ID   SLX1_YEAST              Reviewed;         304 AA.
AC   P38324; D6VQM3;
DT   01-OCT-1994, integrated into UniProtKB/Swiss-Prot.
DT   01-OCT-1994, sequence version 1.
DT   04-NOV-2026, entry version 177.
DE   RecName: Full=Structure-specific endonuclease subunit SLX1 {ECO:0000255|HAMAP-Rule:MF_03100};
DE            EC=3.1.-.- {ECO:0000255|HAMAP-Rule:MF_03100};
DE   AltName: Full=Synthetic lethal of unknown function protein 1;
GN   Name=SLX1 {ECO:0000255|HAMAP-Rule:MF_03100};
GN   OrderedLocusNames=YBR228W; ORFNames=YBR1525;
OS   Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC   Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC   Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX   NCBI_TaxID=559292;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 204508 / S288c;
RX   PubMed=7813418; DOI=10.1002/j.1460-2075.1994.tb06923.x;
RA   Feldmann H., Aigle M., Aljinovic G., Andre B., Baclet M.C., Barthe C.,
RA   Baur A., Becam A.-M., Biteau N., Boles E., Brandt T., Brendel M.,
RA   Brueckner M., Bussereau F., Christiansen C., Contreras R., Crouzet M.,
RA   Cziepluch C., Demolis N., Delaveau T., Doignon F., Domdey H.,
RA   Duesterhus S., Dubois E., Dujon B., El Bakkoury M., Entian K.-D.,
RA   Feuermann M., Fiers W., Fobo G.M., Fritz C., Gassenhuber J., Glansdorff N.,
RA   Goffeau A., Grivell L.A., de Haan M., Hein C., Herbert C.J.,
RA   Hollenberg C.P., Holmstroem K., Jacq C., Jacquet M., Jauniaux J.-C.,
RA   Jonniaux J.-L., Kallesoee T., Kiesau P., Kirchrath L., Koetter P.,
RA   Korol S., Liebl S., Logghe M., Lohan A.J.E., Louis E.J., Li Z.Y.,
RA   Maat M.J., Mallet L., Mannhaupt G., Messenguy F., Miosga T., Molemans F.,
RA   Mueller S., Nasr F., Obermaier B., Perea J., Pierard A., Piravandi E.,
RA   Pohl F.M., Pohl T.M., Potier S., Proft M., Purnelle B., Ramezani Rad M.,
RA   Rieger M., Rose M., Schaaff-Gerstenschlaeger I., Scherens B.,
RA   Schwarzlose C., Skala J., Slonimski P.P., Smits P.H.M., Souciet J.-L.,
RA   Steensma H.Y., Stucka R., Urrestarazu L.A., van der Aart Q.J.M.,
RA   Van Dyck L., Vassarotti A., Vetter I., Vierendeels F., Vissers S.,
RA   Wagner G., de Wergifosse P., Wolfe K.H., Zagulski M., Zimmermann F.K.,
RA   Mewes H.-W., Kleine K.;
RT   "Complete DNA sequence of yeast chromosome II.";
RL   EMBO J. 13:5795-5809(1994).
RN   [2]
RP   GENOME REANNOTATION.
RC   STRAIN=ATCC 204508 / S288c;
RX   PubMed=24374639; DOI=10.1534/g3.113.008995;
RA   Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA   Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA   Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
RT   "The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
RL   G3 (Bethesda) 4:389-398(2014).
RN   [3]
RP   FUNCTION, AND INTERACTION WITH SLX4.
RX   PubMed=11139495; DOI=10.1093/genetics/157.1.103;
RA   Mullen J.R., Kaliraman V., Ibrahim S.S., Brill S.J.;
RT   "Requirement for three novel protein complexes in the absence of the Sgs1
RT   DNA helicase in Saccharomyces cerevisiae.";
RL   Genetics 157:103-118(2001).
RN   [4]
RP   FUNCTION, AND SUBCELLULAR LOCATION.
RX   PubMed=12832395; DOI=10.1101/gad.1105203;
RA   Fricke W.M., Brill S.J.;
RT   "Slx1-Slx4 is a second structure-specific endonuclease functionally
RT   redundant with Sgs1-Top3.";
RL   Genes Dev. 17:1768-1778(2003).
CC   -!- FUNCTION: Catalytic subunit of the SLX1-SLX4 structure-specific
CC       endonuclease that resolves DNA secondary structures generated during
CC       DNA repair and recombination. Has endonuclease activity towards
CC       branched DNA substrates, introducing single-strand cuts in duplex DNA
CC       close to junctions with ss-DNA. Has a preference for simple Y, 5'-flap
CC       and replication fork-like structures. It cleaves the strand bearing the
CC       5'-non-homologous arm at the branch site junction and generates
CC       ligatable, nicked products from the 5'-flap or replication fork
CC       substrates. Plays a critical role in maintaining the integrity of the
CC       ribosomal DNA (rDNA) loci, where it has a role in re-starting stalled
CC       replication forks. Has Holliday junction resolvase activity in vitro.
