Skip Header

You are using a version of Internet Explorer that may not display all features of this website. Please upgrade to a modern browser.
Contribute Send feedback
Read comments (?) or add your own

Q9BQ83 (SLX1_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 100. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Structure-specific endonuclease subunit SLX1

EC=3.6.1.-
Alternative name(s):
GIY-YIG domain-containing protein 1
Gene names
Name:SLX1A
Synonyms:GIYD1, SLX1
AND
Name:SLX1B
Synonyms:GIYD2, SLX1
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length275 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

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 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. Ref.4 Ref.5 Ref.6

Cofactor

Divalent cation.

Subunit structure

Forms a heterodimer with SLX4.

Subcellular location

Nucleus Ref.5.

Sequence similarities

Belongs to the SLX1 family.

Contains 1 GIY-YIG domain.

Contains 1 SLX1-type zinc finger.

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.

Binary interactions

With

Entry

#Exp.

IntAct

Notes

SLX4Q8IY9210EBI-2370858,EBI-2370740

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: Q9BQ83-1)

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.
Isoform 2 (identifier: Q9BQ83-2)

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

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 275275Structure-specific endonuclease subunit SLX1 HAMAP-Rule MF_03100
PRO_0000332120

Regions

Domain12 – 9584GIY-YIG
Zinc finger186 – 23853SLX1-type HAMAP-Rule MF_03100

Natural variations

Alternative sequence81 – 194114Missing in isoform 2.
VSP_033331

Experimental info

Mutagenesis411R → A: Abolishes endonucleolytic activity. Ref.5
Mutagenesis821E → A: Abolishes endonucleolytic activity. Ref.4 Ref.5

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified June 1, 2001. Version 1.
Checksum: 57DF055F2E59CF70

FASTA27530,771
        10         20         30         40         50         60 
MGPAGVAARP GRFFGVYLLY CLNPRYRGRV YVGFTVNTAR RVQQHNGGRK KGGAWRTSGR 

        70         80         90        100        110        120 
GPWEMVLVVH GFPSSVAALR FEWAWQHPHA SRRLAHVGPR LRGETAFAFH LRVLAHMLRA 

       130        140        150        160        170        180 
PPWARLPLTL RWVRPDLRQD LCLPPPPHVP LAFGPPPPQA PAPRRRAGPF DDAEPEPDQG 

       190        200        210        220        230        240 
DPGACCSLCA QTIQDEEGPL CCPHPGCLLR AHVICLAEEF LQEEPGQLLP LEGQCPCCEK 

       250        260        270 
SLLWGDLIWL CQMDTEKEVE DSELEEAHWT DLLET 

« Hide

Isoform 2 [UniParc].

Checksum: 4182E39967F1FDE9
Show »

