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Protein

DNA-(apurinic or apyrimidinic site) lyase 2

Gene

APEX2

Organism
Bos taurus (Bovine)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-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)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi8 – 81Magnesium 1By similarity
Metal bindingi48 – 481Magnesium 1By similarity
Active sitei156 – 1561By similarity
Active sitei197 – 1971Proton donor/acceptorBy similarity
Metal bindingi197 – 1971Magnesium 2By similarity
Metal bindingi199 – 1991Magnesium 2By similarity
Sitei199 – 1991Transition state stabilizerBy similarity
Sitei277 – 2771Important for catalytic activityBy similarity
Metal bindingi303 – 3031Magnesium 1By similarity
Sitei304 – 3041Interaction with DNA substrateBy similarity

GO - Molecular functioni

  1. DNA-(apurinic or apyrimidinic site) lyase activity Source: UniProtKB-EC
  2. DNA binding Source: UniProtKB-KW
  3. exonuclease activity Source: UniProtKB-KW
  4. zinc ion binding Source: InterPro

GO - Biological processi

  1. cell cycle Source: UniProtKB-KW
  2. DNA recombination Source: UniProtKB-KW
  3. DNA repair Source: UniProtKB-KW
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

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
ProteomesiUP000009136: Unplaced

Subcellular locationi

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

GO - Cellular componenti

  1. mitochondrion Source: UniProtKB-SubCell
  2. nucleus Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Mitochondrion, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 514514DNA-(apurinic or apyrimidinic site) lyase 2PRO_0000200013Add
BLAST

Proteomic databases

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

Structurei

3D structure databases

ProteinModelPortaliQ5E9N9.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni390 – 3978Required for the colocalization with PCNA in nuclear foci in presence of oxidative-induced DNA damaging agentsBy similarity

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiCOG0708.
HOGENOMiHOG000231386.
HOVERGENiHBG054715.
InParanoidiQ5E9N9.
KOiK10772.

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.

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

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti369 – 3691K → Q in AAX46554 (PubMed:16305752).Curated

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.

Cross-referencesi

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.

3D structure databases

ProteinModelPortaliQ5E9N9.
ModBaseiSearch...
MobiDBiSearch...

Proteomic databases

PRIDEiQ5E9N9.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi511790.
KEGGibta:511790.

Organism-specific databases

CTDi27301.

Phylogenomic databases

eggNOGiCOG0708.
HOGENOMiHOG000231386.
HOVERGENiHBG054715.
InParanoidiQ5E9N9.
KOiK10772.

Miscellaneous databases

NextBioi20870098.

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...

Publicationsi

  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].

Entry informationi

Entry nameiAPEX2_BOVIN
AccessioniPrimary (citable) accession number: Q5E9N9
Secondary accession number(s): Q58D90
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 30, 2005
Last sequence update: March 15, 2005
Last modified: January 7, 2015
This is version 67 of the entry and version 1 of the sequence. [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

External Data

Dasty 3

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 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.