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Protein

Three-prime repair exonuclease 1

Gene

TREX1

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

Functioni

Major cellular 3'-to-5' DNA exonuclease which digests single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) with mismatched 3' termini. Prevents cell-intrinsic initiation of autoimmunity. Acts by metabolizing DNA fragments from endogenous retroelements, including L1, LTR and SINE elements. Unless degraded, these DNA fragments accumulate in the cytosol and activate the IFN-stimulatory DNA (ISD) response and innate immune signaling. Prevents chronic ATM-dependent checkpoint activation, by processing ssDNA polynucleotide species arising from the processing of aberrant DNA replication intermediates. Inefficiently degrades oxidized DNA, such as that generated upon antimicrobial reactive oxygen production or upon absorption of UV light. During GZMA-mediated cell death, contributes to DNA damage in concert with NME1. NME1 nicks one strand of DNA and TREX1 removes bases from the free 3' end to enhance DNA damage and prevent DNA end reannealing and rapid repair.6 Publications

Catalytic activityi

Exonucleolytic cleavage in the 3'- to 5'-direction to yield nucleoside 5'-phosphates.

Cofactori

Mg2+By similarityNote: Binds 2 Mg2+ per subunit. The second magnesium ion interacts with only one residue. Substitution with Mn2+ results in partial activity.By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi18Magnesium 1By similarity1
Metal bindingi18Magnesium 2By similarity1
Metal bindingi20Magnesium 1By similarity1
Binding sitei129SubstrateBy similarity1
Active sitei195Proton donor/acceptorBy similarity1
Metal bindingi200Magnesium 1By similarity1
Binding sitei200SubstrateBy similarity1

GO - Molecular functioni

  • 3'-5'-exodeoxyribonuclease activity Source: UniProtKB
  • 3'-5' exonuclease activity Source: UniProtKB
  • exodeoxyribonuclease III activity Source: UniProtKB-EC
  • metal ion binding Source: UniProtKB
  • MutLalpha complex binding Source: MGI
  • MutSalpha complex binding Source: MGI
  • protein homodimerization activity Source: UniProtKB
  • single-stranded DNA binding Source: UniProtKB

GO - Biological processi

  • DNA metabolic process Source: UniProtKB
  • DNA recombination Source: UniProtKB
  • DNA repair Source: ProtInc
  • DNA replication Source: UniProtKB
  • mismatch repair Source: UniProtKB
  • regulation of type I interferon production Source: Reactome

Keywordsi

Molecular functionExonuclease, Hydrolase, Nuclease
LigandMagnesium, Metal-binding

Enzyme and pathway databases

ReactomeiR-HSA-3248023. Regulation by TREX1.
R-HSA-3270619. IRF3-mediated induction of type I IFN.

Names & Taxonomyi

Protein namesi
Recommended name:
Three-prime repair exonuclease 1Curated (EC:3.1.11.2)
Alternative name(s):
3'-5' exonuclease TREX11 Publication
Deoxyribonuclease III1 Publication
Short name:
DNase III1 Publication
Gene namesi
Name:TREX1Imported
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 3

Organism-specific databases

EuPathDBiHostDB:ENSG00000213689.10.
HostDB:ENSG00000282827.1.
HGNCiHGNC:12269. TREX1.
MIMi606609. gene.
neXtProtiNX_Q9NSU2.

