Human DNA Ligase IV-Artemis Fragment Complex

Sean Smith '16 and Samantha White '16


Contents:


I. Introduction

DNA ligase IV (LigIV) is an enzyme that helps to repair double strand breaks (DSBs) through nonhomologous end joining (NHEJ). This is accomplished when DNA protein kinase (DNA-PK) binds to the ends of the DSBs and brings them together. The DNA-PK catalytic subunit (DNA-PKcs) then recruits the protein Artemis and this enzyme, along with other proteins, processes the ends of the DNA to be joined. The NHEJ ligase complex is then recruited, and LigIV, XRCC4 and XLF-Cernunnos work to connect the two DNA strands.

 


II. General Structure

Human LigIV has a catalytic region that includes a DNA binding domain (DBD), a nucleotidyltransferase domain (NTD), and an OB-fold domain (OBD) . It also has repeats of a BRCT domain at the carboxy terminus which interact with XRCC4. In comparison to other human DNA ligases, there are unique inserts between alpha chain 5 and alpha chain 6 of the DBD region and between alpha chain 15 and alpha chain 16 of the NTD region. When LigIV is not in complex with Artemis, the conformation of the loop between beta sheet 12 and beta sheet 13 is altered.

III. Artemis-LigIV Interactions

It has been found that LigIV makes contact with Artemis through its first and second alpha helices, found in the DBD domain. This interaction buries 436 2 of the surfaces of the two proteins. A kink in alpha helix 1

exists due to the proline P15 , and this distortion produces a hydrophobic pocket in which the tryptophan W489 from Artemis associates (residues from Artemis italicized). In this pocket, W489 engages in van der Waals interactions with V14 from LigIV This hydrophobic interaction is stabilized by the interactions between F492 of Artemis and F49 of LigIV, and the interactions between F493 of Artemis and F42 of LigIV. The Nsigma of W489 also makes a hydrogen bond with the side chain of D18 from LigIV.

It was found that when W489, F492 or F493 of Artemis was mutated to alanine, the LigIV-Artemis complex could no longer form.


IV. LIG 4 Syndrome Mutations

LIG4 syndrome is a hereditary disorder that results from the disruption of normal NHEJ due to mutations in the LigIV enzyme. This disorder is characterized by microcephaly, growth and developmental delay, and pancytopenia, among other conditions. One of the residues whose mutation causes LIG4 syndrome is T9. This residue interacts in a polar way with S12 and Q146, and when it is mutated, the flexibility of some of the residues in the DBD may be increased and DNA binding may be inhibited. This syndrome also occurs when the M249 residue in the NTD region is mutated. M249 stabilizes W447, which interacts with K432, which are part of the catalytic pocket. Therefore it is probable that the mutation of M249 leads to destabilization of the catalytic pocket due to the decreased rigidity of W447 and K432. The residue G469 interacts with two tryptophan side chains, W471 and W526. When this guanine is mutated, the structure of the OBD region may change, and its adenylation and ligation functions may be inhibited. 


V. References

Ochi, T., Gu, X., and Blundell, T. (2013). Structure of the catalytic region of DNA Ligase IV in complex with an artemis fragment sheds light on double-strand break repair. Structure, 21(4):672-679.

Malu, S., De Ioannes, P., Kozlov, M., Greene, M., Francis, D., Hanna, M., Pena, J., Escalante, C. R., Kurosawa, A., Erdjument-Bromage, H., Tempst, P., Adachi, N., Vezzoni, P., Villa, A., Aggarwal, A. K., and Cortes, P. (2012). Artemis C-terminal region facilitates V(D)J recombination through its interactions with DNA Ligase IV and DNA-PKcs. JEM, 209(5):955-963.

(July 2012). LIG4 syndrome. Orphanet. [Online]. Available: http://www.orpha.net/consor/cgi-bin/OC_Exp.php?lng=en&Expert=99812. [2013, December 9].

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