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Protein

Structure-specific endonuclease subunit SLX1

Gene

SLX1A

more
Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

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 5'-flap structures, and promotes symmetrical cleavage of static and migrating Holliday junctions (HJs). Resolves HJs by generating two pairs of ligatable, nicked duplex products.UniRule annotation3 Publications

Cofactori

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri186 – 238SLX1-typeUniRule annotationAdd BLAST53

GO - Molecular functioni

GO - Biological processi

  • DNA double-strand break processing involved in repair via single-strand annealing Source: UniProtKB
  • DNA repair Source: UniProtKB
  • double-strand break repair via homologous recombination Source: UniProtKB
  • interstrand cross-link repair Source: Reactome
  • positive regulation of t-circle formation Source: BHF-UCL
  • t-circle formation Source: BHF-UCL
Complete GO annotation...

Keywords - Molecular functioni

Endonuclease, Hydrolase, Nuclease

Keywords - Biological processi

DNA damage, DNA recombination, DNA repair

Keywords - Ligandi

Metal-binding, Zinc

Enzyme and pathway databases

ReactomeiR-HSA-5693568. Resolution of D-loop Structures through Holliday Junction Intermediates.
R-HSA-6783310. Fanconi Anemia Pathway.

Names & Taxonomyi

Protein namesi
Recommended name:
Structure-specific endonuclease subunit SLX1UniRule annotation (EC:3.1.-.-UniRule annotation)
Alternative name(s):
GIY-YIG domain-containing protein 1UniRule annotation
Gene namesi
Name:SLX1AUniRule annotation
Synonyms:GIYD1UniRule annotation, SLX1
AND
Name:SLX1BUniRule annotation
Synonyms:GIYD2, SLX1
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 16

Organism-specific databases

HGNCiHGNC:20922. SLX1A.
HGNC:28748. SLX1B.

Subcellular locationi

GO - Cellular componenti

  • nucleoplasm Source: Reactome
  • Slx1-Slx4 complex Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi41R → A: Abolishes endonucleolytic activity. 1 Publication1
Mutagenesisi82E → A: Abolishes endonucleolytic activity. 2 Publications1

Organism-specific databases

OpenTargetsiENSG00000132207.
ENSG00000181625.
PharmGKBiPA142671738.

Polymorphism and mutation databases

BioMutaiSLX1A.
DMDMi74732820.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00003321201 – 275Structure-specific endonuclease subunit SLX1Add BLAST275

Proteomic databases

EPDiQ9BQ83.
PaxDbiQ9BQ83.
PeptideAtlasiQ9BQ83.
PRIDEiQ9BQ83.

PTM databases

PhosphoSitePlusiQ9BQ83.

Expressioni

Gene expression databases

BgeeiENSG00000132207.
ExpressionAtlasiQ9BQ83. baseline and differential.
GenevisibleiQ9BQ83. HS.

Organism-specific databases

HPAiHPA047038.

Interactioni

Subunit structurei

Forms a heterodimer with SLX4.

Binary interactionsi

WithEntry#Exp.IntActNotes
SLX4Q8IY9210EBI-2370858,EBI-2370740

Protein-protein interaction databases

BioGridi122479. 43 interactors.
139225. 24 interactors.
IntActiQ9BQ83. 55 interactors.
STRINGi9606.ENSP00000328940.

Structurei

3D structure databases

ProteinModelPortaliQ9BQ83.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini12 – 95GIY-YIGUniRule annotationAdd BLAST84

Sequence similaritiesi

Belongs to the SLX1 family.UniRule annotation
Contains 1 GIY-YIG domain.UniRule annotation
Contains 1 SLX1-type zinc finger.UniRule annotation

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri186 – 238SLX1-typeUniRule annotationAdd BLAST53

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiKOG3005. Eukaryota.
ENOG411266C. LUCA.
GeneTreeiENSGT00390000013368.
HOGENOMiHOG000008012.
InParanoidiQ9BQ83.
KOiK15078.
OMAiCHMLCLA.
OrthoDBiEOG091G0J09.
PhylomeDBiQ9BQ83.
TreeFamiTF352344.

