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Protein

DNA-(apurinic or apyrimidinic site) lyase 2

Gene

APEX2

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Function as a weak apurinic/apyrimidinic (AP) endodeoxyribonuclease in the DNA base excision repair (BER) pathway of DNA lesions induced by oxidative and alkylating agents. Initiates repair of AP sites in DNA by catalyzing hydrolytic incision of the phosphodiester backbone immediately adjacent to the damage, generating a single-strand break with 5'-deoxyribose phosphate and 3'-hydroxyl ends. Displays also double-stranded DNA 3'-5' exonuclease, 3'-phosphodiesterase activities. Shows robust 3'-5' exonuclease activity on 3'-recessed heteroduplex DNA and is able to remove mismatched nucleotides preferentially. Shows fairly strong 3'-phosphodiesterase activity involved in the removal of 3'-damaged termini formed in DNA by oxidative agents. In the nucleus functions in the PCNA-dependent BER pathway. Required for somatic hypermutation (SHM) and DNA cleavage step of class switch recombination (CSR) of immunoglobulin genes. Required for proper cell cycle progression during proliferation of peripheral lymphocytes.3 Publications

Catalytic activityi

The C-O-P bond 3' to the apurinic or apyrimidinic site in DNA is broken by a beta-elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate.PROSITE-ProRule annotation

Cofactori

Mg2+By similarity, Mn2+By similarityNote: Probably binds two magnesium or manganese ions per subunit.By similarity

Enzyme regulationi

3'-5' exonuclease activity is activated by sodium and manganese. 3'-5' exonuclease and 3'-phosphodiesterase activities are stimulated in presence of PCNA.

pH dependencei

Optimum pH is 6.0-8.0.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi8Magnesium 1By similarity1
Metal bindingi48Magnesium 1By similarity1
Active sitei156By similarity1
Active sitei197Proton donor/acceptorBy similarity1
Metal bindingi197Magnesium 2By similarity1
Metal bindingi199Magnesium 2By similarity1
Sitei199Transition state stabilizerBy similarity1
Sitei277Important for catalytic activityBy similarity1
Metal bindingi303Magnesium 1By similarity1

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Endonuclease, Exonuclease, Hydrolase, Lyase, Nuclease

Keywords - Biological processi

Cell cycle, DNA damage, DNA recombination, DNA repair

Keywords - Ligandi

DNA-binding, Magnesium, Metal-binding

Enzyme and pathway databases

BioCyciZFISH:HS09895-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA-(apurinic or apyrimidinic site) lyase 2 (EC:3.1.-.-, EC:4.2.99.18)
Alternative name(s):
AP endonuclease XTH2
APEX nuclease 2
APEX nuclease-like 2
Apurinic-apyrimidinic endonuclease 2
Short name:
AP endonuclease 2
Gene namesi
Name:APEX2
Synonyms:APE2, APEXL2, XTH2
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome X

Organism-specific databases

HGNCiHGNC:17889. APEX2.

Subcellular locationi

  • Nucleus
  • Cytoplasm
  • Mitochondrion Curated

  • Note: Together with PCNA, is redistributed in discrete nuclear foci in presence of oxidative DNA damaging agents.

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Mitochondrion, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi269H → A: Abolishes AP endodeoxyribonuclease, 3'-5' exonuclease activity and 3'-phosphodiesterase activities. 1
Mutagenesisi277D → A: Abolishes AP endodeoxyribonuclease, 3'-5' exonuclease activity and 3'-phosphodiesterase activities. 1 Publication1
Mutagenesisi396Y → A: Reduces 3'-5' exonuclease activity in presence of PCNA. Does not abolish the 3'-5' exonuclease activity. Does only partially redistributes together with PCNA in nuclear foci in presence of oxidative-induced DNA damaging agents. 1 Publication1
Mutagenesisi397F → A: Reduces 3'-5' exonuclease activity in presence of PCNA. Does not abolish the 3'-5' exonuclease activity. Does only partially redistributes together with PCNA in nuclear foci in presence of oxidative-induced DNA damaging agents. 1 Publication1

Organism-specific databases

DisGeNETi27301.
OpenTargetsiENSG00000169188.
PharmGKBiPA38474.

Polymorphism and mutation databases

DMDMi73921676.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002000141 – 518DNA-(apurinic or apyrimidinic site) lyase 2Add BLAST518

Proteomic databases

EPDiQ9UBZ4.
MaxQBiQ9UBZ4.
PaxDbiQ9UBZ4.
PeptideAtlasiQ9UBZ4.
PRIDEiQ9UBZ4.

