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Protein

DNA-(apurinic or apyrimidinic site) lyase 2

Gene

APEX2

Organism
Bos taurus (Bovine)
Status
Reviewed-Annotation score: -Experimental evidence at transcript 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 (By similarity).By similarity

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 (By similarity).By similarity

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

Keywordsi

Molecular functionDNA-binding, Endonuclease, Exonuclease, Hydrolase, Lyase, Nuclease
Biological processCell cycle, DNA damage, DNA recombination, DNA repair
LigandMagnesium, Metal-binding

Names & Taxonomyi

Protein namesi
Recommended name:
DNA-(apurinic or apyrimidinic site) lyase 2 (EC:3.1.-.-, EC:4.2.99.18)
Alternative name(s):
APEX nuclease 2
Apurinic-apyrimidinic endonuclease 2
Short name:
AP endonuclease 2
Gene namesi
Name:APEX2
OrganismiBos taurus (Bovine)
Taxonomic identifieri9913 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaLaurasiatheriaCetartiodactylaRuminantiaPecoraBovidaeBovinaeBos
Proteomesi

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, Mitochondrion, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002000131 – 514DNA-(apurinic or apyrimidinic site) lyase 2Add BLAST514

Proteomic databases

PaxDbiQ5E9N9
PRIDEiQ5E9N9

Interactioni

Subunit structurei

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

Sites

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

Protein-protein interaction databases

STRINGi9913.ENSBTAP00000017537

Structurei

3D structure databases

ProteinModelPortaliQ5E9N9
SMRiQ5E9N9
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 agentsBy similarity8

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiKOG1294 Eukaryota
COG0708 LUCA
HOGENOMiHOG000231386
HOVERGENiHBG054715
InParanoidiQ5E9N9
KOiK10772

Family and domain databases

Gene3Di3.60.10.10, 1 hit
InterProiView protein in InterPro
IPR004808 AP_endonuc_1
IPR020847 AP_endonuclease_F1_BS
IPR036691 Endo/exonu/phosph_ase_sf
IPR005135 Endo/exonuclease/phosphatase
IPR010666 Znf_GRF
PANTHERiPTHR22748 PTHR22748, 1 hit
PfamiView protein in Pfam
PF03372 Exo_endo_phos, 1 hit
PF06839 zf-GRF, 1 hit
SUPFAMiSSF56219 SSF56219, 1 hit
TIGRFAMsiTIGR00633 xth, 1 hit
PROSITEiView protein in PROSITE
PS00726 AP_NUCLEASE_F1_1, 1 hit
PS51435 AP_NUCLEASE_F1_4, 1 hit

Sequencei

Sequence statusi: Complete.

Q5E9N9-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MLRLVSWNIN GIRSPLQGVR CEEPSSCSAM AMGRILDKLD ADIVCLQETK
60 70 80 90 100
VTRDVLTEPL AIIEGYNSYF SFSRNRSGYS GVATFCKDSA TPVAAEEGLS
110 120 130 140 150
GLLSTQNGDV GCYGNMDDFT QEELRALDSE GRALLTQHKI CTWEGKEKTL
160 170 180 190 200
TLINVYCPHA DPGKPERLTF KMRFYRLLQI RAEALLAAGS HVIILGDLNT
210 220 230 240 250
AHRPIDHWDA VNMECFEEDP GRKWMDGLLS NLGCESGSHM GPFIDSYRCF
260 270 280 290 300
QPKQKGAFTC WSTVSGARHL NYGSRLDYVL GDRTLVIDTF QSSFLLPEVM
310 320 330 340 350
GSDHCPVGAV LSVSSVPAKQ CPPLCTCFLP EFAGTQLKIL RFLVHFKQDP
360 370 380 390 400
VFKQSALQPS NQTQVHMRKN KARVRSTRSR PSKTGSSRGQ KNLMSYFQPS
410 420 430 440 450
SSGPQTSNLD LPSLGTLITP KTSEEDVMAN VVEGQTKASE AKDEKEIRTS
460 470 480 490 500
FWKSLLGGPS PMPLCGGHRE PCVMRTVKKP GPNLGRHFYM CARPQGPPTD
510
PSSRCNFFLW SRPS
Length:514
Mass (Da):56,938
Last modified:March 15, 2005 - v1
Checksum:iD22E64035623C993
GO

Sequence cautioni

The sequence AAX46554 differs from that shown. Reason: Frameshift at position 392.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti369K → Q in AAX46554 (PubMed:16305752).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BT020881 mRNA Translation: AAX08898.1
BT021707 mRNA Translation: AAX46554.1 Frameshift.
RefSeqiNP_001015577.1, NM_001015577.1
UniGeneiBt.1184

Genome annotation databases

GeneIDi511790
KEGGibta:511790

Similar proteinsi

Entry informationi

Entry nameiAPEX2_BOVIN
AccessioniPrimary (citable) accession number: Q5E9N9
Secondary accession number(s): Q58D90
Entry historyiIntegrated into UniProtKB/Swiss-Prot: August 30, 2005
Last sequence update: March 15, 2005
Last modified: May 23, 2018
This is version 75 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families

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