CC       {ECO:0000255|HAMAP-Rule:MF_03100, ECO:0000269|PubMed:11139495,
CC       ECO:0000269|PubMed:12832395}.
CC   -!- COFACTOR:
CC       Name=a divalent metal cation; Xref=ChEBI:CHEBI:60240;
CC         Evidence={ECO:0000255|HAMAP-Rule:MF_03100};
CC   -!- SUBUNIT: Forms a heterodimer with SLX4.
CC   -!- INTERACTION:
CC       P38324; Q12098: SLX4; NbExp=6; IntAct=EBI-21016, EBI-37788;
CC   -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000255|HAMAP-Rule:MF_03100,
CC       ECO:0000269|PubMed:12832395}.
CC   -!- SIMILARITY: Belongs to the SLX1 family. {ECO:0000255|HAMAP-
CC       Rule:MF_03100}.
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DR   EMBL; Z36097; CAA85191.1; -; Genomic_DNA.
DR   EMBL; BK006936; DAA07343.1; -; Genomic_DNA.
DR   PIR; S46104; S46104.
DR   RefSeq; NP_009787.3; NM_001178576.3.
DR   PDB; 7CQ2; X-ray; 2.50 A; A/B=1-304.
DR   PDB; 7CQ3; X-ray; 1.45 A; A=1-304.
DR   PDB; 7CQ4; X-ray; 3.29 A; A=1-304.
DR   AlphaFoldDB; P38324; -.
DR   SMR; P38324; -.
DR   BioGRID; 32923; 103.
DR   ComplexPortal; CPX-1355; RTT107-SLX4-SLX1 complex.
DR   ComplexPortal; CPX-3159; SLX1-SLX4 structure-specific endonuclease complex.
DR   DIP; DIP-1770N; -.
DR   FunCoup; P38324; 502.
DR   IntAct; P38324; 4.
DR   STRING; 4932.YBR228W; -.
DR   PaxDb; 4932-YBR228W; -.
DR   PeptideAtlas; P38324; -.
DR   EnsemblFungi; YBR228W_mRNA; YBR228W; YBR228W.
DR   GeneID; 852529; -.
DR   KEGG; sce:YBR228W; -.
DR   AGR; SGD:S000000432; -.
DR   SGD; S000000432; SLX1.
DR   VEuPathDB; FungiDB:YBR228W; -.
DR   eggNOG; KOG3005; Eukaryota.
DR   HOGENOM; CLU_030739_1_1_1; -.
DR   InParanoid; P38324; -.
DR   OMA; AAHIFCL; -.
DR   OrthoDB; 24645at2759; -.
DR   BioCyc; YEAST:G3O-29161-MONOMER; -.
DR   BioGRID-ORCS; 852529; 2 hits in 10 CRISPR screens.
DR   PRO; PR:P38324; -.
DR   Proteomes; UP000002311; Chromosome II.
DR   RNAct; P38324; protein.
DR   GO; GO:0000228; C:nuclear chromosome; NAS:ComplexPortal.
DR   GO; GO:0005634; C:nucleus; NAS:ComplexPortal.
DR   GO; GO:0033557; C:Slx1-Slx4 complex; IPI:SGD.
DR   GO; GO:0017108; F:5'-flap endonuclease activity; IDA:SGD.
DR   GO; GO:0008821; F:crossover junction DNA endonuclease activity; IBA:GO_Central.
DR   GO; GO:0006261; P:DNA-templated DNA replication; IGI:SGD.
DR   GO; GO:0000724; P:double-strand break repair via homologous recombination; IBA:GO_Central.
DR   GO; GO:2000001; P:regulation of DNA damage checkpoint; NAS:ComplexPortal.
DR   GO; GO:0031297; P:replication fork processing; NAS:ComplexPortal.
DR   CDD; cd10455; GIY-YIG_SLX1; 1.
DR   FunFam; 3.40.1440.10:FF:000006; Structure-specific endonuclease subunit SLX1; 1.
DR   Gene3D; 3.40.1440.10; GIY-YIG endonuclease; 1.
DR   Gene3D; 3.30.40.10; Zinc/RING finger domain, C3HC4 (zinc finger); 1.
DR   HAMAP; MF_03100; Endonuc_su_Slx1; 1.
DR   InterPro; IPR000305; GIY-YIG_endonuc.
DR   InterPro; IPR035901; GIY-YIG_endonuc_sf.
DR   InterPro; IPR027520; Slx1.
DR   InterPro; IPR048749; SLX1_C.
DR   InterPro; IPR050381; SLX1_endonuclease.
DR   InterPro; IPR013083; Znf_RING/FYVE/PHD.
DR   PANTHER; PTHR20208; STRUCTURE-SPECIFIC ENDONUCLEASE SUBUNIT SLX1; 1.
