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Protein

X-ray repair cross-complementing protein 6

Gene

XRCC6

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

Functioni

Single-stranded DNA-dependent ATP-dependent helicase. Has a role in chromosome translocation. The DNA helicase II complex binds preferentially to fork-like ends of double-stranded DNA in a cell cycle-dependent manner. It works in the 3'-5' direction. Binding to DNA may be mediated by XRCC6. Involved in DNA non-homologous end joining (NHEJ) required for double-strand break repair and V(D)J recombination. The XRCC5/6 dimer acts as regulatory subunit of the DNA-dependent protein kinase complex DNA-PK by increasing the affinity of the catalytic subunit PRKDC to DNA by 100-fold. The XRCC5/6 dimer is probably involved in stabilizing broken DNA ends and bringing them together. The assembly of the DNA-PK complex to DNA ends is required for the NHEJ ligation step. Required for osteocalcin gene expression. Probably also acts as a 5'-deoxyribose-5-phosphate lyase (5'-dRP lyase), by catalyzing the beta-elimination of the 5' deoxyribose-5-phosphate at an abasic site near double-strand breaks. 5'-dRP lyase activity allows to 'clean' the termini of abasic sites, a class of nucleotide damage commonly associated with strand breaks, before such broken ends can be joined. The XRCC5/6 dimer together with APEX1 acts as a negative regulator of transcription. Plays a role in the regulation of DNA virus-mediated innate immune response by assembling into the HDP-RNP complex, a complex that serves as a platform for IRF3 phosphorylation and subsequent innate immune response activation through the cGAS-STING pathway.8 Publications

Miscellaneous

Individuals with systemic lupus erythematosus (SLE) and related disorders produce extremely large amounts of autoantibodies to XRCC5 and XRCC6. Existence of a major autoantigenic epitope or epitopes on the C-terminal 190 amino acids of XRCC6 containing the leucine repeat. The majority of autoantibodies to XRCC6 in most sera from patients with SLE seem to be reactive with this region.

Caution

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Active sitei31Schiff-base intermediate with DNA; for 5'-deoxyribose-5-phosphate lyase activityCurated1

GO - Molecular functioni

  • 5'-deoxyribose-5-phosphate lyase activity Source: UniProtKB
  • ATP binding Source: UniProtKB-KW
  • ATP-dependent DNA helicase activity Source: ProtInc
  • cyclin binding Source: UniProtKB
  • damaged DNA binding Source: InterPro
  • DNA binding Source: UniProtKB
  • double-stranded DNA binding Source: ProtInc
  • protein-containing complex binding Source: BHF-UCL
  • protein C-terminus binding Source: UniProtKB
  • RNA binding Source: UniProtKB
  • telomeric DNA binding Source: InterPro
  • transcription regulatory region DNA binding Source: BHF-UCL

GO - Biological processi

  • activation of innate immune response Source: UniProtKB
  • brain development Source: Ensembl
  • cellular hyperosmotic salinity response Source: Ensembl
  • cellular response to gamma radiation Source: UniProtKB
  • cellular response to X-ray Source: Ensembl
  • DNA ligation Source: ProtInc
  • DNA recombination Source: UniProtKB-KW
  • double-strand break repair via classical nonhomologous end joining Source: BHF-UCL
  • double-strand break repair via nonhomologous end joining Source: UniProtKB
  • establishment of integrated proviral latency Source: Reactome
  • innate immune response Source: UniProtKB-KW
  • negative regulation of transcription, DNA-templated Source: UniProtKB
  • neutrophil degranulation Source: Reactome
  • positive regulation of protein kinase activity Source: CAFA
  • positive regulation of transcription, DNA-templated Source: UniProtKB
  • positive regulation of transcription by RNA polymerase II Source: BHF-UCL
  • positive regulation of type I interferon production Source: Reactome
  • protein heterotetramerization Source: BHF-UCL
  • regulation of smooth muscle cell proliferation Source: UniProtKB
  • telomere maintenance Source: BHF-UCL
  • transcription, DNA-templated Source: UniProtKB-KW

