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Structure-specific endonuclease subunit SLX4 (Synthetic lethal of unknown function protein 4)

 SLX4_YEAST              Reviewed;         748 AA.
Q12098; D6VYD0;
09-JAN-2007, integrated into UniProtKB/Swiss-Prot.
01-NOV-1996, sequence version 1.
22-NOV-2017, entry version 130.
RecName: Full=Structure-specific endonuclease subunit SLX4 {ECO:0000255|HAMAP-Rule:MF_03110};
AltName: Full=Synthetic lethal of unknown function protein 4;
Name=SLX4 {ECO:0000255|HAMAP-Rule:MF_03110};
OrderedLocusNames=YLR135W; ORFNames=L3140;
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina;
Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces.
NCBI_TaxID=559292;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 204508 / S288c;
PubMed=9169871;
Johnston M., Hillier L.W., Riles L., Albermann K., Andre B.,
Ansorge W., Benes V., Brueckner M., Delius H., Dubois E.,
Duesterhoeft A., Entian K.-D., Floeth M., Goffeau A., Hebling U.,
Heumann K., Heuss-Neitzel D., Hilbert H., Hilger F., Kleine K.,
Koetter P., Louis E.J., Messenguy F., Mewes H.-W., Miosga T.,
Moestl D., Mueller-Auer S., Nentwich U., Obermaier B., Piravandi E.,
Pohl T.M., Portetelle D., Purnelle B., Rechmann S., Rieger M.,
Rinke M., Rose M., Scharfe M., Scherens B., Scholler P., Schwager C.,
Schwarz S., Underwood A.P., Urrestarazu L.A., Vandenbol M.,
Verhasselt P., Vierendeels F., Voet M., Volckaert G., Voss H.,
Wambutt R., Wedler E., Wedler H., Zimmermann F.K., Zollner A.,
Hani J., Hoheisel J.D.;
"The nucleotide sequence of Saccharomyces cerevisiae chromosome XII.";
Nature 387:87-90(1997).
[2]
GENOME REANNOTATION.
STRAIN=ATCC 204508 / S288c;
PubMed=24374639; DOI=10.1534/g3.113.008995;
Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M.,
Cherry J.M.;
"The reference genome sequence of Saccharomyces cerevisiae: Then and
now.";
G3 (Bethesda) 4:389-398(2014).
[3]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
STRAIN=ATCC 204508 / S288c;
PubMed=17322287; DOI=10.1101/gr.6037607;
Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F.,
Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A.,
Raphael J., Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F.,
Williamson J., Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G.,
Kolodner R.D., LaBaer J.;
"Approaching a complete repository of sequence-verified protein-
encoding clones for Saccharomyces cerevisiae.";
Genome Res. 17:536-543(2007).
[4]
FUNCTION, AND INTERACTION WITH SLX1.
PubMed=11139495;
Mullen J.R., Kaliraman V., Ibrahim S.S., Brill S.J.;
"Requirement for three novel protein complexes in the absence of the
Sgs1 DNA helicase in Saccharomyces cerevisiae.";
Genetics 157:103-118(2001).
[5]
FUNCTION.
PubMed=12228808; DOI=10.1007/s00294-002-0319-6;
Kaliraman V., Brill S.J.;
"Role of SGS1 and SLX4 in maintaining rDNA structure in Saccharomyces
cerevisiae.";
Curr. Genet. 41:389-400(2002).
[6]
FUNCTION, AND SUBCELLULAR LOCATION.
PubMed=12832395; DOI=10.1101/gad.1105203;
Fricke W.M., Brill S.J.;
"Slx1-Slx4 is a second structure-specific endonuclease functionally
redundant with Sgs1-Top3.";
Genes Dev. 17:1768-1778(2003).
[7]
SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
PubMed=14562095; DOI=10.1038/nature02026;
Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W.,
Weissman J.S., O'Shea E.K.;
"Global analysis of protein localization in budding yeast.";
Nature 425:686-691(2003).
