Crystal structure of the Mus81–Eme1 complex

Chang, Jeong Ho; Kim, Jeong Joo; Choi, Jung Min; Lee, Jung Hoon; Cho, Yunje

doi:10.1101/gad.1618708

Cited by 53 publications

(102 citation statements)

References 48 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…5B). Although not directly analogous, Mus81-Eme1 also recognizes the 39 flap substrate through four domains (nuclease, nuclease-like, and two helix-hairpinhelix [HhH 2 ] domains) and undergoes a gross rigid body movement of the HhH 2 domain to place the scissile bond into the active site (Chang et al 2008;Gwon et al 2014). Such rotation has been proposed to provide Mus81-Eme1 with exonuclease activity.…”

Section: Fan1 Shares Several Common Features With Other Structure-selmentioning

confidence: 99%

Crystal structure of a Fanconi anemia-associated nuclease homolog bound to 5′ flap DNA: basis of interstrand cross-link repair by FAN1

et al. 2014

Self Cite

View full text Add to dashboard Cite

Fanconi anemia (FA) is an autosomal recessive genetic disorder caused by defects in any of 15 FA genes responsible for processing DNA interstrand cross-links (ICLs). The ultimate outcome of the FA pathway is resolution of crosslinks, which requires structure-selective nucleases. FA-associated nuclease 1 (FAN1) is believed to be recruited to lesions by a monoubiquitinated FANCI-FANCD2 (ID) complex and participates in ICL repair. Here, we determined the crystal structure of Pseudomonas aeruginosa FAN1 (PaFAN1) lacking the UBZ (ubiquitin-binding zinc) domain in complex with 59 flap DNA. All four domains of the right-hand-shaped PaFAN1 are involved in DNA recognition, with each domain playing a specific role in bending DNA at the nick. The six-helix bundle that binds the junction connects to the catalytic viral replication and repair (VRR) nuclease (VRR nuc) domain, enabling FAN1 to incise the scissile phosphate a few bases distant from the junction. The six-helix bundle also inhibits the cleavage of intact Holliday junctions. PaFAN1 shares several conserved features with other flap structure-selective nucleases despite structural differences. A clamping motion of the domains around the wedge helix, which acts as a pivot, facilitates nucleolytic cleavage. The PaFAN1 structure provides insights into how archaeal Holliday junction resolvases evolved to incise 59 flap substrates and how FAN1 integrates with the FA complex to participate in ICL repair.

show abstract

Section: Fan1 Shares Several Common Features With Other Structure-selmentioning

confidence: 99%

Crystal structure of a Fanconi anemia-associated nuclease homolog bound to 5′ flap DNA: basis of interstrand cross-link repair by FAN1

et al. 2014

Self Cite

View full text Add to dashboard Cite

show abstract

“…A fundamental question is, what are the DNA joint molecules targeted by Mus81-Mms4 in vivo? Biochemical analysis of purified and partially purified Mus81-Mms4 protein shows catalytic and robust cleavage of nicked, 3=-flap, and displacement loop (D-loop) substrates to be the preferential in vitro target for Mus81 (5,9,13,14,21,23,26,45). Yet, it is the highly inefficient incision of intact, four-way HJs that has resulted in widely discussed models suggesting that intact HJs or dHJs are the physiological substrates for Mus81-Mms4 in CO formation (9,14,26,38,52,57).…”

mentioning

confidence: 99%

Mus81-Mms4 Functions as a Single Heterodimer To Cleave Nicked Intermediates in Recombinational DNA Repair

Schwartz

Wright

Ehmsen

et al. 2012

Molecular and Cellular Biology

View full text Add to dashboard Cite

The formation of crossovers is a fundamental genetic process. The XPF-family endonuclease Mus81-Mms4 (Eme1) contributes significantly to crossing over in eukaryotes. A key question is whether Mus81-Mms4 can process Holliday junctions that contain four uninterrupted strands. Holliday junction cleavage requires the coordination of two active sites, necessitating the assembly of two Mus81-Mms4 heterodimers. Contrary to this expectation, we show that Saccharomyces cerevisiae Mus81-Mms4 exists as a single heterodimer both in solution and when bound to DNA substrates in vitro. Consistently, immunoprecipitation experiments demonstrate that Mus81-Mms4 does not multimerize in vivo. Moreover, chromatin-bound Mus81-Mms4 does not detectably form higher-order multimers. We show that Cdc5 kinase activates Mus81-Mms4 nuclease activity on 3= flaps and Holliday junctions in vitro but that activation does not induce a preference for Holliday junctions and does not induce multimerization of the Mus81-Mms4 heterodimer. These data support a model in which Mus81-Mms4 cleaves nicked recombination intermediates such as displacement loops (D-loops), nicked Holliday junctions, or 3= flaps but not intact Holliday junctions with four uninterrupted strands. We infer that Mus81-dependent crossing over occurs in a noncanonical manner that does not involve the coordinated cleavage of classic Holliday junctions. Robin Holliday first proposed a mechanism for crossover formation (29). Based on fungal tetrad data, he envisioned that nick-induced heteroduplex formation could result in a DNA intermediate composed of four intact strands after ligation of the strand interruptions. This intermediate was later termed the Holliday junction (HJ). Cleavage across the two alternative planes of this junction would result in crossover (CO) or noncrossover (NCO) products, depending on the orientation of cleavage. Biochemical analysis of the bacterial RuvC nuclease supports this model and provides a paradigm for a class of enzymes called Holliday junction resolvases. These nucleases form homodimeric complexes to deliver two coordinated and symmetric endonucleolytic cuts that generate DNA ends that can be directly ligated to form recombinant products (reviewed in reference 38). However, RuvC is not evolutionarily conserved in eukaryotes, and the specific mechanisms of crossover formation in eukaryotes are still undefined. Refinement and expansion of the original Holliday model have produced the current model of double-strand break repair, in which one subpathway is defined by the formation of a double Holliday junction (dHJ) (46). Physical analysis has demonstrated the existence of dHJs in meiotic and mitotic recombination (12, 48). However, these studies could not establish whether these junctions were truly dHJs, i.e., with each individual junction having four uninterrupted strands, or were nicked junctions in a dHJ population where each strand could be found to be full length (for more discussion, see reference 49). Hence, the importance of Holliday junctions...