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

Cytoplasm, Endoplasmic reticulum, Membrane, Nucleus

Pathology & Biotechi

Involvement in diseasei

Aicardi-Goutieres syndrome 1 (AGS1)8 Publications
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA form of Aicardi-Goutieres syndrome, a genetically heterogeneous disease characterized by cerebral atrophy, leukoencephalopathy, intracranial calcifications, chronic cerebrospinal fluid (CSF) lymphocytosis, increased CSF alpha-interferon, and negative serologic investigations for common prenatal infection. Clinical features as thrombocytopenia, hepatosplenomegaly and elevated hepatic transaminases along with intermittent fever may erroneously suggest an infective process. Severe neurological dysfunctions manifest in infancy as progressive microcephaly, spasticity, dystonic posturing and profound psychomotor retardation. Death often occurs in early childhood.
See also OMIM:225750
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_070899122V → A in AGS1; increases ubiquitination levels; no effect on exonuclease activity. 2 PublicationsCorresponds to variant dbSNP:rs79993407Ensembl.1
Natural variantiVAR_070900198E → K in AGS1; increases ubiquitination levels; no effect on exonuclease activity. 2 Publications1
Natural variantiVAR_028320200D → DD in AGS1; heterozygous compound with H-169; loss of activity. 2 Publications1
Natural variantiVAR_032940200D → N in AGS1; autosomal dominant form; no effect on dsDNA exonuclease activity; abolishes ssDNA exonuclease activity. 3 PublicationsCorresponds to variant dbSNP:rs78846775Ensembl.1
Natural variantiVAR_028321201V → D in AGS1; reduces activity by 75%. 3 PublicationsCorresponds to variant dbSNP:rs78408272Ensembl.1
Natural variantiVAR_070902303T → P in AGS1; decreases ubiquitination levels; decreases colocalization with UBQLN1; no effect on exonuclease activity. 2 PublicationsCorresponds to variant dbSNP:rs76224909Ensembl.1
Systemic lupus erythematosus (SLE)3 Publications
Disease susceptibility is associated with variations affecting the gene represented in this entry. Enhanced immune sensing of oxidized DNA may be involved in the phototoxicity experienced by SLE patients. Exposure to UV-light produces DNA oxidative damage. Oxidized DNA being a poor TREX1 substrate, it accumulates in skin, leading to enhanced auto-immune reactivity and eventually skin lesions (PubMed:23993650).1 Publication
Disease descriptionA chronic, relapsing, inflammatory, and often febrile multisystemic disorder of connective tissue, characterized principally by involvement of the skin, joints, kidneys and serosal membranes. It is of unknown etiology, but is thought to represent a failure of the regulatory mechanisms of the autoimmune system. The disease is marked by a wide range of system dysfunctions, an elevated erythrocyte sedimentation rate, and the formation of LE cells in the blood or bone marrow.
See also OMIM:152700
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_037949158A → V in SLE. 1 PublicationCorresponds to variant dbSNP:rs762011967Ensembl.1
Natural variantiVAR_037950227G → S in SLE; associated in cis with P-302. 1 PublicationCorresponds to variant dbSNP:rs113107733Ensembl.1
Natural variantiVAR_037951240R → S in SLE. 1 PublicationCorresponds to variant dbSNP:rs72556555Ensembl.1
Natural variantiVAR_037952247A → P in SLE; associated in cis with S-282. 1 PublicationCorresponds to variant dbSNP:rs112741962Ensembl.1
Natural variantiVAR_037954290P → L in SLE; increases ubiquitination levels; no effect on exonuclease activity. 2 PublicationsCorresponds to variant dbSNP:rs148833270Ensembl.1
Natural variantiVAR_037955305Y → C in SLE; decreases ubiquitination levels; decreases colocalization with UBQLN1; no effect on exonuclease activity. 2 PublicationsCorresponds to variant dbSNP:rs370504038Ensembl.1
Natural variantiVAR_037956306G → A in SLE. 1 PublicationCorresponds to variant dbSNP:rs780022923Ensembl.1
Chilblain lupus 1 (CHBL1)2 Publications
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA rare cutaneous form of lupus erythematosus. Affected individuals present with painful bluish-red papular or nodular lesions of the skin in acral locations precipitated by cold and wet exposure at temperatures less than 10 degrees centigrade.
See also OMIM:610448
Vasculopathy, retinal, with cerebral leukodystrophy (RVCL)1 Publication
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA microvascular endotheliopathy resulting in central nervous system degeneration and retinopathy, with progressive loss of vision, stroke, motor impairment, and cognitive decline. The ocular manifestations are characterized by telangiectasias, microaneurysms and retinal capillary obliteration starting in the macula. Diseased cerebral white matter has prominent small infarcts that often coalesce to pseudotumors.
See also OMIM:192315