Keywordsi

Molecular functionActivator, DNA-binding, Helicase, Hydrolase, Lyase, Multifunctional enzyme
Biological processDNA damage, DNA recombination, DNA repair, Immunity, Innate immunity, Transcription, Transcription regulation
LigandATP-binding, Nucleotide-binding

Enzyme and pathway databases

ReactomeiR-HSA-164843 2-LTR circle formation
R-HSA-1834949 Cytosolic sensors of pathogen-associated DNA
R-HSA-3270619 IRF3-mediated induction of type I IFN
R-HSA-5693571 Nonhomologous End-Joining (NHEJ)
R-HSA-6798695 Neutrophil degranulation
SIGNORiP12956

Names & Taxonomyi

Protein namesi
Recommended name:
X-ray repair cross-complementing protein 6 (EC:3.6.4.-, EC:4.2.99.-)
Alternative name(s):
5'-deoxyribose-5-phosphate lyase Ku70
Short name:
5'-dRP lyase Ku70
70 kDa subunit of Ku antigen
ATP-dependent DNA helicase 2 subunit 1
ATP-dependent DNA helicase II 70 kDa subunit
CTC box-binding factor 75 kDa subunit
Short name:
CTC75
Short name:
CTCBF
DNA repair protein XRCC6
Lupus Ku autoantigen protein p70
Short name:
Ku70
Thyroid-lupus autoantigen
Short name:
TLAA
X-ray repair complementing defective repair in Chinese hamster cells 6
Gene namesi
Name:XRCC6
Synonyms:G22P1
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 22

Organism-specific databases

EuPathDBiHostDB:ENSG00000196419.12
HGNCiHGNC:4055 XRCC6
MIMi152690 gene
neXtProtiNX_P12956

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Chromosome, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi31K → A: Diminishes the ability to form a Schiff base. Abolishes adduct formation; when associated with A-160 and A-164. 1 Publication1
Mutagenesisi160K → A: Abolishes adduct formation; when associated with A-31 and A-160. 1 Publication1
Mutagenesisi164K → A: Abolishes adduct formation; when associated with A-31 and A-164. 1 Publication1

Keywords - Diseasei

Systemic lupus erythematosus

Organism-specific databases

DisGeNETi2547
OpenTargetsiENSG00000196419
PharmGKBiPA28467

Polymorphism and mutation databases

DMDMi125729

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedCombined sources
ChainiPRO_00002101792 – 609X-ray repair cross-complementing protein 6Add BLAST608

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylserineCombined sources1
Modified residuei2PhosphoserineCombined sources1
Modified residuei6Phosphoserine; by PRKDC1 Publication1
Modified residuei27PhosphoserineCombined sources1
Modified residuei31N6-acetyllysineCombined sources1
Modified residuei51Phosphoserine; by PRKDC1 Publication1
Cross-linki287Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Modified residuei306PhosphoserineCombined sources1
Cross-linki317Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Modified residuei331N6-acetyllysineCombined sources1
Modified residuei338N6-acetyllysineCombined sources1
Modified residuei455PhosphothreonineCombined sources1
Modified residuei461N6-acetyllysineCombined sources1
Modified residuei477PhosphoserineCombined sources1
Modified residuei520PhosphoserineCombined sources1
Modified residuei550PhosphoserineCombined sources1
Cross-linki556Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Modified residuei560PhosphoserineCombined sources1

Post-translational modificationi

Phosphorylation by PRKDC may enhance helicase activity. Phosphorylation of Ser-51 does not affect DNA repair.3 Publications

Keywords - PTMi

Acetylation, Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

EPDiP12956
MaxQBiP12956
PaxDbiP12956
PeptideAtlasiP12956
PRIDEiP12956

2D gel databases

SWISS-2DPAGEiP12956

PTM databases

iPTMnetiP12956
PhosphoSitePlusiP12956
SwissPalmiP12956

Miscellaneous databases

PMAP-CutDBiP12956

Expressioni

Developmental stagei

Expression does not increase during promyelocyte differentiation.1 Publication

Inductioni

In osteoblasts, by FGF2.