FASTA16118,012

References

« Hide 'large scale' references
[1]"The sequence and analysis of duplication-rich human chromosome 16."
Martin J., Han C., Gordon L.A., Terry A., Prabhakar S., She X., Xie G., Hellsten U., Chan Y.M., Altherr M., Couronne O., Aerts A., Bajorek E., Black S., Blumer H., Branscomb E., Brown N.C., Bruno W.J. expand/collapse author list , Buckingham J.M., Callen D.F., Campbell C.S., Campbell M.L., Campbell E.W., Caoile C., Challacombe J.F., Chasteen L.A., Chertkov O., Chi H.C., Christensen M., Clark L.M., Cohn J.D., Denys M., Detter J.C., Dickson M., Dimitrijevic-Bussod M., Escobar J., Fawcett J.J., Flowers D., Fotopulos D., Glavina T., Gomez M., Gonzales E., Goodstein D., Goodwin L.A., Grady D.L., Grigoriev I., Groza M., Hammon N., Hawkins T., Haydu L., Hildebrand C.E., Huang W., Israni S., Jett J., Jewett P.B., Kadner K., Kimball H., Kobayashi A., Krawczyk M.-C., Leyba T., Longmire J.L., Lopez F., Lou Y., Lowry S., Ludeman T., Manohar C.F., Mark G.A., McMurray K.L., Meincke L.J., Morgan J., Moyzis R.K., Mundt M.O., Munk A.C., Nandkeshwar R.D., Pitluck S., Pollard M., Predki P., Parson-Quintana B., Ramirez L., Rash S., Retterer J., Ricke D.O., Robinson D.L., Rodriguez A., Salamov A., Saunders E.H., Scott D., Shough T., Stallings R.L., Stalvey M., Sutherland R.D., Tapia R., Tesmer J.G., Thayer N., Thompson L.S., Tice H., Torney D.C., Tran-Gyamfi M., Tsai M., Ulanovsky L.E., Ustaszewska A., Vo N., White P.S., Williams A.L., Wills P.L., Wu J.-R., Wu K., Yang J., DeJong P., Bruce D., Doggett N.A., Deaven L., Schmutz J., Grimwood J., Richardson P., Rokhsar D.S., Eichler E.E., Gilna P., Lucas S.M., Myers R.M., Rubin E.M., Pennacchio L.A.
Nature 432:988-994(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[2]"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
The MGC Project Team
Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2).
Tissue: B-cell, Lung and Placenta.
[3]"Human SULT1A3 pharmacogenetics: gene duplication and functional genomic studies."
Hildebrandt M.A.T., Salavaggione O.E., Martin Y.N., Flynn H.C., Jalal S., Wieben E.D., Weinshilboum R.M.
Biochem. Biophys. Res. Commun. 321:870-878(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION.
[4]"Mammalian BTBD12/SLX4 assembles a Holliday junction resolvase and is required for DNA repair."
Svendsen J.M., Smogorzewska A., Sowa M.E., O'Connell B.C., Gygi S.P., Elledge S.J., Harper J.W.
Cell 138:63-77(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, INTERACTION WITH SLX4, MUTAGENESIS OF GLU-82.
[5]"Human SLX4 is a Holliday junction resolvase subunit that binds multiple DNA repair/recombination endonucleases."
Fekairi S., Scaglione S., Chahwan C., Taylor E.R., Tissier A., Coulon S., Dong M.-Q., Ruse C., Yates J.R. III, Russell P., Fuchs R.P., McGowan C.H., Gaillard P.-H.L.
Cell 138:78-89(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, INTERACTION WITH SLX4, MUTAGENESIS OF ARG-41 AND GLU-82, SUBCELLULAR LOCATION.
[6]"Coordination of structure-specific nucleases by human SLX4/BTBD12 is required for DNA repair."
Munoz I.M., Hain K., Declais A.-C., Gardiner M., Toh G.W., Sanchez-Pulido L., Heuckmann J.M., Toth R., Macartney T., Eppink B., Kanaar R., Ponting C.P., Lilley D.M.J., Rouse J.
Mol. Cell 35:116-127(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, INTERACTION WITH SLX4.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
CCDSCCDS10648.1. [Q9BQ83-1]
CCDS10649.1. [Q9BQ83-2]
CCDS32431.1. [Q9BQ83-1]
CCDS32432.1. [Q9BQ83-2]
RefSeqNP_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]
UniGeneHs.728161.
Hs.729791.

3D structure databases

ProteinModelPortalQ9BQ83.
SMRQ9BQ83. Positions 16-93, 184-243.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid122479. 42 interactions.
139225. 6 interactions.
IntActQ9BQ83. 53 interactions.
STRING9606.ENSP00000328940.

Polymorphism databases

DMDM74732820.

Proteomic databases

PaxDbQ9BQ83.
PRIDEQ9BQ83.

Protocols and materials databases

DNASU548593.
79008.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000251303; ENSP00000251303; ENSG00000132207. [Q9BQ83-1]
ENST00000330181; ENSP00000328940; ENSG00000181625. [Q9BQ83-1]
ENST00000345535; ENSP00000333945; ENSG00000132207. [Q9BQ83-2]
ENST00000351581; ENSP00000335316; ENSG00000181625. [Q9BQ83-2]
GeneID548593.
79008.
KEGGhsa:548593.
hsa:79008.
UCSCuc002dsx.3. human. [Q9BQ83-1]
uc002dsy.3. human. [Q9BQ83-2]

Organism-specific databases

CTD548593.
79008.
GeneCardsGC16P029481.
GC16P030215.
HGNCHGNC:20922. SLX1A.
HGNC:28748. SLX1B.
HPAHPA047038.
neXtProtNX_Q9BQ83.
PharmGKBPA142671738.
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG296745.
HOGENOMHOG000008012.
InParanoidQ9BQ83.
KOK15078.
OMAGRIYIGF.
PhylomeDBQ9BQ83.
TreeFamTF352344.

Gene expression databases

BgeeQ9BQ83.
GenevestigatorQ9BQ83.

Family and domain databases

HAMAPMF_03100. Endonuc_su_Slx1.
InterProIPR000305. GIY-YIG_SF.
IPR027520. Slx1.
[Graphical view]
PfamPF01541. GIY-YIG. 1 hit.
[Graphical view]
SUPFAMSSF82771. SSF82771. 1 hit.
PROSITEPS50164. GIY_YIG. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

NextBio112282.

Entry information

Entry nameSLX1_HUMAN
AccessionPrimary (citable) accession number: Q9BQ83
Secondary accession number(s): B7ZME1, Q6NTG6
Entry history
Integrated into UniProtKB/Swiss-Prot: April 29, 2008
Last sequence update: June 1, 2001
Last modified: July 9, 2014
This is version 100 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (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.

Relevant documents

SIMILARITY comments

Index of protein domains and families

Human chromosome 16

Human chromosome 16: entries, gene names and cross-references to MIM