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Q5E9N9 (APEX2_BOVIN) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 63. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (1) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended 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 names
Name:APEX2
OrganismBos taurus (Bovine) [Reference proteome]
Taxonomic identifier9913 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaLaurasiatheriaCetartiodactylaRuminantiaPecoraBovidaeBovinaeBos

Protein attributes

Sequence length514 AA.
Sequence statusComplete.
Protein existenceEvidence at transcript level

General annotation (Comments)

Function

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.

Catalytic activity

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.

Cofactor

Magnesium. Can also utilize manganese. Probably binds two magnesium or manganese ions per subunit By similarity.

Enzyme regulation

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.

Subunit structure

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

Subcellular location

Nucleus By similarity. Cytoplasm By similarity. Mitochondrion By similarity. Note: Together with PCNA, is redistributed in discrete nuclear foci in presence of oxidative DNA damaging agents By similarity.

Sequence similarities

Belongs to the DNA repair enzymes AP/ExoA family.

Sequence caution

The sequence AAX46554.1 differs from that shown. Reason: Frameshift at position 392.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 514514DNA-(apurinic or apyrimidinic site) lyase 2
PRO_0000200013

Regions

Region390 – 3978Required for the colocalization with PCNA in nuclear foci in presence of oxidative-induced DNA damaging agents By similarity

Sites

Active site1561 By similarity
Active site1971Proton donor/acceptor By similarity
Metal binding81Magnesium 1 By similarity
Metal binding481Magnesium 1 By similarity
Metal binding1971Magnesium 2 By similarity
Metal binding1991Magnesium 2 By similarity
Metal binding3031Magnesium 1 By similarity
Site1991Transition state stabilizer By similarity
Site2771Important for catalytic activity By similarity
Site3041Interaction with DNA substrate By similarity

Experimental info

Sequence conflict3691K → Q in AAX46554. Ref.1

Sequences

Sequence LengthMass (Da)Tools
Q5E9N9 [UniParc].

Last modified March 15, 2005. Version 1.
Checksum: D22E64035623C993

FASTA51456,938
        10         20         30         40         50         60 
MLRLVSWNIN GIRSPLQGVR CEEPSSCSAM AMGRILDKLD ADIVCLQETK VTRDVLTEPL 

        70         80         90        100        110        120 
AIIEGYNSYF SFSRNRSGYS GVATFCKDSA TPVAAEEGLS GLLSTQNGDV GCYGNMDDFT 

       130        140        150        160        170        180 
QEELRALDSE GRALLTQHKI CTWEGKEKTL TLINVYCPHA DPGKPERLTF KMRFYRLLQI 

       190        200        210        220        230        240 
RAEALLAAGS HVIILGDLNT AHRPIDHWDA VNMECFEEDP GRKWMDGLLS NLGCESGSHM 

       250        260        270        280        290        300 
GPFIDSYRCF QPKQKGAFTC WSTVSGARHL NYGSRLDYVL GDRTLVIDTF QSSFLLPEVM 

       310        320        330        340        350        360 
GSDHCPVGAV LSVSSVPAKQ CPPLCTCFLP EFAGTQLKIL RFLVHFKQDP VFKQSALQPS 

       370        380        390        400        410        420 
NQTQVHMRKN KARVRSTRSR PSKTGSSRGQ KNLMSYFQPS SSGPQTSNLD LPSLGTLITP 

       430        440        450        460        470        480 
KTSEEDVMAN VVEGQTKASE AKDEKEIRTS FWKSLLGGPS PMPLCGGHRE PCVMRTVKKP 

       490        500        510 
GPNLGRHFYM CARPQGPPTD PSSRCNFFLW SRPS 

« Hide

References

[1]"Characterization of 954 bovine full-CDS cDNA sequences."
Harhay G.P., Sonstegard T.S., Keele J.W., Heaton M.P., Clawson M.L., Snelling W.M., Wiedmann R.T., Van Tassell C.P., Smith T.P.L.
BMC Genomics 6:166-166(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
BT020881 mRNA. Translation: AAX08898.1.
BT021707 mRNA. Translation: AAX46554.1. Frameshift.
RefSeqNP_001015577.1. NM_001015577.1.
UniGeneBt.1184.

3D structure databases

ProteinModelPortalQ5E9N9.
ModBaseSearch...
MobiDBSearch...

Proteomic databases

PRIDEQ5E9N9.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

GeneID511790.
KEGGbta:511790.

Organism-specific databases

CTD27301.

Phylogenomic databases

eggNOGCOG0708.
HOGENOMHOG000231386.
HOVERGENHBG054715.
InParanoidQ5E9N9.
KOK10772.

Family and domain databases

Gene3D3.60.10.10. 1 hit.
InterProIPR004808. AP_endonuc_1.
IPR020847. AP_endonuclease_F1_BS.
IPR005135. Endo/exonuclease/phosphatase.
IPR010666. Znf_GRF.
[Graphical view]
PANTHERPTHR22748. PTHR22748. 1 hit.
PfamPF03372. Exo_endo_phos. 1 hit.
PF06839. zf-GRF. 1 hit.
[Graphical view]
SUPFAMSSF56219. SSF56219. 1 hit.
TIGRFAMsTIGR00633. xth. 1 hit.
PROSITEPS00726. AP_NUCLEASE_F1_1. 1 hit.
PS51435. AP_NUCLEASE_F1_4. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

NextBio20870098.

Entry information

Entry nameAPEX2_BOVIN
AccessionPrimary (citable) accession number: Q5E9N9
Secondary accession number(s): Q58D90
Entry history
Integrated into UniProtKB/Swiss-Prot: August 30, 2005
Last sequence update: March 15, 2005
Last modified: April 16, 2014
This is version 63 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families