Gene expression databases

BgeeiENSG00000196419
CleanExiHS_XRCC6
ExpressionAtlasiP12956 baseline and differential
GenevisibleiP12956 HS

Organism-specific databases

HPAiCAB004254
HPA047549
HPA062226

Interactioni

Subunit structurei

Heterodimer composed of XRCC5/Ku80 and XRCC6/Ku70. The dimer associates in a DNA-dependent manner with PRKDC to form the DNA-dependent protein kinase complex DNA-PK, and with the LIG4-XRCC4 complex to form the core of the non-homologous end joining (NHEJ) complex. Additional components of the NHEJ complex include NHEJ1/XLF and PAXX (PubMed:25574025, PubMed:25941166, PubMed:25670504). The dimer also associates with NAA15, and this complex binds to the osteocalcin promoter and activates osteocalcin expression. In addition, XRCC6 interacts with the osteoblast-specific transcription factors MSX2, RUNX2 and DLX5. Interacts with ELF3. Interacts with ATP23. The XRCC5/6 dimer associates in a DNA-dependent manner with APEX1. Binds to CDK9 isoform 2. Identified in a complex with DEAF1 and XRCC5. Interacts with DEAF1 (via the SAND domain); the interaction is direct and may be inhibited by DNA-binding (PubMed:10219089, PubMed:11493912, PubMed:12145306, PubMed:12509254, PubMed:12547193, PubMed:15075319, PubMed:20493174, PubMed:22442688, PubMed:8621488, PubMed:9742108). Interacts with CLU (By similarity). Interacts with NR4A3; the DNA-dependent protein kinase complex DNA-PK phosphorylates and activates NR4A3 and prevents NR4A3 ubiquitinylation and degradation (PubMed:25852083). Interacts with C7orf49/CYREN isoform 1 (CYREN-1) and isoform 4 (CYREN-2) (PubMed:24610814, PubMed:28959974). Interacts (via N-terminus) with HSF1 (via N-terminus); this interaction is direct and prevents XRCC5/XRCC6 heterodimeric binding and non-homologous end joining (NHEJ) repair activities induced by ionizing radiation (IR) (PubMed:26359349). Part of the HDP-RNP complex composed of at least HEXIM1, PRKDC, XRCC5, XRCC6, paraspeckle proteins (SFPQ, NONO, PSPC1, RBM14, and MATR3) and NEAT1 RNA (PubMed:28712728).By similarity15 Publications

Binary interactionsi

Show more details

GO - Molecular functioni

  • cyclin binding Source: UniProtKB
  • protein C-terminus binding Source: UniProtKB

Protein-protein interaction databases

BioGridi108822294 interactors.
CORUMiP12956
DIPiDIP-24188N
ELMiP12956
IntActiP12956 158 interactors.
MINTiP12956
STRINGi9606.ENSP00000352257

Structurei

Secondary structure

1609
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi35 – 43Combined sources9
Helixi46 – 49Combined sources4
Beta strandi53 – 56Combined sources4
Helixi59 – 76Combined sources18
Beta strandi82 – 89Combined sources8
Beta strandi102 – 109Combined sources8
Helixi113 – 120Combined sources8
Helixi124 – 135Combined sources12
Helixi143 – 155Combined sources13
Beta strandi161 – 171Combined sources11
Turni175 – 178Combined sources4
Helixi180 – 196Combined sources17
Beta strandi198 – 205Combined sources8
Turni213 – 216Combined sources4
Helixi217 – 219Combined sources3
Helixi239 – 250Combined sources12
Beta strandi256 – 266Combined sources11
Beta strandi268 – 274Combined sources7
Beta strandi286 – 289Combined sources4
Turni290 – 292Combined sources3
Beta strandi295 – 304Combined sources10
Turni305 – 307Combined sources3
Helixi313 – 315Combined sources3
Beta strandi316 – 322Combined sources7
Beta strandi325 – 329Combined sources5
Helixi331 – 336Combined sources6
Beta strandi343 – 352Combined sources10
Helixi353 – 355Combined sources3
Helixi358 – 360Combined sources3
Beta strandi366 – 370Combined sources5
Turni372 – 374Combined sources3
Helixi378 – 391Combined sources14
Beta strandi394 – 401Combined sources8
Beta strandi403 – 405Combined sources3
Beta strandi409 – 416Combined sources8
Beta strandi426 – 428Combined sources3
Beta strandi430 – 436Combined sources7
Helixi440 – 442Combined sources3
Helixi456 – 468Combined sources13
Helixi481 – 494Combined sources14
Helixi511 – 518Combined sources8
Helixi521 – 529Combined sources9
Helixi561 – 569Combined sources9
Helixi573 – 575Combined sources3
Helixi578 – 587Combined sources10
Helixi596 – 607Combined sources12