PTM databases

iPTMnetiQ9UBZ4.
PhosphoSitePlusiQ9UBZ4.

Expressioni

Tissue specificityi

Highly expressed in brain and kidney. Weakly expressed in the fetal brain.1 Publication

Gene expression databases

BgeeiENSG00000169188.
CleanExiHS_APEX2.
ExpressionAtlasiQ9UBZ4. baseline and differential.
GenevisibleiQ9UBZ4. HS.

Organism-specific databases

HPAiHPA030872.
HPA048577.

Interactioni

Subunit structurei

Interacts with PCNA; this interaction is triggered by reactive oxygen species and increased by misincorporation of uracil in nuclear DNA.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei304Interaction with DNA substrateBy similarity1

Protein-protein interaction databases

BioGridi118124. 21 interactors.
IntActiQ9UBZ4. 13 interactors.
MINTiMINT-1439290.
STRINGi9606.ENSP00000364126.

Structurei

3D structure databases

ProteinModelPortaliQ9UBZ4.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni390 – 397Required for the colocalization with PCNA in nuclear foci in presence of oxidative-induced DNA damaging agents8

Sequence similaritiesi

Belongs to the DNA repair enzymes AP/ExoA family.Curated

Phylogenomic databases

eggNOGiKOG1294. Eukaryota.
COG0708. LUCA.
GeneTreeiENSGT00530000063540.
HOGENOMiHOG000231386.
HOVERGENiHBG054715.
InParanoidiQ9UBZ4.
KOiK10772.
OMAiAVNLECF.
OrthoDBiEOG091G0IPG.
PhylomeDBiQ9UBZ4.
TreeFamiTF328442.

Family and domain databases

Gene3Di3.60.10.10. 1 hit.
InterProiIPR004808. AP_endonuc_1.
IPR020847. AP_endonuclease_F1_BS.
IPR005135. Endo/exonuclease/phosphatase.
IPR010666. Znf_GRF.
[Graphical view]
PANTHERiPTHR22748. PTHR22748. 1 hit.
PfamiPF03372. Exo_endo_phos. 1 hit.
PF06839. zf-GRF. 1 hit.
[Graphical view]
SUPFAMiSSF56219. SSF56219. 1 hit.
TIGRFAMsiTIGR00633. xth. 1 hit.
PROSITEiPS00726. AP_NUCLEASE_F1_1. 1 hit.
PS51435. AP_NUCLEASE_F1_4. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q9UBZ4-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MLRVVSWNIN GIRRPLQGVA NQEPSNCAAV AVGRILDELD ADIVCLQETK
60 70 80 90 100
VTRDALTEPL AIVEGYNSYF SFSRNRSGYS GVATFCKDNA TPVAAEEGLS
110 120 130 140 150
GLFATQNGDV GCYGNMDEFT QEELRALDSE GRALLTQHKI RTWEGKEKTL
160 170 180 190 200
TLINVYCPHA DPGRPERLVF KMRFYRLLQI RAEALLAAGS HVIILGDLNT
210 220 230 240 250
AHRPIDHWDA VNLECFEEDP GRKWMDSLLS NLGCQSASHV GPFIDSYRCF
260 270 280 290 300
QPKQEGAFTC WSAVTGARHL NYGSRLDYVL GDRTLVIDTF QASFLLPEVM
310 320 330 340 350
GSDHCPVGAV LSVSSVPAKQ CPPLCTRFLP EFAGTQLKIL RFLVPLEQSP
360 370 380 390 400
VLEQSTLQHN NQTRVQTCQN KAQVRSTRPQ PSQVGSSRGQ KNLKSYFQPS
410 420 430 440 450
PSCPQASPDI ELPSLPLMSA LMTPKTPEEK AVAKVVKGQA KTSEAKDEKE
460 470 480 490 500
LRTSFWKSVL AGPLRTPLCG GHREPCVMRT VKKPGPNLGR RFYMCARPRG
510
PPTDPSSRCN FFLWSRPS
Length:518
Mass (Da):57,401
Last modified:May 1, 2000 - v1
Checksum:i08464806153F8832
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti399P → S in AAD43041 (Ref. 4) Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_023390141R → C.1 PublicationCorresponds to variant rs2301416dbSNPEnsembl.1
Natural variantiVAR_048261141R → W.Corresponds to variant rs2301416dbSNPEnsembl.1
Natural variantiVAR_064033269H → Y Identified in a patient with mtDNA maintenance disorders. 1 PublicationCorresponds to variant rs145122391dbSNPEnsembl.1
Natural variantiVAR_064034392N → H Identified in a patient with mtDNA maintenance disorders. 1 PublicationCorresponds to variant rs201964062dbSNPEnsembl.1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB049211 mRNA. Translation: BAB13764.1.
AJ011311 mRNA. Translation: CAB45242.1.
AB021260 mRNA. Translation: BAA78422.1.
AF119046 mRNA. Translation: AAD43041.1.
AY884244 Genomic DNA. Translation: AAW56941.1.
AL020991 Genomic DNA. Translation: CAI43126.1.
BC002959 mRNA. Translation: AAH02959.1.
CCDSiCCDS14365.1.
RefSeqiNP_055296.2. NM_014481.3.
UniGeneiHs.659558.

