| SMART accession number: | SM00891
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| Description: |
This entry represents a structural motif found in several DNA repair nucleases, such as Rad1/Mus81/XPF endonucleases, and in ATP-dependent helicases. The XPF/Rad1/Mus81-dependent nuclease family specifically cleaves branched structures generated during DNA repair, replication, and recombination, and is essential for maintaining genome stability. The nuclease domain architecture exhibits remarkable similarity to those of restriction endonucleases. |
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| Interpro abstract (IPR006166): |
This entry represents a structural motif found in several DNA repair nucleases, such as Rad1/Mus81/XPF endonucleases (EC 3.1.22) [(PUBMED:12679022)], and in ATP-dependent helicases. The XPF/Rad1/Mus81-dependent nuclease family specifically cleaves branched structures generated during DNA repair, replication, and recombination, and is essential for maintaining genome stability. The nuclease domain architecture exhibits remarkable similarity to those of restriction endonucleases.
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| GO process: | DNA metabolic process (GO:0006259) |
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| GO function: | DNA binding (GO:0003677), nuclease activity (GO:0004518) |
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| Family alignment: |
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Click on the following links for more information.
- Evolution (species in which this domain is found)
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- Cellular role (predicted cellular role)
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Cellular role: chromatin
- Literature (relevant references for this domain)
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Primary literature is listed below; Automatically-derived, secondary literature is also avaliable.
- Gaillard PH, Noguchi E, Shanahan P, Russell P
- The endogenous Mus81-Eme1 complex resolves Holliday junctions by a nickand counternick mechanism.
- Mol Cell. 2003; 12: 747-59
- Display abstract
Functional studies strongly suggest that the Mus81-Eme1 complex resolvesHolliday junctions (HJs) in fission yeast, but in vitro it preferentiallycleaves flexible three-way branched structures that model replicationforks or 3' flaps. Here we report that a nicked HJ is the preferredsubstrate of endogenous and recombinant Mus81-Eme1. Cleavage occursspecifically on the strand that opposes the nick, resulting in resolutionof the structure into linear duplex products. Resolving cuts made by theendogenous Mus81-Eme1 complex on an intact HJ are quasi-simultaneous,indicating that Mus81-Eme1 resolves HJs by a nick and counternickmechanism, with a large rate enhancement of the second cut arising fromthe flexible nature of the nicked HJ intermediate. Recombinant Mus81-Eme1is ineffective at making the first cut. We also report that HJs accumulatein a DNA polymerase alpha mutant that lacks Mus81, providing furtherevidence that the Mus81-Eme1 complex targets HJs in vivo.
- Nishino T, Komori K, Ishino Y, Morikawa K
- X-ray and biochemical anatomy of an archaeal XPF/Rad1/Mus81 familynuclease: similarity between its endonuclease domain and restrictionenzymes.
- Structure. 2003; 11: 445-57
- Display abstract
The XPF/Rad1/Mus81-dependent nuclease family specifically cleaves branchedstructures generated during DNA repair, replication, and recombination,and is essential for maintaining genome stability. Here, we report thedomain organization of an archaeal homolog (Hef) of this family and theX-ray crystal structure of the middle domain, with the nuclease activity.The nuclease domain architecture exhibits remarkable similarity to thoseof restriction endonucleases, including the correspondence of theGDX(n)ERKX(3)D signature motif in Hef to the PDX(n)(E/D)XK motif inrestriction enzymes. This structural study also suggests that theXPF/Rad1/Mus81/ERCC1 proteins form a dimer through each interface of thenuclease domain and the helix-hairpin-helix domain. Simultaneousdisruptions of both interfaces result in their dissociation into separatemonomers, with strikingly reduced endonuclease activities.
- Boddy MN, Gaillard PH, McDonald WH, Shanahan P, Yates JR 3rd, Russell P
- Mus81-Eme1 are essential components of a Holliday junction resolvase.
- Cell. 2001; 107: 537-48
- Display abstract
Mus81, a fission yeast protein related to the XPF subunit of ERCC1-XPFnucleotide excision repair endonuclease, is essential for meiosis andimportant for coping with stalled replication forks. These processesrequire resolution of X-shaped DNA structures known as Holliday junctions.We report that Mus81 and an associated protein Eme1 are components of anendonuclease that resolves Holliday junctions into linear duplex products.Mus81 and Eme1 are required during meiosis at a late step of meioticrecombination. The mus81 meiotic defect is rescued by expression of abacterial Holliday junction resolvase. These findings constitute strongevidence that Mus81 and Eme1 are subunits of a nuclear Holliday junctionresolvase.
- Structure (3D structures containing this domain)
3D Structures of ERCC4 domains in PDB
| PDB code | Main view | Title | | 1j22 |  | Crystal structure of archaeal xpf/mus81 homolog, hef from pyrococcus furiosus, nuclease domain, selenomet derivative |
| 1j23 |  | Crystal structure of archaeal xpf/mus81 homolog, hef from pyrococcus furiosus, nuclease domain |
| 1j24 |  | Crystal structure of archaeal xpf/mus81 homolog, hef from pyrococcus furiosus, nuclease domain, ca cocrystal |
| 1j25 |  | Crystal structure of archaeal xpf/mus81 homolog, hef from pyrococcus furiosus, nuclease domain, mn cocrystal |
| 2bgw |  | Xpf from aeropyrum pernix, complex with dna |
| 2bhn |  | Xpf from aeropyrum pernix |
| 2ziu |  | Crystal structure of the mus81-eme1 complex |
| 2ziv |  | Crystal structure of the mus81-eme1 complex |
| 2ziw |  | Crystal structure of the mus81-eme1 complex |
| 2zix |  | Crystal structure of the mus81-eme1 complex |
- Links (links to other resources describing this domain)
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to expand nodes. To display all proteins with a ERCC4 domain in a specific node, click on it.