Protein: Structure-specific endonuclease subunit slx1 (EC 3.1.-.-) (Q9P7M3)
Organism: Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast)
Function: Catalytic subunit of the slx1-slx4 structure-specific endonuclease that resolves DNA secondary structures generated during DNA repair and recombination. Has endonuclease activity towards branched DNA substrates, introducing single-strand cuts in duplex DNA close to junctions with ss-DNA. Has a preference for stem-loop (SL) and splayed arm Y structures. Introduces a single-strand cut in duplex DNA on the 3' side of a double-strand/single-strand junction with respect to the single-strand moving 3' to 5' away from the junction. Plays a critical role in maintaining the integrity of the ribosomal DNA (rDNA) loci, where it has a role in re-starting stalled replication forks. The complex initiates homologous recombination (HR) events, used to maintain rDNA copy number, in the rDNA repeats that are processed by a mechanism that requires rad22, but not rhp51. It is also required for suppression of methyl methanesulfonate (MMS) and UV-C irradiation hypersensitivity of the structural maintenance of chromosome (SMC) protein mutant, smc6-74, by overexpression of brc1. Has Holliday junction resolvase activity in vitro.
Subcellular location: Nucleus, nucleolus {ECO:0000269|PubMed:14528010, ECO:0000269|PubMed:16467377}. Note=Associates with chromatin at rDNA repeat protrusions. {ECO:0000269|PubMed:14528010, ECO:0000269|PubMed:16467377}.
Sequence: MDLCNFYCCYLLKSNRTQSSGAVYIGSTPDPPRRLRQHNGEIVGGASKTKHGRPWSISCLVYGFPNKVSALKFEWNWQNLGISRYTKDCDFRSKKQKTIMYCLKGLKHLVDSDTWRRWPLNITFLNKTAFSKWNQLGKTYGNINVYFDEEWLNGFHEKVIQKTYDHKLCLRKTISEPVKCNLCYECIESDELRANCPFTDCNSINHLTCLASSFLTEECQVLPIEGMCTKCKRVLRWREFLSTVFTTSLETDERDFESENRIEIIDLELEK
InterPro domains: - IPR050381: SLX1 structure-specific endonuclease (family) [5-258]
- IPR027520: Structure-specific endonuclease subunit Slx1 (family) [2-253]
- IPR048749: Structure-specific endonuclease subunit SLX1, C-terminal domain (domain) [179-239]
- IPR000305: GIY-YIG endonuclease (domain) [5-87]
- IPR013083: Zinc finger, RING/FYVE/PHD-type (homologous_superfamily) [175-247]
- IPR035901: GIY-YIG endonuclease superfamily (homologous_superfamily) [4-108]
Interaction partners: - Structure-specific endonuclease subunit slx4
- Crossover junction endonuclease mus81
- Crossover junction endonuclease eme1
- RecQ-mediated genome instability protein 1
- Exodeoxyribonuclease 1
- Probable asparagine--tRNA ligase, cytoplasmic
- DNA topoisomerase 3
- ATP-dependent DNA helicase hus2/rqh1
- DNA mismatch repair protein msh3
- DNA repair protein rhp51
Gene Ontology annotations:
Molecular Function (MF): GO:0003674 (molecular function), GO:0005488 (binding), GO:0003824 (catalytic activity), GO:0140640 (catalytic activity, acting on a nucleic acid), GO:0016787 (hydrolase activity), GO:0005515 (protein binding), GO:0016788 (hydrolase activity, acting on ester bonds), GO:0140097 (catalytic activity, acting on DNA), GO:0004518 (nuclease activity), GO:0004536 (deoxyribonuclease activity), GO:0004520 (DNA endonuclease activity), GO:0004519 (endonuclease activity), GO:0016894 (endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 3'-phosphomonoesters), GO:0016889 (DNA endonuclease activity, producing 3'-phosphomonoesters), GO:0016893 (endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters), GO:0016888 (endodeoxyribonuclease activity, producing 5'-phosphomonoesters), GO:0048256 (flap endonuclease activity), GO:0017108 (5'-flap endonuclease activity), GO:0008821 (crossover junction DNA endonuclease activity)
Biological Process (BP): GO:0008150 (biological process), GO:0008152 (metabolic process), GO:0009987 (cellular process), GO:0044237 (cellular metabolic process), GO:0071704 (organic substance metabolic process), GO:0044238 (primary metabolic process), GO:0006807 (nitrogen compound metabolic process), GO:0006725 (cellular aromatic compound metabolic process), GO:0034641 (cellular nitrogen compound metabolic process), GO:1901360 (organic cyclic compound metabolic process), GO:0044260 (cellular macromolecule metabolic process), GO:0006139 (nucleobase-containing compound metabolic process), GO:0043170 (macromolecule metabolic process), GO:0046483 (heterocycle metabolic process), GO:0006259 (DNA metabolic process), GO:0090304 (nucleic acid metabolic process), GO:0006260 (DNA replication), GO:0006261 (DNA-templated DNA replication)
Cellular Component (CC): GO:0005575 (cellular component), GO:0032991 (protein-containing complex), GO:0110165 (cellular anatomical entity), GO:0005622 (intracellular anatomical structure), GO:0043226 (organelle), GO:0005829 (cytosol), GO:0140513 (nuclear protein-containing complex), GO:0005737 (cytoplasm), GO:0031974 (membrane-enclosed lumen), GO:0043233 (organelle lumen), GO:0043229 (intracellular organelle), GO:0043227 (membrane-bounded organelle), GO:0043228 (non-membrane-bounded organelle), GO:0043231 (intracellular membrane-bounded organelle), GO:0070013 (intracellular organelle lumen), GO:0043232 (intracellular non-membrane-bounded organelle), GO:0031981 (nuclear lumen), GO:0005694 (chromosome), GO:0005634 (nucleus), GO:0000228 (nuclear chromosome)