Genome annotation databases

EnsembliENST00000374987; ENSP00000364126; ENSG00000169188.
GeneIDi27301.
KEGGihsa:27301.
UCSCiuc004dtz.5. human.

Keywords - Coding sequence diversityi

Polymorphism

Cross-referencesi

Web resourcesi

NIEHS-SNPs

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB049211 mRNA. Translation: BAB13764.1.
AJ011311 mRNA. Translation: CAB45242.1.
AB021260 mRNA. Translation: BAA78422.1.
AF119046 mRNA. Translation: AAD43041.1.
AY884244 Genomic DNA. Translation: AAW56941.1.
AL020991 Genomic DNA. Translation: CAI43126.1.
BC002959 mRNA. Translation: AAH02959.1.
CCDSiCCDS14365.1.
RefSeqiNP_055296.2. NM_014481.3.
UniGeneiHs.659558.

3D structure databases

ProteinModelPortaliQ9UBZ4.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi118124. 21 interactors.
IntActiQ9UBZ4. 13 interactors.
MINTiMINT-1439290.
STRINGi9606.ENSP00000364126.

PTM databases

iPTMnetiQ9UBZ4.
PhosphoSitePlusiQ9UBZ4.

Polymorphism and mutation databases

DMDMi73921676.

Proteomic databases

EPDiQ9UBZ4.
MaxQBiQ9UBZ4.
PaxDbiQ9UBZ4.
PeptideAtlasiQ9UBZ4.
PRIDEiQ9UBZ4.

Protocols and materials databases

DNASUi27301.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000374987; ENSP00000364126; ENSG00000169188.
GeneIDi27301.
KEGGihsa:27301.
UCSCiuc004dtz.5. human.

Organism-specific databases

CTDi27301.
DisGeNETi27301.
GeneCardsiAPEX2.
HGNCiHGNC:17889. APEX2.
HPAiHPA030872.
HPA048577.
MIMi300773. gene.
neXtProtiNX_Q9UBZ4.
OpenTargetsiENSG00000169188.
PharmGKBiPA38474.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG1294. Eukaryota.
COG0708. LUCA.
GeneTreeiENSGT00530000063540.
HOGENOMiHOG000231386.
HOVERGENiHBG054715.
InParanoidiQ9UBZ4.
KOiK10772.
OMAiAVNLECF.
OrthoDBiEOG091G0IPG.
PhylomeDBiQ9UBZ4.
TreeFamiTF328442.

Enzyme and pathway databases

BioCyciZFISH:HS09895-MONOMER.

Miscellaneous databases

ChiTaRSiAPEX2. human.
GenomeRNAii27301.
PROiQ9UBZ4.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000169188.
CleanExiHS_APEX2.
ExpressionAtlasiQ9UBZ4. baseline and differential.
GenevisibleiQ9UBZ4. HS.

Family and domain databases

Gene3Di3.60.10.10. 1 hit.
InterProiIPR004808. AP_endonuc_1.
IPR020847. AP_endonuclease_F1_BS.
IPR005135. Endo/exonuclease/phosphatase.
IPR010666. Znf_GRF.
[Graphical view]
PANTHERiPTHR22748. PTHR22748. 1 hit.
PfamiPF03372. Exo_endo_phos. 1 hit.
PF06839. zf-GRF. 1 hit.
[Graphical view]
SUPFAMiSSF56219. SSF56219. 1 hit.
TIGRFAMsiTIGR00633. xth. 1 hit.
PROSITEiPS00726. AP_NUCLEASE_F1_1. 1 hit.
PS51435. AP_NUCLEASE_F1_4. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiAPEX2_HUMAN
AccessioniPrimary (citable) accession number: Q9UBZ4
Secondary accession number(s): Q9Y5X7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 30, 2005
Last sequence update: May 1, 2000
Last modified: November 30, 2016
This is version 140 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

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Human chromosome X
    Human chromosome X: 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. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.