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi30K → R: Reduces ubiquitination. 1 Publication1
Mutagenesisi66K → R: No effect on ubiquitination. 1 Publication1
Mutagenesisi75K → R: Reduces ubiquitination. 1 Publication1
Mutagenesisi160K → R: Reduces ubiquitination. 1 Publication1
Mutagenesisi175K → R: Reduces ubiquitination. 1 Publication1
Mutagenesisi242K → R: Reduces ubiquitination. 1 Publication1
Mutagenesisi271K → R: Reduces ubiquitination. Strongly reduces ubiquitination; when associated with R-277. 1 Publication1
Mutagenesisi277K → R: Reduces ubiquitination. Strongly reduces ubiquitination; when associated with R-271. 1 Publication1

Keywords - Diseasei

Aicardi-Goutieres syndrome, Disease mutation, Neurodegeneration, Systemic lupus erythematosus

Organism-specific databases

DisGeNETi11277.
GeneReviewsiTREX1.
MalaCardsiTREX1.
MIMi152700. phenotype.
192315. phenotype.
225750. phenotype.
610448. phenotype.
OpenTargetsiENSG00000213689.
Orphaneti51. Aicardi-Goutieres syndrome.
3421. Cerebroretinal vasculopathy.
90280. Chilblain lupus.
71291. Hereditary vascular retinopathy.
63261. HERNS syndrome.
536. Systemic lupus erythematosus.
PharmGKBiPA36949.

Polymorphism and mutation databases

DMDMi47606216.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001098681 – 314Three-prime repair exonuclease 1Add BLAST314

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei78PhosphoserineCombined sources1
Modified residuei167PhosphoserineCombined sources1
Modified residuei261PhosphoserineCombined sources1

Post-translational modificationi

Ubiquitinated, but not targeted to proteasomal degradation. Ubiquitination may be important for interaction with UBQLN1.1 Publication

Keywords - PTMi

Phosphoprotein, Ubl conjugation

Proteomic databases

EPDiQ9NSU2.
PaxDbiQ9NSU2.
PeptideAtlasiQ9NSU2.
PRIDEiQ9NSU2.

PTM databases

iPTMnetiQ9NSU2.
PhosphoSitePlusiQ9NSU2.

Expressioni

Tissue specificityi

Detected in thymus, spleen, liver, brain, heart, small intestine and colon.2 Publications

Inductioni

Induced by cytosolic DNA. Induced by inflammatory stimuli such as IFN-alpha and IFN-gamma in B cells and also by LPS and viral and bacterial DNA (via TLR9) in dendritic cells and macrophages (By similarity).By similarity

Gene expression databases

BgeeiENSG00000213689.
CleanExiHS_TREX1.
ExpressionAtlasiQ9NSU2. baseline.
GenevisibleiQ9NSU2. HS.

Organism-specific databases

HPAiHPA035437.

Interactioni

Subunit structurei

Homodimer. Interacts (via proline-rich region) with TCERG1/CA150 (via the second WW domain). Component of the SET complex, composed of at least ANP32A, APEX1, HMGB2, NME1, SET and TREX1. Within this complex, directly interacts with SET; this interaction does not result in TREX1 inhibition. Also interacts with NME1, but only following translocation to the nucleus. Directly interacts with UBQLN1 (via ubiquitin-like domain); the interaction may control TREX1 subcellular location.2 Publications

Binary interactionsi

Show more details

GO - Molecular functioni

  • MutLalpha complex binding Source: MGI
  • MutSalpha complex binding Source: MGI
  • protein homodimerization activity Source: UniProtKB

Protein-protein interaction databases

BioGridi116433. 12 interactors.
IntActiQ9NSU2. 5 interactors.
STRINGi9606.ENSP00000390478.

