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Protein

Non-homologous end-joining factor 1

Gene

NHEJ1

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

Functioni

DNA repair protein involved in DNA nonhomologous end joining (NHEJ) required for double-strand break (DSB) repair and V(D)J recombination. May serve as a bridge between XRCC4 and the other NHEJ factors located at DNA ends, or may participate in reconfiguration of the end bound NHEJ factors to allow XRCC4 access to the DNA termini. It may act in concert with XRCC6/XRCC5 (Ku) to stimulate XRCC4-mediated joining of blunt ends and several types of mismatched ends that are noncomplementary or partially complementary (PubMed:16439204, PubMed:16439205, PubMed:17470781). Binds DNA in a length-dependent manner (PubMed:17317666).4 Publications

Miscellaneous

Was named 'Cernunnos' after the enigmatic Celtic god of hunting, the underworld and fertility.

GO - Molecular functioni

GO - Biological processi

  • B cell differentiation Source: UniProtKB
  • central nervous system development Source: UniProtKB
  • double-strand break repair via nonhomologous end joining Source: UniProtKB
  • positive regulation of ligase activity Source: UniProtKB
  • response to ionizing radiation Source: UniProtKB
  • T cell differentiation Source: UniProtKB

Keywordsi

Molecular functionDNA-binding
Biological processDNA damage, DNA repair

Enzyme and pathway databases

ReactomeiR-HSA-5693571 Nonhomologous End-Joining (NHEJ)
SIGNORiQ9H9Q4

Names & Taxonomyi

Protein namesi
Recommended name:
Non-homologous end-joining factor 1
Alternative name(s):
Protein cernunnos
XRCC4-like factor
Gene namesi
Name:NHEJ1
Synonyms:XLF
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 2

Organism-specific databases

EuPathDBiHostDB:ENSG00000187736.12
HGNCiHGNC:25737 NHEJ1
MIMi611290 gene
neXtProtiNX_Q9H9Q4

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

Nucleus

Pathology & Biotechi

Involvement in diseasei

Severe combined immunodeficiency due to NHEJ1 deficiency (NHEJ1-SCID)3 Publications
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionSCID refers to a genetically and clinically heterogeneous group of rare congenital disorders characterized by impairment of both humoral and cell-mediated immunity, leukopenia and low or absent antibody levels. Patients with SCID present in infancy with recurrent, persistent infections by opportunistic organisms. The common characteristic of all types of SCID is absence of T-cell-mediated cellular immunity due to a defect in T-cell development. NHEJ1-SCID is characterized by a profound T- and B-lymphocytopenia associated with increased cellular sensitivity to ionizing radiation, microcephaly and growth retardation. Some patients may manifest SCID with sensitivity to ionizing radiation without microcephaly and mild growth retardation, probably due to hypomorphic NHEJ1 mutations.
See also OMIM:611291
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_02570457R → G in NHEJ1-SCID; fails to translocate to the nucleus. 2 PublicationsCorresponds to variant dbSNP:rs118204451EnsemblClinVar.1
Natural variantiVAR_025705123C → R in NHEJ1-SCID. 1 PublicationCorresponds to variant dbSNP:rs118204452EnsemblClinVar.1
A chromosomal aberration involving NHEJ1 is found in a patient with polymicrogyria. Translocation t(2;7)(q35;p22).1 Publication

Keywords - Diseasei

Disease mutation, SCID

Organism-specific databases

DisGeNETi79840
MalaCardsiNHEJ1
MIMi611291 phenotype
OpenTargetsiENSG00000187736
Orphaneti208447 Bilateral generalized polymicrogyria
169079 Cernunnos-XLF deficiency
PharmGKBiPA144596401

Polymorphism and mutation databases

BioMutaiNHEJ1
DMDMi74734059

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002286541 – 299Non-homologous end-joining factor 1Add BLAST299

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei245PhosphoserineBy similarity1
Modified residuei287PhosphoserineCombined sources1

Keywords - PTMi

Phosphoprotein

Proteomic databases

EPDiQ9H9Q4
MaxQBiQ9H9Q4
PaxDbiQ9H9Q4
PeptideAtlasiQ9H9Q4
PRIDEiQ9H9Q4
ProteomicsDBi81350
81351 [Q9H9Q4-2]

PTM databases

iPTMnetiQ9H9Q4
PhosphoSitePlusiQ9H9Q4

Expressioni

Tissue specificityi

Ubiquitously expressed.1 Publication

Gene expression databases

BgeeiENSG00000187736
CleanExiHS_NHEJ1
ExpressionAtlasiQ9H9Q4 baseline and differential
GenevisibleiQ9H9Q4 HS

Organism-specific databases

HPAiCAB012334
HPA043869

Interactioni

Subunit structurei

Exists mainly as a homodimer. Associates with the non-homologous end joining (NHEJ) complex which is at least composed of the core proteins XRCC5/Ku80, XRCC6/Ku70, PRKDC/DNA-PKcs, LIG4 and XRCC4.7 Publications

Binary interactionsi

Show more details

Protein-protein interaction databases

BioGridi122931, 7 interactors
CORUMiQ9H9Q4
DIPiDIP-37959N
IntActiQ9H9Q4, 7 interactors
MINTiQ9H9Q4
STRINGi9606.ENSP00000349313

Structurei

Secondary structure

1299
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi1 – 9Combined sources9
Beta strandi14 – 17Combined sources4
Beta strandi19 – 30Combined sources12
Beta strandi33 – 39Combined sources7
Beta strandi44 – 49Combined sources6
Helixi51 – 61Combined sources11
Helixi69 – 85Combined sources17
Beta strandi94 – 100Combined sources7
Beta strandi103 – 112Combined sources10
Beta strandi115 – 125Combined sources11
Helixi128 – 134Combined sources7
Helixi136 – 169Combined sources34
Helixi186 – 196Combined sources11
Helixi198 – 201Combined sources4
Helixi208 – 213Combined sources6
Helixi215 – 228Combined sources14

3D structure databases

ProteinModelPortaliQ9H9Q4
SMRiQ9H9Q4
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9H9Q4

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni1 – 135Globular headAdd BLAST135

Coiled coil

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Coiled coili128 – 1701 PublicationAdd BLAST43

Domaini

The coiled-coil region mediates homodimerization.