DR   PANTHER; PTHR20208:SF10; STRUCTURE-SPECIFIC ENDONUCLEASE SUBUNIT SLX1; 1.
DR   Pfam; PF01541; GIY-YIG; 1.
DR   Pfam; PF21202; SLX1_C; 1.
DR   SMART; SM00465; GIYc; 1.
DR   SUPFAM; SSF82771; GIY-YIG endonuclease; 1.
DR   PROSITE; PS50164; GIY_YIG; 1.
PE   1: Evidence at protein level;
KW   3D-structure; DNA damage; DNA recombination; DNA repair; Endonuclease;
KW   Hydrolase; Metal-binding; Nuclease; Nucleus; Reference proteome; Zinc;
KW   Zinc-finger.
FT   CHAIN           1..304
FT                   /note="Structure-specific endonuclease subunit SLX1"
FT                   /id="PRO_0000202517"
FT   DOMAIN          12..95
FT                   /note="GIY-YIG"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_03100"
FT   ZN_FING         218..282
FT                   /note="SLX1-type"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_03100"
FT   STRAND          15..23
FT                   /evidence="ECO:0007829|PDB:7CQ3"
FT   STRAND          28..34
FT                   /evidence="ECO:0007829|PDB:7CQ3"
FT   HELIX           36..44
FT                   /evidence="ECO:0007829|PDB:7CQ3"
FT   STRAND          45..47
FT                   /evidence="ECO:0007829|PDB:7CQ3"
FT   HELIX           53..56
FT                   /evidence="ECO:0007829|PDB:7CQ3"
FT   TURN            58..60
FT                   /evidence="ECO:0007829|PDB:7CQ3"
FT   STRAND          62..70
FT                   /evidence="ECO:0007829|PDB:7CQ3"
FT   HELIX           75..86
FT                   /evidence="ECO:0007829|PDB:7CQ3"
FT   HELIX           88..90
FT                   /evidence="ECO:0007829|PDB:7CQ3"
FT   HELIX           96..98
FT                   /evidence="ECO:0007829|PDB:7CQ3"
FT   STRAND          103..106
FT                   /evidence="ECO:0007829|PDB:7CQ2"
FT   HELIX           110..122
FT                   /evidence="ECO:0007829|PDB:7CQ3"
FT   HELIX           124..127
FT                   /evidence="ECO:0007829|PDB:7CQ3"
FT   TURN            128..130
FT                   /evidence="ECO:0007829|PDB:7CQ3"
FT   STRAND          132..137
FT                   /evidence="ECO:0007829|PDB:7CQ3"
FT   HELIX           138..146
FT                   /evidence="ECO:0007829|PDB:7CQ3"
FT   TURN            152..154
FT                   /evidence="ECO:0007829|PDB:7CQ2"
FT   STRAND          159..167
FT                   /evidence="ECO:0007829|PDB:7CQ3"
FT   HELIX           175..211
FT                   /evidence="ECO:0007829|PDB:7CQ3"
FT   TURN            219..221
FT                   /evidence="ECO:0007829|PDB:7CQ3"
FT   HELIX           232..234
FT                   /evidence="ECO:0007829|PDB:7CQ3"
FT   STRAND          238..240
FT                   /evidence="ECO:0007829|PDB:7CQ3"
FT   TURN            244..246
FT                   /evidence="ECO:0007829|PDB:7CQ3"
FT   STRAND          249..251
FT                   /evidence="ECO:0007829|PDB:7CQ3"
FT   HELIX           252..267
FT                   /evidence="ECO:0007829|PDB:7CQ3"
FT   STRAND          275..278
FT                   /evidence="ECO:0007829|PDB:7CQ3"
FT   TURN            280..282
FT                   /evidence="ECO:0007829|PDB:7CQ3"
FT   STRAND          285..287
FT                   /evidence="ECO:0007829|PDB:7CQ3"
FT   HELIX           288..302
FT                   /evidence="ECO:0007829|PDB:7CQ3"
SQ   SEQUENCE   304 AA;  35857 MW;  4C676E877FDF7A7A CRC64;
     MSQKIQQHQF PDFYCCYLLQ SINKRQSFYV GSTPNPVRRL RQHNGKLAVG GAYRTKRDGS
     RPWEMIMIVR GFPSKIAALQ FEHAWQHGYQ THYIAEKDRV VKHKAGGRTL HHKVALMKLL
     LKHEFFQRMN LIVEVFNIKA WEVWKQDKFF IERDRFPINI QINENALEEP KEKTVDVLMD
     HSDENLKVVE AVYTKVIENE RNIFETFEKK LTTGVVRCEI CEKEIDYTSE EQNLKPFVAL
     CNNKDCGCVN HLKCLHRYFL DDEQLMVGRR NLIPRGGKCP KCDMFCDWTT LVKFSTRMKL
     AHGK
//