Structurei

3D structure databases

ProteinModelPortaliQ9NSU2.
SMRiQ9NSU2.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni20 – 21Substrate bindingBy similarity2
Regioni54 – 63Proline-rich regionBy similarity10
Regioni236 – 314Necessary for endoplasmic reticulum localizationBy similarityAdd BLAST79
Regioni243 – 314Interaction with UBQLN11 PublicationAdd BLAST72
Regioni281 – 314Necessary for cytoplasmic retentionBy similarityAdd BLAST34

Sequence similaritiesi

Belongs to the exonuclease superfamily. TREX family.Curated

Phylogenomic databases

eggNOGiKOG4793. Eukaryota.
ENOG4111YSP. LUCA.
GeneTreeiENSGT00390000012715.
HOGENOMiHOG000118119.
HOVERGENiHBG079278.
InParanoidiQ9NSU2.
KOiK10790.
OMAiLLSICQW.
OrthoDBiEOG091G0LSM.
PhylomeDBiQ9NSU2.
TreeFamiTF323333.

Family and domain databases

Gene3Di3.30.420.10. 1 hit.
InterProiView protein in InterPro
IPR013520. Exonuclease_RNaseT/DNA_pol3.
IPR012337. RNaseH-like_sf.
IPR036397. RNaseH_sf.
SMARTiView protein in SMART
SM00479. EXOIII. 1 hit.
SUPFAMiSSF53098. SSF53098. 1 hit.

Sequences (3)i

Sequence statusi: Complete.

This entry describes 3 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 3 (identifier: Q9NSU2-3) [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
MGSQALPPGP MQTLIFFDME ATGLPFSQPK VTELCLLAVH RCALESPPTS
60 70 80 90 100
QGPPPTVPPP PRVVDKLSLC VAPGKACSPA ASEITGLSTA VLAAHGRQCF
110 120 130 140 150
DDNLANLLLA FLRRQPQPWC LVAHNGDRYD FPLLQAELAM LGLTSALDGA
160 170 180 190 200
FCVDSITALK ALERASSPSE HGPRKSYSLG SIYTRLYGQS PPDSHTAEGD
210 220 230 240 250
VLALLSICQW RPQALLRWVD AHARPFGTIR PMYGVTASAR TKPRPSAVTT
260 270 280 290 300
TAHLATTRNT SPSLGESRGT KDLPPVKDPG ALSREGLLAP LGLLAILTLA
310
VATLYGLSLA TPGE
Length:314
Mass (Da):33,212
Last modified:December 20, 2017 - v2
Checksum:iEE8F63B6496D72F4
GO
Isoform 1 (identifier: Q9NSU2-1) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-1: M → MGPGARRQGRIVQGRPEMCFCPPPTPLPPLRILTLGTHTPTPCSSPGSAAGTYPTM

Show »
Length:369
Mass (Da):38,923
Checksum:i42B79047A9AD9837
GO
Isoform 2 (identifier: Q9NSU2-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-10: Missing.