show abstract

“…In normal cells, these resultant DSBs can be repaired by HR, but in cancer cells that are defective in HR, these DSBs will accumulate and eventually induce cell death (54). This explanation, however, has been challenged by alternative models.…”

Section: Sl-based Targeted Therapymentioning

confidence: 92%

“…For example, the protein p73 (also known as TP73), which belongs to the same family as the well-known tumour suppressor p53, was recently discovered to regulate DNA repair gene expression [54]. As another example, MXD3, whose role in human DNA repair has not begun to be explored, was recently proposed to be involved in DNA repair in mouse [55].…”

Section: Selected(tfs(that(may(be(major(drivers(of(dna(repair(dysregumentioning

confidence: 99%

See 1 more Smart Citation

Computational analysis of DNA repair pathways in breast cancer

Liu¹

View full text Add to dashboard Cite

The integrity of the human genome is constantly challenged by a variety of endogenous and exogenous factors such as ultraviolet radiation and cigarette smoke. To deal with these threats, five major DNA repair pathways, which are principally defined by the type of lesions they repair, have evolved. Defects in these repair pathways predispose individuals to a wide variety of cancers, and at the same time can be therapeutically exploited to target tumours with defective DNA repair.Dysregulation of these repair pathways are also frequently observed in cancer, presenting both opportunities and challenges for cancer therapy: downregulated repair pathways sensitise tumours to DNA-damaging therapies, while upregulated repair pathways cause resistance to these therapies.The primary aim of this thesis is to obtain a comprehensive and in-depth understanding of the mechanisms and roles of these major DNA repair pathways in the context of breast cancer. This will be beneficial for predicting response to radiation and chemotherapy, and for developing novel targeted therapies in this common type of malignancy.By careful literature search and consulting a domain expert, the research presented in this thesis started with a manual curation of six DNA repair pathways, including the five major repair pathways and the Fanconi anaemia pathway that is closely associated with breast cancer susceptibility. Six comprehensive pathway figures were generated, each for one repair pathway, describing in total 195 genes and 138 reactions with direct relevance to DNA repair. Moreover, to facilitate a deep understanding of the repair mechanisms, a detailed description for each reaction was given, importantly including the literature references used for curating the reaction. This curation work enables a mechanistic understanding of how cells respond to DNA damage, and provides a solid foundation for the subsequent computational analyses.In the second study of this PhD research, I performed a personalised pathway analysis to investigate the status of homologous recombination (HR) pathway dysregulation in individual sporadic breast tumours, its association with HR repair deficiency and its impact on tumour characteristics.Specifically, using the expression values of the HR genes curated in the previous study, I calculated an HR score for each tumour that quantifies the extent of HR pathway dysregulation in that tumour.Based on that score, I observed a great diversity in HR dysregulation between and within gene expression-based breast cancer subtypes. And by comparing to two published HR-defect signatures, I found HR pathway dysregulation reflects HR repair deficiency. Furthermore, I uncovered a novel association between HR pathway dysregulation and chromosomal instability (CIN): tumours with more-dysregulated HR tend to have higher CIN. Although CIN has long been considered to be a iii hallmark of most solid tumours, with recent studies highlighting its importance in tumour evolution and drug resistance, the molecular basis of CIN in spora...

show abstract

Crystal structure of the Mus81–Eme1 complex

Cited by 53 publications

References 48 publications

Crystal structure of a Fanconi anemia-associated nuclease homolog bound to 5′ flap DNA: basis of interstrand cross-link repair by FAN1

Crystal structure of a Fanconi anemia-associated nuclease homolog bound to 5′ flap DNA: basis of interstrand cross-link repair by FAN1

Mus81-Mms4 Functions as a Single Heterodimer To Cleave Nicked Intermediates in Recombinational DNA Repair

Computational analysis of DNA repair pathways in breast cancer

Contact Info

Product

Resources

About