[8]
LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
PubMed=14562106; DOI=10.1038/nature02046;
Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A.,
Dephoure N., O'Shea E.K., Weissman J.S.;
"Global analysis of protein expression in yeast.";
Nature 425:737-741(2003).
[9]
FUNCTION, AND PHOSPHORYLATION BY MEC1 AND TEL1.
PubMed=15975089; DOI=10.1042/BJ20050768;
Flott S., Rouse J.;
"Slx4 becomes phosphorylated after DNA damage in a Mec1/Tel1-dependent
manner and is required for repair of DNA alkylation damage.";
Biochem. J. 391:325-333(2005).
[10]
FUNCTION.
PubMed=15834151; DOI=10.1534/genetics.104.028795;
Deng C., Brown J.A., You D., Brown J.M.;
"Multiple endonucleases function to repair covalent topoisomerase I
complexes in Saccharomyces cerevisiae.";
Genetics 170:591-600(2005).
[11]
INTERACTION WITH RTT107.
PubMed=17094803; DOI=10.1186/1471-2199-7-40;
Zappulla D.C., Maharaj A.S.R., Connelly J.J., Jockusch R.A.,
Sternglanz R.;
"Rtt107/Esc4 binds silent chromatin and DNA repair proteins using
different BRCT motifs.";
BMC Mol. Biol. 7:40-40(2006).
[12]
FUNCTION, AND INTERACTION WITH RTT107.
PubMed=16267268; DOI=10.1091/mbc.E05-08-0785;
Roberts T.M., Kobor M.S., Bastin-Shanower S.A., Ii M., Horte S.A.,
Gin J.W., Emili A., Rine J., Brill S.J., Brown G.W.;
"Slx4 regulates DNA damage checkpoint-dependent phosphorylation of the
BRCT domain protein Rtt107/Esc4.";
Mol. Biol. Cell 17:539-548(2006).
[13]
FUNCTION, INTERACTION WITH RAD1 AND SLX1, AND PHOSPHORYLATION AT
THR-72; SER-289 AND SER-329 BY MEC1 AND TEL1.
PubMed=17636031; DOI=10.1128/MCB.00135-07;
Flott S., Alabert C., Toh G.W., Toth R., Sugawara N., Campbell D.G.,
Haber J.E., Pasero P., Rouse J.;
"Phosphorylation of Slx4 by Mec1 and Tel1 regulates the single-strand
annealing mode of DNA repair in budding yeast.";
Mol. Cell. Biol. 27:6433-6445(2007).
[14]
FUNCTION.
PubMed=18579504; DOI=10.1534/genetics.108.090654;
Lyndaker A.M., Goldfarb T., Alani E.;
"Mutants defective in Rad1-Rad10-Slx4 exhibit a unique pattern of
viability during mating-type switching in Saccharomyces cerevisiae.";
Genetics 179:1807-1821(2008).
[15]
FUNCTION, AND INTERACTION WITH RAD1.
PubMed=18471978; DOI=10.1016/j.molcel.2008.02.028;
Li F., Dong J., Pan X., Oum J.-H., Boeke J.D., Lee S.E.;
"Microarray-based genetic screen defines SAW1, a gene required for
Rad1/Rad10-dependent processing of recombination intermediates.";
Mol. Cell 30:325-335(2008).
[16]
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=18407956; DOI=10.1074/mcp.M700468-MCP200;
Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.;
"A multidimensional chromatography technology for in-depth
phosphoproteome analysis.";
Mol. Cell. Proteomics 7:1389-1396(2008).