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1JEQX-ray2.70A1-609[»]
1JEYX-ray2.50A1-609[»]
1JJRNMR-A556-609[»]
3RZXX-ray2.61B537-558[»]
5Y3Relectron microscopy6.60A34-534[»]
ProteinModelPortaliP12956
SMRiP12956
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP12956

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini261 – 468KuAdd BLAST208
Domaini573 – 607SAPPROSITE-ProRule annotationAdd BLAST35

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni550 – 609Interaction with DEAF11 PublicationAdd BLAST60

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi2 – 61Ser-rich (potentially targets for phosphorylation)Add BLAST60
Compositional biasi11 – 29Asp/Glu-rich (acidic)Add BLAST19
Compositional biasi330 – 342Asp/Glu-rich (acidic)Add BLAST13

Sequence similaritiesi

Belongs to the ku70 family.Curated

Phylogenomic databases

eggNOGiKOG2327 Eukaryota
ENOG410XNXU LUCA
GeneTreeiENSGT00390000001422
HOGENOMiHOG000006588
HOVERGENiHBG006236
InParanoidiP12956
KOiK10884
OMAiDVFTSCN
OrthoDBiEOG091G04AI
PhylomeDBiP12956
TreeFamiTF315101

Family and domain databases

Gene3Di1.10.720.301 hit
2.40.290.102 hits
3.40.50.4101 hit
4.10.970.101 hit
InterProiView protein in InterPro
IPR006165 Ku70
IPR006164 Ku70/Ku80_beta-barrel_dom
IPR027388 Ku70_bridge/pillars_dom_sf
IPR005160 Ku_C
IPR005161 Ku_N
IPR003034 SAP_dom
IPR036361 SAP_dom_sf
IPR016194 SPOC-like_C_dom_sf
IPR036465 vWFA_dom_sf
PANTHERiPTHR12604:SF2 PTHR12604:SF2, 1 hit
PfamiView protein in Pfam
PF02735 Ku, 1 hit
PF03730 Ku_C, 1 hit
PF03731 Ku_N, 1 hit
PF02037 SAP, 1 hit
PIRSFiPIRSF003033 Ku70, 1 hit
SMARTiView protein in SMART
SM00559 Ku78, 1 hit
SM00513 SAP, 1 hit
SUPFAMiSSF100939 SSF100939, 1 hit
SSF53300 SSF53300, 1 hit
SSF68906 SSF68906, 1 hit
TIGRFAMsiTIGR00578 ku70, 1 hit
PROSITEiView protein in PROSITE
PS50800 SAP, 1 hit

