Q9BQ83 (SLX1_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended 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

Organism

Homo sapiens (Human) [Reference proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Primates › Haplorrhini › Simiiformes › Catarrhini › Hominoidea › Hominidae › Homininae › Homo

Protein attributes

Sequence length	275 AA.
Sequence status	Complete.
Protein existence	Evidence 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.

Ontologies

Keywords
Biological process	DNA damage DNA recombination DNA repair
Cellular component	Nucleus
Coding sequence diversity	Alternative splicing
Domain	Zinc-finger
Ligand	Metal-binding Zinc
Molecular function	Endonuclease Hydrolase Nuclease
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	DNA double-strand break processing involved in repair via single-strand annealing Inferred from mutant phenotype Ref.6. Source: UniProtKB double-strand break repair via homologous recombination Inferred from mutant phenotype Ref.6. Source: UniProtKB
Cellular_component	Slx1-Slx4 complex Inferred from direct assay Ref.6Ref.4Ref.5. Source: UniProtKB
Molecular_function	5'-flap endonuclease activity Inferred from direct assay Ref.4Ref.5. Source: UniProtKB crossover junction endodeoxyribonuclease activity Inferred from direct assay Ref.6Ref.4Ref.5. Source: UniProtKB metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
SLX4	Q8IY92	10	EBI-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 key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 275	275	Structure-specific endonuclease subunit SLX1 HAMAP-Rule MF_03100		PRO_0000332120
Regions
	Domain	12 – 95	84	GIY-YIG
	Zinc finger	186 – 238	53	SLX1-type HAMAP-Rule MF_03100
Natural variations
	Alternative sequence	81 – 194	114	Missing in isoform 2.		VSP_033331
Experimental info
	Mutagenesis	41	1	R → A: Abolishes endonucleolytic activity. Ref.5
	Mutagenesis	82	1	E → A: Abolishes endonucleolytic activity. Ref.4 Ref.5

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 [UniParc]. Last modified June 1, 2001. Version 1. Checksum: 57DF055F2E59CF70	FASTA	275	30,771
	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
	Isoform 2 [UniParc]. Checksum: 4182E39967F1FDE9	FASTA	161	18,012
	10 20 30 40 50 60 MGPAGVAARP GRFFGVYLLY CLNPRYRGRV YVGFTVNTAR RVQQHNGGRK KGGAWRTSGR 70 80 90 100 110 120 GPWEMVLVVH GFPSSVAALR DEEGPLCCPH PGCLLRAHVI CLAEEFLQEE PGQLLPLEGQ 130 140 150 160 CPCCEKSLLW GDLIWLCQMD TEKEVEDSEL EEAHWTDLLE T

References

	« Hide 'large scale' referencesShow '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. , 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.

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.
IPI	IPI00031535. IPI00376968.
RefSeq	NP_001014999.1. NM_001014999.2. NP_001015000.1. NM_001015000.2. NP_076949.1. NM_024044.3. NP_835145.1. NM_178044.2.
UniGene	Hs.728161. Hs.729791.
3D structure databases
HSSP	HSSP built from PDB template 1ZG2 based on UniProtKB Q9KGL3.
ProteinModelPortal	Q9BQ83.
ModBase	Search...
Protein-protein interaction databases
IntAct	Q9BQ83. 53 interactions.
STRING	9606.ENSP00000328940.
Proteomic databases
PaxDb	Q9BQ83.
PRIDE	Q9BQ83.
Protocols and materials databases
DNASU	548593. 79008.
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
Ensembl	ENST00000251303; ENSP00000251303; ENSG00000132207. ENST00000330181; ENSP00000328940; ENSG00000181625. ENST00000345535; ENSP00000333945; ENSG00000132207. ENST00000351581; ENSP00000335316; ENSG00000181625.
GeneID	548593. 79008.
KEGG	hsa:548593. hsa:79008.
UCSC	uc002dsx.3. human. uc002dsy.3. human.
Organism-specific databases
CTD	548593. 79008.
GeneCards	GC16P029471. GC16P030208.
HGNC	HGNC:20922. SLX1A. HGNC:28748. SLX1B.
HPA	HPA047038.
neXtProt	NX_Q9BQ83.
PharmGKB	PA142671738.
GenAtlas	Search...
Phylogenomic databases
eggNOG	NOG296745.
HOGENOM	HOG000008012.
InParanoid	Q9BQ83.
KO	K15078.
OMA	GRIYIGF.
OrthoDB	EOG4Z62P9.
Gene expression databases
ArrayExpress	Q9BQ83.
Bgee	Q9BQ83.
Genevestigator	Q9BQ83.
Family and domain databases
HAMAP	MF_03100. Endonuc_su_Slx1.
InterPro	IPR027299. GIY-YIG_dom. IPR000305. GIY-YIG_SF. [Graphical view]
Pfam	PF01541. GIY-YIG. 1 hit. [Graphical view]
PROSITE	PS50164. GIY_YIG. 1 hit. [Graphical view]
ProtoNet	Search...
Other
NextBio	112282.

Entry information

Entry name

SLX1_HUMAN

Accession

Primary (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:	May 1, 2013
This is version 88 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

Disclaimer

Any 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.