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Protein

Structure-specific endonuclease subunit SLX4

Gene

SLX4

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

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.UniRule annotation9 Publications

GO - Molecular functioni

  • 5'-flap endonuclease activity Source: SGD

GO - Biological processi

  • cellular response to DNA damage stimulus Source: SGD
  • DNA-dependent DNA replication Source: SGD
  • DNA replication Source: SGD
  • double-strand break repair via break-induced replication Source: SGD
  • double-strand break repair via single-strand annealing, removal of nonhomologous ends Source: SGD
  • interstrand cross-link repair Source: SGD
Complete GO annotation...

Keywords - Biological processi

DNA damage, DNA recombination, DNA repair

Enzyme and pathway databases

BioCyciYEAST:G3O-32275-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Structure-specific endonuclease subunit SLX4UniRule annotation
Alternative name(s):
Synthetic lethal of unknown function protein 4
Gene namesi
Name:SLX4UniRule annotation
Ordered Locus Names:YLR135W
ORF Names:L3140
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome XII

Organism-specific databases

EuPathDBiFungiDB:YLR135W.
SGDiS000004125. SLX4.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: UniProtKB-SubCell
  • nucleus Source: SGD
  • Slx1-Slx4 complex Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 748748Structure-specific endonuclease subunit SLX4PRO_0000270574Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei72 – 721Phosphothreonine; by ATR and ATM1 Publication
Modified residuei113 – 1131Phosphothreonine; by ATR and ATMSequence analysis
Modified residuei289 – 2891Phosphoserine; by ATR and ATM1 Publication
Modified residuei319 – 3191Phosphothreonine; by ATR and ATMSequence analysis
Modified residuei329 – 3291Phosphoserine; by ATR and ATM1 Publication
Modified residuei355 – 3551Phosphoserine; by ATR and ATMSequence analysis

Post-translational modificationi

Phosphorylated by ATR (MEC1) and ATM (TEL1) upon DNA damage. This appears to be required for the function with the RAD1-RAD10 endonuclease.UniRule annotation2 Publications

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiQ12098.

PTM databases

iPTMnetiQ12098.

Interactioni

Subunit structurei

Forms a heterodimer with SLX1. Interacts with RAD1; catalytic subunit of the RAD1-RAD10 endonuclease. Interacts with RTT107.UniRule annotation5 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
SLX1P383244EBI-37788,EBI-21016

Protein-protein interaction databases

BioGridi31404. 221 interactions.
DIPiDIP-1771N.
IntActiQ12098. 4 interactions.
MINTiMINT-402900.

Structurei

3D structure databases

ProteinModelPortaliQ12098.
SMRiQ12098. Positions 680-745.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi568 – 5736Poly-Glu

Sequence similaritiesi

Belongs to the SLX4 family.UniRule annotation

Phylogenomic databases

InParanoidiQ12098.
KOiK15079.
OMAiNTQIQSR.
OrthoDBiEOG74TX75.

Family and domain databases

HAMAPiMF_03110. Endonuc_su_Slx4.
InterProiIPR027784. Slx4_ascomycetes.
IPR018574. Structure-sp_endonuc_su_Slx4.
[Graphical view]
PfamiPF09494. Slx4. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q12098-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MELQRAQRNL KFLQNEDYVN VTDQTNLNGE SQNAYSLGME TQVPEMQFSL
60 70 80 90 100
SSDDDSIGTQ VKSVTAQKSP MTQETTKNDT ERNKDVDKSC NPVSTSHPDL
110 120 130 140 150
GGSNIEENIF INTQIQSRLD DAEEETNLKL KLEKFKYSFK SSNADDTHSN
160 170 180 190 200
ANVTAKRRPA IRKANSKLKT KPKTKRDPKI IKNITDFNIN NYERSRTASL
210 220 230 240 250
LKQLSGKHKK VLDIIKTQNE GNSDKPPRAR NNKGEKATFD TYSEQEWKDI
260 270 280 290 300
MKLLLQKFPQ SEETDLNEVQ KFLYGSEKSS NSLDNQESSQ QRLWTASQLP
310 320 330 340 350
PELPDEAIQP EQEERIRDTQ SAVNFLSLSQ VMDDKSEIMK DEESIIISRG
360 370 380 390 400
DSTSSQEYGN GLEPQQPVGN VVGEDIELAV GTRINAFSLT DYKACKPMSV
410 420 430 440 450
EVSRRCENST DNDYDNISIV SDTTDETSTL FPLDQYRYVF IENDERPPLA
460 470 480 490 500
TDTIGSTQFF TPNTSPLDGI IDLTQESFKA VRSLISPLKV ENNKTGVTSQ
510 520 530 540 550
ASNQVQVPAT RTPTIIPQKN LTTTLKTEEE KNNIGSSIRV KLLQESVVKL
560 570 580 590 600
NPKLVKHNFY RVEANDSEEE ETEFDDQFCI ADIQLVDSSK ISTKDSTQNP
610 620 630 640 650
TTSNDIIDTS AASSIASPEK FCEIMMSQSM KELRQSLKTV GLKPMRTKVE
660 670 680 690 700
IIQSLQTASQ ILSTANPDNK GEHGGVANFS KIEIFDHLTE LIEAFPDFLE
710 720 730 740
RIYTFEPIPL NELIEKLFSA EPFVSQIDEM TIREWADVQG ICLRNDKK
Length:748
Mass (Da):84,362
Last modified:November 1, 1996 - v1
Checksum:i52C0FD889C8C5835
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z73307 Genomic DNA. Translation: CAA97706.1.
U53881 Genomic DNA. Translation: AAB82394.1.
X91258 Genomic DNA. Translation: CAA62650.1.
AY692839 Genomic DNA. Translation: AAT92858.1.
BK006945 Genomic DNA. Translation: DAA09446.1.
PIRiS59327.
RefSeqiNP_013236.1. NM_001182022.1.