Family and domain databases

HAMAPiMF_03100. Endonuc_su_Slx1. 1 hit.
InterProiIPR000305. GIY-YIG_SF.
IPR027520. Slx1.
[Graphical view]
PfamiPF01541. GIY-YIG. 1 hit.
[Graphical view]
SUPFAMiSSF82771. SSF82771. 1 hit.
PROSITEiPS50164. GIY_YIG. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q9BQ83-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MGPAGVAARP GRFFGVYLLY CLNPRYRGRV YVGFTVNTAR RVQQHNGGRK
60 70 80 90 100
KGGAWRTSGR GPWEMVLVVH GFPSSVAALR FEWAWQHPHA SRRLAHVGPR
110 120 130 140 150
LRGETAFAFH LRVLAHMLRA PPWARLPLTL RWVRPDLRQD LCLPPPPHVP
160 170 180 190 200
LAFGPPPPQA PAPRRRAGPF DDAEPEPDQG DPGACCSLCA QTIQDEEGPL
210 220 230 240 250
CCPHPGCLLR AHVICLAEEF LQEEPGQLLP LEGQCPCCEK SLLWGDLIWL
260 270
CQMDTEKEVE DSELEEAHWT DLLET
Length:275
Mass (Da):30,771
Last modified:June 1, 2001 - v1
Checksum:i57DF055F2E59CF70
GO
Isoform 2 (identifier: Q9BQ83-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     81-194: Missing.

Show »
Length:161
Mass (Da):18,012
Checksum:i4182E39967F1FDE9
GO

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_03333181 – 194Missing in isoform 2. 1 PublicationAdd BLAST114

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AC106782 Genomic DNA. No translation available.
AC133555 Genomic DNA. No translation available.
BC000754 mRNA. Translation: AAH00754.1.
BC000803 mRNA. Translation: AAH00803.1.
BC015990 mRNA. Translation: AAH15990.1.
BC019306 mRNA. Translation: AAH19306.1.
BC069007 mRNA. Translation: AAH69007.1.
BC130545 mRNA. Translation: AAI30546.1.
BC130547 mRNA. Translation: AAI30548.1.
BC144462 mRNA. Translation: AAI44463.1.
CCDSiCCDS10648.1. [Q9BQ83-1]
CCDS10649.1. [Q9BQ83-2]
CCDS32431.1. [Q9BQ83-1]
CCDS32432.1. [Q9BQ83-2]
RefSeqiNP_001014999.1. NM_001014999.2. [Q9BQ83-1]
NP_001015000.1. NM_001015000.2. [Q9BQ83-2]
NP_076949.1. NM_024044.3. [Q9BQ83-1]
NP_835145.1. NM_178044.2. [Q9BQ83-2]
UniGeneiHs.728161.
Hs.729791.

Genome annotation databases

EnsembliENST00000251303; ENSP00000251303; ENSG00000132207. [Q9BQ83-1]
ENST00000330181; ENSP00000328940; ENSG00000181625. [Q9BQ83-1]
ENST00000345535; ENSP00000333945; ENSG00000132207. [Q9BQ83-2]
ENST00000351581; ENSP00000335316; ENSG00000181625. [Q9BQ83-2]
GeneIDi548593.
79008.
KEGGihsa:548593.
hsa:79008.
UCSCiuc002dsx.4. human. [Q9BQ83-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AC106782 Genomic DNA. No translation available.
AC133555 Genomic DNA. No translation available.
BC000754 mRNA. Translation: AAH00754.1.
BC000803 mRNA. Translation: AAH00803.1.
BC015990 mRNA. Translation: AAH15990.1.
BC019306 mRNA. Translation: AAH19306.1.
BC069007 mRNA. Translation: AAH69007.1.
BC130545 mRNA. Translation: AAI30546.1.
BC130547 mRNA. Translation: AAI30548.1.
BC144462 mRNA. Translation: AAI44463.1.
CCDSiCCDS10648.1. [Q9BQ83-1]
CCDS10649.1. [Q9BQ83-2]
CCDS32431.1. [Q9BQ83-1]
CCDS32432.1. [Q9BQ83-2]
RefSeqiNP_001014999.1. NM_001014999.2. [Q9BQ83-1]
NP_001015000.1. NM_001015000.2. [Q9BQ83-2]
NP_076949.1. NM_024044.3. [Q9BQ83-1]
NP_835145.1. NM_178044.2. [Q9BQ83-2]
UniGeneiHs.728161.
Hs.729791.