-!- FUNCTION: Regulatory subunit that interacts with and increases the
activity of different structure-specific endonucleases. Has
several distinct roles in protecting genome stability by resolving
diverse forms of deleterious DNA structures. Component 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 simple Y, 5'-flap and
replication fork-like structures. It cleaves the strand bearing
the 5'-non-homologous arm at the branch site junction and
generates ligatable, nicked products from the 5'-flap or
replication fork substrates. 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. Has Holliday
junction resolvase activity in vitro. Interacts with the
structure-specific RAD1-RAD10 endonuclease and promotes RAD1-
RAD10-dependent 3'-non-homologous tail removal (NHTR) during
repair of double-strand breaks by single-strand annealing. SLX4
also promotes recovery from DNA-alkylation-induced replisome
stalling during DNA replication by facilitating the error-free
mode of lesion bypass. This does not require SLX1 or RAD1-RAD10,
but probably RTT107. {ECO:0000255|HAMAP-Rule:MF_03110,
ECO:0000269|PubMed:11139495, ECO:0000269|PubMed:12228808,
ECO:0000269|PubMed:12832395, ECO:0000269|PubMed:15834151,
ECO:0000269|PubMed:15975089, ECO:0000269|PubMed:16267268,
ECO:0000269|PubMed:17636031, ECO:0000269|PubMed:18471978,
ECO:0000269|PubMed:18579504}.
-!- SUBUNIT: Forms a heterodimer with SLX1. Interacts with RAD1;
catalytic subunit of the RAD1-RAD10 endonuclease. Interacts with
RTT107. {ECO:0000255|HAMAP-Rule:MF_03110,
ECO:0000269|PubMed:11139495, ECO:0000269|PubMed:16267268,
ECO:0000269|PubMed:17094803, ECO:0000269|PubMed:17636031,
ECO:0000269|PubMed:18471978}.
-!- INTERACTION:
P47027:DPB11; NbExp=2; IntAct=EBI-37788, EBI-25984;
P38324:SLX1; NbExp=4; IntAct=EBI-37788, EBI-21016;
-!- SUBCELLULAR LOCATION: Nucleus. Cytoplasm.
-!- PTM: Phosphorylated by ATR (MEC1) and ATM (TEL1) upon DNA damage.
This appears to be required for the function with the RAD1-RAD10
endonuclease. {ECO:0000255|HAMAP-Rule:MF_03110,
ECO:0000269|PubMed:15975089, ECO:0000269|PubMed:17636031}.
-!- MISCELLANEOUS: Present with 274 molecules/cell in log phase SD
medium. {ECO:0000269|PubMed:14562106}.
-!- SIMILARITY: Belongs to the SLX4 family. {ECO:0000255|HAMAP-
Rule:MF_03110}.
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EMBL; Z73307; CAA97706.1; -; Genomic_DNA.
EMBL; U53881; AAB82394.1; -; Genomic_DNA.
EMBL; X91258; CAA62650.1; -; Genomic_DNA.
EMBL; AY692839; AAT92858.1; -; Genomic_DNA.
EMBL; BK006945; DAA09446.1; -; Genomic_DNA.
PIR; S59327; S59327.
RefSeq; NP_013236.1; NM_001182022.1.
ProteinModelPortal; Q12098; -.
SMR; Q12098; -.
BioGrid; 31404; 256.
DIP; DIP-1771N; -.
IntAct; Q12098; 6.
MINT; MINT-402900; -.
STRING; 4932.YLR135W; -.
iPTMnet; Q12098; -.
MaxQB; Q12098; -.
PRIDE; Q12098; -.
EnsemblFungi; YLR135W; YLR135W; YLR135W.
GeneID; 850826; -.
KEGG; sce:YLR135W; -.
EuPathDB; FungiDB:YLR135W; -.
SGD; S000004125; SLX4.
InParanoid; Q12098; -.
KO; K15079; -.
OMA; NTQIQSR; -.
OrthoDB; EOG092C0S5M; -.
BioCyc; YEAST:G3O-32275-MONOMER; -.
PRO; PR:Q12098; -.
Proteomes; UP000002311; Chromosome XII.
GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
GO; GO:0005634; C:nucleus; IMP:SGD.
GO; GO:0033557; C:Slx1-Slx4 complex; IPI:SGD.
GO; GO:0017108; F:5'-flap endonuclease activity; IDA:SGD.
GO; GO:0006974; P:cellular response to DNA damage stimulus; IGI:SGD.