Sequence similaritiesi

Belongs to the XLF family.Curated

Keywords - Domaini

Coiled coil

Phylogenomic databases

eggNOGiENOG410IT7Y Eukaryota
ENOG411291V LUCA
GeneTreeiENSGT00390000009940
HOGENOMiHOG000089974
HOVERGENiHBG080703
InParanoidiQ9H9Q4
KOiK10980
OMAiYWNFHCI
OrthoDBiEOG091G1269
PhylomeDBiQ9H9Q4
TreeFamiTF328567

Family and domain databases

InterProiView protein in InterPro
IPR015381 XLF_fam
PfamiView protein in Pfam
PF09302 XLF, 1 hit

Sequences (2)i

Sequence statusi: Complete.

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

Isoform 1 (identifier: Q9H9Q4-1) [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
MEELEQGLLM QPWAWLQLAE NSLLAKVFIT KQGYALLVSD LQQVWHEQVD
60 70 80 90 100
TSVVSQRAKE LNKRLTAPPA AFLCHLDNLL RPLLKDAAHP SEATFSCDCV
110 120 130 140 150
ADALILRVRS ELSGLPFYWN FHCMLASPSL VSQHLIRPLM GMSLALQCQV
160 170 180 190 200
RELATLLHMK DLEIQDYQES GATLIRDRLK TEPFEENSFL EQFMIEKLPE
210 220 230 240 250
ACSIGDGKPF VMNLQDLYMA VTTQEVQVGQ KHQGAGDPHT SNSASLQGID
260 270 280 290
SQCVNQPEQL VSSAPTLSAP EKESTGTSGP LQRPQLSKVK RKKPRGLFS
Length:299
Mass (Da):33,337
Last modified:March 1, 2001 - v1
Checksum:iBC5C68076A5E7A96
GO
Isoform 2 (identifier: Q9H9Q4-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     276-299: GTSGPLQRPQLSKVKRKKPRGLFS → ALCRDLSCQRSRGRSQGVSSVNLLWPQLLRMDLENSFQASP

Note: No experimental confirmation available.
Show »
Length:316
Mass (Da):35,291
Checksum:i11CAF1C6543580CE
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti256Q → R in CAG33572 (Ref. 3) Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_03879014A → T. Corresponds to variant dbSNP:rs34689457EnsemblClinVar.1
Natural variantiVAR_02570457R → G in NHEJ1-SCID; fails to translocate to the nucleus. 2 PublicationsCorresponds to variant dbSNP:rs118204451EnsemblClinVar.1
Natural variantiVAR_03879189H → R. Corresponds to variant dbSNP:rs1056296Ensembl.1
Natural variantiVAR_025705123C → R in NHEJ1-SCID. 1 PublicationCorresponds to variant dbSNP:rs118204452EnsemblClinVar.1
Natural variantiVAR_038792256Q → L. Corresponds to variant dbSNP:rs35270667EnsemblClinVar.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_017689276 – 299GTSGP…RGLFS → ALCRDLSCQRSRGRSQGVSS VNLLWPQLLRMDLENSFQAS P in isoform 2. 1 PublicationAdd BLAST24

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ972687 mRNA Translation: CAI99410.1
AK022672 mRNA Translation: BAB14168.1
CR457291 mRNA Translation: CAG33572.1
AC020575 Genomic DNA No translation available.
AC068946 Genomic DNA No translation available.
AC097468 Genomic DNA Translation: AAX88921.1
BC008210 mRNA Translation: AAH08210.2
BC012732 mRNA Translation: AAH12732.1
BC030986 mRNA Translation: AAH30986.1
CCDSiCCDS2432.1 [Q9H9Q4-1]
RefSeqiNP_079058.1, NM_024782.2 [Q9H9Q4-1]
UniGeneiHs.225988

Genome annotation databases

EnsembliENST00000356853; ENSP00000349313; ENSG00000187736 [Q9H9Q4-1]
ENST00000409720; ENSP00000387290; ENSG00000187736 [Q9H9Q4-2]
GeneIDi79840
KEGGihsa:79840
UCSCiuc002vjp.5 human [Q9H9Q4-1]

Keywords - Coding sequence diversityi

Alternative splicing, Chromosomal rearrangement, Polymorphism

Similar proteinsi

Entry informationi

Entry nameiNHEJ1_HUMAN
AccessioniPrimary (citable) accession number: Q9H9Q4
Secondary accession number(s): B8ZZA4
, Q4ZFW7, Q6IA64, Q96JS9
Entry historyiIntegrated into UniProtKB/Swiss-Prot: March 21, 2006
Last sequence update: March 1, 2001
Last modified: June 20, 2018
This is version 136 of the entry and version 1 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, Reference proteome

Documents

  1. Human chromosome 2
    Human chromosome 2: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. SIMILARITY comments
    Index of protein domains and families

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