Genome annotation databases

EnsemblFungiiYLR135W; YLR135W; YLR135W.
GeneIDi850826.
KEGGisce:YLR135W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z73307 Genomic DNA. Translation: CAA97706.1.
U53881 Genomic DNA. Translation: AAB82394.1.
X91258 Genomic DNA. Translation: CAA62650.1.
AY692839 Genomic DNA. Translation: AAT92858.1.
BK006945 Genomic DNA. Translation: DAA09446.1.
PIRiS59327.
RefSeqiNP_013236.1. NM_001182022.1.

3D structure databases

ProteinModelPortaliQ12098.
SMRiQ12098. Positions 680-745.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi31404. 221 interactions.
DIPiDIP-1771N.
IntActiQ12098. 4 interactions.
MINTiMINT-402900.

PTM databases

iPTMnetiQ12098.

Proteomic databases

MaxQBiQ12098.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYLR135W; YLR135W; YLR135W.
GeneIDi850826.
KEGGisce:YLR135W.

Organism-specific databases

EuPathDBiFungiDB:YLR135W.
SGDiS000004125. SLX4.

Phylogenomic databases

InParanoidiQ12098.
KOiK15079.
OMAiNTQIQSR.
OrthoDBiEOG74TX75.

Enzyme and pathway databases

BioCyciYEAST:G3O-32275-MONOMER.

Miscellaneous databases

NextBioi967085.
PROiQ12098.

Family and domain databases

HAMAPiMF_03110. Endonuc_su_Slx4.
InterProiIPR027784. Slx4_ascomycetes.
IPR018574. Structure-sp_endonuc_su_Slx4.
[Graphical view]
PfamiPF09494. Slx4. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The nucleotide sequence of Saccharomyces cerevisiae chromosome XII."
    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.
    Nature 387:87-90(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  2. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  3. Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  4. "Requirement for three novel protein complexes in the absence of the Sgs1 DNA helicase in Saccharomyces cerevisiae."
    Mullen J.R., Kaliraman V., Ibrahim S.S., Brill S.J.
    Genetics 157:103-118(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INTERACTION WITH SLX1.
  5. "Role of SGS1 and SLX4 in maintaining rDNA structure in Saccharomyces cerevisiae."
    Kaliraman V., Brill S.J.
    Curr. Genet. 41:389-400(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  6. "Slx1-Slx4 is a second structure-specific endonuclease functionally redundant with Sgs1-Top3."
    Fricke W.M., Brill S.J.
    Genes Dev. 17:1768-1778(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBCELLULAR LOCATION.
  7. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
  8. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  9. "Slx4 becomes phosphorylated after DNA damage in a Mec1/Tel1-dependent manner and is required for repair of DNA alkylation damage."
    Flott S., Rouse J.
    Biochem. J. 391:325-333(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, PHOSPHORYLATION BY MEC1 AND TEL1.
  10. "Multiple endonucleases function to repair covalent topoisomerase I complexes in Saccharomyces cerevisiae."
    Deng C., Brown J.A., You D., Brown J.M.
    Genetics 170:591-600(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  11. "Rtt107/Esc4 binds silent chromatin and DNA repair proteins using different BRCT motifs."
    Zappulla D.C., Maharaj A.S.R., Connelly J.J., Jockusch R.A., Sternglanz R.
    BMC Mol. Biol. 7:40-40(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH RTT107.
  12. "Slx4 regulates DNA damage checkpoint-dependent phosphorylation of the BRCT domain protein Rtt107/Esc4."
    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.
    Mol. Biol. Cell 17:539-548(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INTERACTION WITH RTT107.
  13. "Phosphorylation of Slx4 by Mec1 and Tel1 regulates the single-strand annealing mode of DNA repair in budding yeast."
    Flott S., Alabert C., Toh G.W., Toth R., Sugawara N., Campbell D.G., Haber J.E., Pasero P., Rouse J.
    Mol. Cell. Biol. 27:6433-6445(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INTERACTION WITH RAD1 AND SLX1, PHOSPHORYLATION AT THR-72; SER-289 AND SER-329 BY MEC1 AND TEL1.
  14. "Mutants defective in Rad1-Rad10-Slx4 exhibit a unique pattern of viability during mating-type switching in Saccharomyces cerevisiae."
    Lyndaker A.M., Goldfarb T., Alani E.
    Genetics 179:1807-1821(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  15. "Microarray-based genetic screen defines SAW1, a gene required for Rad1/Rad10-dependent processing of recombination intermediates."
    Li F., Dong J., Pan X., Oum J.-H., Boeke J.D., Lee S.E.
    Mol. Cell 30:325-335(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INTERACTION WITH RAD1.
  16. "A multidimensional chromatography technology for in-depth phosphoproteome analysis."
    Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.
    Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

Entry informationi

Entry nameiSLX4_YEAST
AccessioniPrimary (citable) accession number: Q12098
Secondary accession number(s): D6VYD0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 9, 2007
Last sequence update: November 1, 1996
Last modified: May 11, 2016
This is version 117 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 274 molecules/cell in log phase SD medium.1 Publication

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  3. Yeast chromosome XII
    Yeast (Saccharomyces cerevisiae) chromosome XII: entries and gene names

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.