GO; GO:0006260; P:DNA replication; IMP:SGD.
GO; GO:0006261; P:DNA-dependent DNA replication; IGI:SGD.
GO; GO:0000727; P:double-strand break repair via break-induced replication; IGI:SGD.
GO; GO:0000736; P:double-strand break repair via single-strand annealing, removal of nonhomologous ends; IMP:SGD.
GO; GO:0036297; P:interstrand cross-link repair; IGI:SGD.
GO; GO:2000001; P:regulation of DNA damage checkpoint; IMP:SGD.
GO; GO:1903775; P:regulation of DNA double-strand break processing; IMP:SGD.
GO; GO:1905261; P:regulation of meiotic DNA double-strand break formation involved in reciprocal meiotic recombination; IMP:SGD.
HAMAP; MF_03110; Endonuc_su_Slx4; 1.
InterPro; IPR027784; Slx4_ascomycetes.
InterPro; IPR018574; Structure-sp_endonuc_su_Slx4.
Pfam; PF09494; Slx4; 1.
1: Evidence at protein level;
Complete proteome; Cytoplasm; DNA damage; DNA recombination;
DNA repair; Nucleus; Phosphoprotein; Reference proteome.
CHAIN 1 748 Structure-specific endonuclease subunit
SLX4.
/FTId=PRO_0000270574.
COMPBIAS 568 573 Poly-Glu.
MOD_RES 72 72 Phosphothreonine; by ATR and ATM.
{ECO:0000269|PubMed:17636031}.
MOD_RES 113 113 Phosphothreonine; by ATR and ATM.
{ECO:0000255}.
MOD_RES 289 289 Phosphoserine; by ATR and ATM.
{ECO:0000269|PubMed:17636031}.
MOD_RES 319 319 Phosphothreonine; by ATR and ATM.
{ECO:0000255}.
MOD_RES 329 329 Phosphoserine; by ATR and ATM.
{ECO:0000269|PubMed:17636031}.
MOD_RES 355 355 Phosphoserine; by ATR and ATM.
{ECO:0000255}.
SEQUENCE 748 AA; 84362 MW; 52C0FD889C8C5835 CRC64;
MELQRAQRNL KFLQNEDYVN VTDQTNLNGE SQNAYSLGME TQVPEMQFSL SSDDDSIGTQ
VKSVTAQKSP MTQETTKNDT ERNKDVDKSC NPVSTSHPDL GGSNIEENIF INTQIQSRLD
DAEEETNLKL KLEKFKYSFK SSNADDTHSN ANVTAKRRPA IRKANSKLKT KPKTKRDPKI
IKNITDFNIN NYERSRTASL LKQLSGKHKK VLDIIKTQNE GNSDKPPRAR NNKGEKATFD
TYSEQEWKDI MKLLLQKFPQ SEETDLNEVQ KFLYGSEKSS NSLDNQESSQ QRLWTASQLP
PELPDEAIQP EQEERIRDTQ SAVNFLSLSQ VMDDKSEIMK DEESIIISRG DSTSSQEYGN
GLEPQQPVGN VVGEDIELAV GTRINAFSLT DYKACKPMSV EVSRRCENST DNDYDNISIV
SDTTDETSTL FPLDQYRYVF IENDERPPLA TDTIGSTQFF TPNTSPLDGI IDLTQESFKA
VRSLISPLKV ENNKTGVTSQ ASNQVQVPAT RTPTIIPQKN LTTTLKTEEE KNNIGSSIRV
KLLQESVVKL NPKLVKHNFY RVEANDSEEE ETEFDDQFCI ADIQLVDSSK ISTKDSTQNP
TTSNDIIDTS AASSIASPEK FCEIMMSQSM KELRQSLKTV GLKPMRTKVE IIQSLQTASQ
ILSTANPDNK GEHGGVANFS KIEIFDHLTE LIEAFPDFLE RIYTFEPIPL NELIEKLFSA
EPFVSQIDEM TIREWADVQG ICLRNDKK


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