRCC1, have been implicated in A-EJ. To determine its role in A-EJ and CSR, Xrcc1 was deleted by targeted mutation in the CSR proficient mouse B-cell line, CH12F3. Here we demonstrate that XRCC1 deficiency slightly increases the efficiency of CSR. More importantly, Lig4 and XRCC1 double-deficient cells switch as efficiently as Lig4-deficient cells, clearly indicating that XRCC1 is dispensable for A-EJ in CH12F3 cells during CSR.A DNA double-strand break (DSB) is one of the most severe forms of DNA damage and can result in chromosome loss or translocations. A variety of endogenous and exogenous sources can induce DSBs, including ionizing radiation, reactive oxygen species, and some chemicals. On the other hand, physiological processes during lymphocyte development such as V(D)J and Ig class switch recombination (CSR) rely on DSBs to rearrange genetic information in somatic cells.V(D)J recombination is a site-specific DNA recombination initiated by the RAG proteins, which are evolved from an ancient DNA transposase. The RAG complex recognizes specific DNA sequences called recombination signal sequences (RSS) and cuts the DNA on one side of the RSS. The ensuing repair of the four DNA ends that are produced from a pair of cleavage events results in joining of subexonic coding fragments to form an exon encoding the antigen-binding domain of a B-or T-cell receptor. In contrast, CSR in antigen-stimulated mature B cells is a regionally specific recombination between two repetitive regions [called switch (S) regions] that precede each of the constant regions (1). Looping out intervening sequences between two S regions allows the expression of a new constant region that was further downstream and results in a switch of Ig class (or isotype) from IgM to IgG, IgE, or IgA (2). CSR is initiated by activation-induced cytidine deaminase (AID) that converts DNA cytosines into uracils at S regions. Through mechanisms that are not yet fully understood, repair of AID-generated uracils in the S region ultimately results in DSBs (2), which serve as critical intermediates in an overall cut-and-paste chromosomal deletion (2).In vertebrate cells, DSB repair mechanisms generally fall into two major categories: homologous recombination (HR) and nonhomologous end joining (NHEJ) (3). HR relies on the presence of another copy of DNA sequences that are highly similar to the one harboring the DSB. Copying genetic information from the intact copy allows high-fidelity repair of the DSB. In complex genomes rich in repetitive DNA sequences, HR is restricted to S and G2 phase of the ce...

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Eukaryotic DNA Ligases: Structural and Functional Insights

Cited by 298 publications

References 157 publications

Proliferating cell nuclear antigen restores the enzymatic activity of a DNA ligase I deficient in DNA binding

Proliferating cell nuclear antigen restores the enzymatic activity of a DNA ligase I deficient in DNA binding

Mechanism of replication machinery assembly as revealed by the DNA ligase–PCNA–DNA complex architecture

X-ray repair cross-complementing protein 1 (XRCC1) deficiency enhances class switch recombination and is permissive for alternative end joining

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