Sequences (2)i

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

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

Isoform 1 (identifier: P12956-1) [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
MSGWESYYKT EGDEEAEEEQ EENLEASGDY KYSGRDSLIF LVDASKAMFE
60 70 80 90 100
SQSEDELTPF DMSIQCIQSV YISKIISSDR DLLAVVFYGT EKDKNSVNFK
110 120 130 140 150
NIYVLQELDN PGAKRILELD QFKGQQGQKR FQDMMGHGSD YSLSEVLWVC
160 170 180 190 200
ANLFSDVQFK MSHKRIMLFT NEDNPHGNDS AKASRARTKA GDLRDTGIFL
210 220 230 240 250
DLMHLKKPGG FDISLFYRDI ISIAEDEDLR VHFEESSKLE DLLRKVRAKE
260 270 280 290 300
TRKRALSRLK LKLNKDIVIS VGIYNLVQKA LKPPPIKLYR ETNEPVKTKT
310 320 330 340 350
RTFNTSTGGL LLPSDTKRSQ IYGSRQIILE KEETEELKRF DDPGLMLMGF
360 370 380 390 400
KPLVLLKKHH YLRPSLFVYP EESLVIGSST LFSALLIKCL EKEVAALCRY
410 420 430 440 450
TPRRNIPPYF VALVPQEEEL DDQKIQVTPP GFQLVFLPFA DDKRKMPFTE
460 470 480 490 500
KIMATPEQVG KMKAIVEKLR FTYRSDSFEN PVLQQHFRNL EALALDLMEP
510 520 530 540 550
EQAVDLTLPK VEAMNKRLGS LVDEFKELVY PPDYNPEGKV TKRKHDNEGS
560 570 580 590 600
GSKRPKVEYS EEELKTHISK GTLGKFTVPM LKEACRAYGL KSGLKKQELL

EALTKHFQD
Length:609
Mass (Da):69,843
Last modified:January 23, 2007 - v2
Checksum:iBBD3CD434526DFCB
GO
Isoform 2 (identifier: P12956-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     65-105: Missing.

Note: No experimental confirmation available.
Show »
Length:568
Mass (Da):65,149
Checksum:iB6DBBED4C80118C1
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti20Q → D AA sequence (PubMed:1537839).Curated1
Sequence conflicti101N → K AA sequence (PubMed:8605992).Curated1
Sequence conflicti103Y → L AA sequence (PubMed:8605992).Curated1
Sequence conflicti116I → S AA sequence (PubMed:8605992).Curated1
Sequence conflicti125Q → S AA sequence (PubMed:8605992).Curated1
Sequence conflicti181A → T in CAG47015 (Ref. 5) Curated1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_05603065 – 105Missing in isoform 2. 1 PublicationAdd BLAST41

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J04607 mRNA Translation: AAA61177.1
J04611 mRNA Translation: AAA51733.1
M32865 mRNA Translation: AAA36155.1
S38729 mRNA Translation: AAB22381.1
AK055786 mRNA Translation: BAG51575.1
CR542219 mRNA Translation: CAG47015.1
AY870329 Genomic DNA Translation: AAW34364.1
Z83840 Genomic DNA No translation available.
CH471095 Genomic DNA Translation: EAW60448.1
BC008343 mRNA Translation: AAH08343.1
BC010034 mRNA Translation: AAH10034.1
BC012154 mRNA Translation: AAH12154.1
BC018259 mRNA Translation: AAH18259.1
BC072449 mRNA Translation: AAH72449.1
CCDSiCCDS14021.1 [P12956-1]
CCDS74870.1 [P12956-2]
PIRiA30299 A30894
RefSeqiNP_001275905.1, NM_001288976.1 [P12956-1]
NP_001275906.1, NM_001288977.1 [P12956-2]
NP_001460.1, NM_001469.4 [P12956-1]
UniGeneiHs.292493
Hs.730702

Genome annotation databases

EnsembliENST00000359308; ENSP00000352257; ENSG00000196419 [P12956-1]
ENST00000360079; ENSP00000353192; ENSG00000196419 [P12956-1]
ENST00000402580; ENSP00000384941; ENSG00000196419 [P12956-2]
ENST00000405878; ENSP00000384257; ENSG00000196419 [P12956-1]
GeneIDi2547
KEGGihsa:2547
UCSCiuc003bao.3 human [P12956-1]

Keywords - Coding sequence diversityi

Alternative splicing

Similar proteinsi

Entry informationi

Entry nameiXRCC6_HUMAN
AccessioniPrimary (citable) accession number: P12956
Secondary accession number(s): B1AHC8
, Q6FG89, Q9UCQ2, Q9UCQ3
Entry historyiIntegrated into UniProtKB/Swiss-Prot: January 1, 1990
Last sequence update: January 23, 2007
Last modified: April 25, 2018
This is version 218 of the entry and version 2 of the sequence. See 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

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome