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Q9BQ83

- SLX1_HUMAN

UniProt

Q9BQ83 - SLX1_HUMAN

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Protein
Structure-specific endonuclease subunit SLX1
Gene
SLX1A, GIYD1, SLX1
SLX1B, GIYD2, SLX1
Organism
Homo sapiens (Human)
Status
Reviewed - 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.3 Publications

Cofactori

Divalent cation.

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri186 – 23853SLX1-typeUniRule annotation
Add
BLAST

GO - Molecular functioni

  1. 5'-flap endonuclease activity Source: UniProtKB
  2. crossover junction endodeoxyribonuclease activity Source: UniProtKB
  3. metal ion binding Source: UniProtKB-KW
  4. protein binding Source: UniProtKB

GO - Biological processi

  1. DNA catabolic process, endonucleolytic Source: GOC
  2. DNA double-strand break processing involved in repair via single-strand annealing Source: UniProtKB
  3. DNA repair Source: UniProtKB
  4. double-strand break repair via homologous recombination Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Endonuclease, Hydrolase, Nuclease

Keywords - Biological processi

DNA damage, DNA recombination, DNA repair

Keywords - Ligandi

Metal-binding, Zinc

Names & Taxonomyi

Organism-specific databases

Protein namesi
Recommended name:
Structure-specific endonuclease subunit SLX1 (EC:3.6.1.-)
Alternative name(s):
GIY-YIG domain-containing protein 1
Gene namesi
Name:SLX1A
Synonyms:GIYD1, SLX1
AND
Name:SLX1B
Synonyms:GIYD2, SLX1
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640: Chromosome 16
HGNCiHGNC:20922. SLX1A.
HGNC:28748. SLX1B.

Subcellular locationi

Nucleus 1 Publication

GO - Cellular componenti

  1. Slx1-Slx4 complex Source: UniProtKB

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi41 – 411R → A: Abolishes endonucleolytic activity. 1 Publication
Mutagenesisi82 – 821E → A: Abolishes endonucleolytic activity. 2 Publications

Organism-specific databases

PharmGKBiPA142671738.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 275275Structure-specific endonuclease subunit SLX1UniRule annotation
PRO_0000332120Add
BLAST

Proteomic databases

PaxDbiQ9BQ83.
PRIDEiQ9BQ83.

Expressioni

Gene expression databases

BgeeiQ9BQ83.
GenevestigatoriQ9BQ83.

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. 42 interactions.
139225. 6 interactions.
IntActiQ9BQ83. 53 interactions.
STRINGi9606.ENSP00000328940.

Structurei

3D structure databases

ProteinModelPortaliQ9BQ83.
SMRiQ9BQ83. Positions 16-93, 184-243.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini12 – 9584GIY-YIG
Add
BLAST

Sequence similaritiesi

Belongs to the SLX1 family.
Contains 1 GIY-YIG domain.

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiNOG296745.
HOGENOMiHOG000008012.
InParanoidiQ9BQ83.
KOiK15078.
OMAiGRIYIGF.
PhylomeDBiQ9BQ83.
TreeFamiTF352344.

Family and domain databases

HAMAPiMF_03100. Endonuc_su_Slx1.
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. Align

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

MGPAGVAARP GRFFGVYLLY CLNPRYRGRV YVGFTVNTAR RVQQHNGGRK    50
KGGAWRTSGR GPWEMVLVVH GFPSSVAALR FEWAWQHPHA SRRLAHVGPR 100
LRGETAFAFH LRVLAHMLRA PPWARLPLTL RWVRPDLRQD LCLPPPPHVP 150
LAFGPPPPQA PAPRRRAGPF DDAEPEPDQG DPGACCSLCA QTIQDEEGPL 200
CCPHPGCLLR AHVICLAEEF LQEEPGQLLP LEGQCPCCEK SLLWGDLIWL 250
CQMDTEKEVE DSELEEAHWT DLLET 275
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)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei81 – 194114Missing in isoform 2.
VSP_033331Add
BLAST

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
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.3. human. [Q9BQ83-1]
uc002dsy.3. human. [Q9BQ83-2]

Polymorphism databases

DMDMi74732820.

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
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 .
CCDSi CCDS10648.1. [Q9BQ83-1 ]
CCDS10649.1. [Q9BQ83-2 ]
CCDS32431.1. [Q9BQ83-1 ]
CCDS32432.1. [Q9BQ83-2 ]
RefSeqi NP_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 ]
UniGenei Hs.728161.
Hs.729791.

3D structure databases

ProteinModelPortali Q9BQ83.
SMRi Q9BQ83. Positions 16-93, 184-243.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 122479. 42 interactions.
139225. 6 interactions.
IntActi Q9BQ83. 53 interactions.
STRINGi 9606.ENSP00000328940.

Polymorphism databases

DMDMi 74732820.

Proteomic databases

PaxDbi Q9BQ83.
PRIDEi Q9BQ83.

Protocols and materials databases

DNASUi 548593.
79008.
Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENST00000251303 ; ENSP00000251303 ; ENSG00000132207 . [Q9BQ83-1 ]
ENST00000330181 ; ENSP00000328940 ; ENSG00000181625 . [Q9BQ83-1 ]
ENST00000345535 ; ENSP00000333945 ; ENSG00000132207 . [Q9BQ83-2 ]
ENST00000351581 ; ENSP00000335316 ; ENSG00000181625 . [Q9BQ83-2 ]
GeneIDi 548593.
79008.
KEGGi hsa:548593.
hsa:79008.
UCSCi uc002dsx.3. human. [Q9BQ83-1 ]
uc002dsy.3. human. [Q9BQ83-2 ]

Organism-specific databases

CTDi 548593.
79008.
GeneCardsi GC16P029481.
GC16P030215.
HGNCi HGNC:20922. SLX1A.
HGNC:28748. SLX1B.
HPAi HPA047038.
MIMi 615822. gene.
615823. gene.
neXtProti NX_Q9BQ83.
PharmGKBi PA142671738.
GenAtlasi Search...

Phylogenomic databases

eggNOGi NOG296745.
HOGENOMi HOG000008012.
InParanoidi Q9BQ83.
KOi K15078.
OMAi GRIYIGF.
PhylomeDBi Q9BQ83.
TreeFami TF352344.

Miscellaneous databases

NextBioi 112282.
SOURCEi Search...

Gene expression databases

Bgeei Q9BQ83.
Genevestigatori Q9BQ83.

Family and domain databases

HAMAPi MF_03100. Endonuc_su_Slx1.
InterProi IPR000305. GIY-YIG_SF.
IPR027520. Slx1.
[Graphical view ]
Pfami PF01541. GIY-YIG. 1 hit.
[Graphical view ]
SUPFAMi SSF82771. SSF82771. 1 hit.
PROSITEi PS50164. GIY_YIG. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

  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. 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. Cited for: FUNCTION, INTERACTION WITH SLX4.

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: September 3, 2014
This is version 101 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.

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

External Data

Dasty 3

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