3D structure databases

ProteinModelPortaliQ9BQ83.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi122479. 43 interactors.
139225. 24 interactors.
IntActiQ9BQ83. 55 interactors.
STRINGi9606.ENSP00000328940.

PTM databases

PhosphoSitePlusiQ9BQ83.

Polymorphism and mutation databases

BioMutaiSLX1A.
DMDMi74732820.

Proteomic databases

EPDiQ9BQ83.
PaxDbiQ9BQ83.
PeptideAtlasiQ9BQ83.
PRIDEiQ9BQ83.

Protocols and materials databases

DNASUi548593.
79008.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000251303; ENSP00000251303; ENSG00000132207. [Q9BQ83-1]
ENST00000330181; ENSP00000328940; ENSG00000181625. [Q9BQ83-1]
ENST00000345535; ENSP00000333945; ENSG00000132207. [Q9BQ83-2]
ENST00000351581; ENSP00000335316; ENSG00000181625. [Q9BQ83-2]
GeneIDi548593.
79008.
KEGGihsa:548593.
hsa:79008.
UCSCiuc002dsx.4. human. [Q9BQ83-1]

Organism-specific databases

CTDi548593.
79008.
GeneCardsiSLX1A.
SLX1B.
HGNCiHGNC:20922. SLX1A.
HGNC:28748. SLX1B.
HPAiHPA047038.
MIMi615822. gene.
615823. gene.
neXtProtiNX_Q9BQ83.
OpenTargetsiENSG00000132207.
ENSG00000181625.
PharmGKBiPA142671738.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG3005. Eukaryota.
ENOG411266C. LUCA.
GeneTreeiENSGT00390000013368.
HOGENOMiHOG000008012.
InParanoidiQ9BQ83.
KOiK15078.
OMAiCHMLCLA.
OrthoDBiEOG091G0J09.
PhylomeDBiQ9BQ83.
TreeFamiTF352344.

Enzyme and pathway databases

ReactomeiR-HSA-5693568. Resolution of D-loop Structures through Holliday Junction Intermediates.
R-HSA-6783310. Fanconi Anemia Pathway.

Miscellaneous databases

PROiQ9BQ83.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000132207.
ExpressionAtlasiQ9BQ83. baseline and differential.
GenevisibleiQ9BQ83. HS.

Family and domain databases

HAMAPiMF_03100. Endonuc_su_Slx1. 1 hit.
InterProiIPR000305. GIY-YIG_SF.
IPR027520. Slx1.
[Graphical view]
PfamiPF01541. GIY-YIG. 1 hit.
[Graphical view]
SUPFAMiSSF82771. SSF82771. 1 hit.
PROSITEiPS50164. GIY_YIG. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiSLX1_HUMAN
AccessioniPrimary (citable) accession number: Q9BQ83
Secondary accession number(s): B7ZME1, Q6NTG6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 29, 2008
Last sequence update: June 1, 2001
Last modified: November 30, 2016
This is version 120 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Caution

Found in a segmental duplication on p arm of chromosome 16 giving rise to two identical copies of this gene sharing exons with SULT1A3 and SULT1A4.Curated

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Human chromosome 16
    Human chromosome 16: entries, gene names and cross-references to MIM
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. SIMILARITY comments
    Index of protein domains and families

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.