Show »
Length:304
Mass (Da):32,276
Checksum:i922048DCC4122124
GO

Sequence cautioni

The sequence AAD48774 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated
The sequence AAL82504 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti265G → R in CAB50866 (PubMed:10393201).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_03794818D → N in CHBL1 and AGS1; loss of function. 2 PublicationsCorresponds to variant dbSNP:rs121908117Ensembl.1
Natural variantiVAR_028319114R → H in AGS1 and SLE; primary fibroblasts from an AGS1 patient carrying H-169 show defective G1/S transition and chronic G2/M DNA damage checkpoint activation; strongly reduces activity. 6 PublicationsCorresponds to variant dbSNP:rs72556554Ensembl.1
Natural variantiVAR_070899122V → A in AGS1; increases ubiquitination levels; no effect on exonuclease activity. 2 PublicationsCorresponds to variant dbSNP:rs79993407Ensembl.1
Natural variantiVAR_037949158A → V in SLE. 1 PublicationCorresponds to variant dbSNP:rs762011967Ensembl.1
Natural variantiVAR_070900198E → K in AGS1; increases ubiquitination levels; no effect on exonuclease activity. 2 Publications1
Natural variantiVAR_028320200D → DD in AGS1; heterozygous compound with H-169; loss of activity. 2 Publications1
Natural variantiVAR_070901200D → H in AGS1 and SLE. 1 Publication1
Natural variantiVAR_032940200D → N in AGS1; autosomal dominant form; no effect on dsDNA exonuclease activity; abolishes ssDNA exonuclease activity. 3 PublicationsCorresponds to variant dbSNP:rs78846775Ensembl.1
Natural variantiVAR_028321201V → D in AGS1; reduces activity by 75%. 3 PublicationsCorresponds to variant dbSNP:rs78408272Ensembl.1
Natural variantiVAR_037950227G → S in SLE; associated in cis with P-302. 1 PublicationCorresponds to variant dbSNP:rs113107733Ensembl.1
Natural variantiVAR_037951240R → S in SLE. 1 PublicationCorresponds to variant dbSNP:rs72556555Ensembl.1
Natural variantiVAR_037952247A → P in SLE; associated in cis with S-282. 1 PublicationCorresponds to variant dbSNP:rs112741962Ensembl.1
Natural variantiVAR_037953266E → G1 PublicationCorresponds to variant dbSNP:rs55999987Ensembl.1
Natural variantiVAR_037954290P → L in SLE; increases ubiquitination levels; no effect on exonuclease activity. 2 PublicationsCorresponds to variant dbSNP:rs148833270Ensembl.1
Natural variantiVAR_070902303T → P in AGS1; decreases ubiquitination levels; decreases colocalization with UBQLN1; no effect on exonuclease activity. 2 PublicationsCorresponds to variant dbSNP:rs76224909Ensembl.1
Natural variantiVAR_037955305Y → C in SLE; decreases ubiquitination levels; decreases colocalization with UBQLN1; no effect on exonuclease activity. 2 PublicationsCorresponds to variant dbSNP:rs370504038Ensembl.1
Natural variantiVAR_037956306G → A in SLE. 1 PublicationCorresponds to variant dbSNP:rs780022923Ensembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0104451 – 10Missing in isoform 2. 1 Publication10
Alternative sequenceiVSP_0592791M → MGPGARRQGRIVQGRPEMCF CPPPTPLPPLRILTLGTHTP TPCSSPGSAAGTYPTM in isoform 1. 1 Publication1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ243797 mRNA. Translation: CAB50866.1.
AF151105 mRNA. Translation: AAD48774.2. Different initiation.
AF319566 mRNA. Translation: AAK07613.1.
AF319567 mRNA. Translation: AAK07614.1.
AF319568 mRNA. Translation: AAK07615.1.
AF319569 mRNA. Translation: AAK07616.1.
AK315196 mRNA. Translation: BAG37636.1.
AL137745 mRNA. No translation available.
AF483777 Genomic DNA. Translation: AAL82504.1. Different initiation.
BC023630 mRNA. Translation: AAH23630.1.
CCDSiCCDS2769.1. [Q9NSU2-3]
CCDS59451.1. [Q9NSU2-2]
PIRiT46299.
RefSeqiNP_009179.2. NM_007248.3. [Q9NSU2-2]
NP_057465.1. NM_016381.5. [Q9NSU2-1]
NP_338599.1. NM_033629.4. [Q9NSU2-3]
UniGeneiHs.707026.
Hs.713742.
Hs.744646.

Genome annotation databases

EnsembliENST00000444177; ENSP00000415972; ENSG00000213689. [Q9NSU2-2]
ENST00000625293; ENSP00000486676; ENSG00000213689. [Q9NSU2-1]
ENST00000629913; ENSP00000486444; ENSG00000213689. [Q9NSU2-3]
GeneIDi11277.
KEGGihsa:11277.
UCSCiuc031rzp.2. human. [Q9NSU2-3]

Keywords - Coding sequence diversityi

Alternative splicing

Similar proteinsi

Entry informationi

Entry nameiTREX1_HUMAN
AccessioniPrimary (citable) accession number: Q9NSU2
Secondary accession number(s): B2RCN9
, Q8TEU2, Q9BPW1, Q9Y4X2
Entry historyiIntegrated into UniProtKB/Swiss-Prot: May 24, 2004
Last sequence update: December 20, 2017
Last modified: March 28, 2018
This is version 167 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

Caution

The gene for this protein is either identical to or adjacent to that of ATRIP. Some of the mRNAs that encode ATRIP also encode TREX1 in another reading frame.Curated

Keywords - Technical termi

Complete proteome, Reference proteome