DNA-(apurinic or apyrimidinic site) lyase 2

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Q5E9N9 (APEX2_BOVIN) Reviewed, UniProtKB/Swiss-Prot

Last modified May 29, 2013. Version 57. History...

Clusters with 100%, 90%, 50% identity |

Documents (1) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

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 names

Name:

APEX2

Organism

Bos taurus (Bovine) [Reference proteome]

Taxonomic identifier

9913 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Laurasiatheria › Cetartiodactyla › Ruminantia › Pecora › Bovidae › Bovinae › Bos

Protein attributes

Sequence length	514 AA.
Sequence status	Complete.
Protein existence	Evidence 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.

Ontologies

Keywords
Biological process	Cell cycle DNA damage DNA recombination DNA repair
Cellular component	Cytoplasm Mitochondrion Nucleus
Ligand	DNA-binding Magnesium Metal-binding
Molecular function	Endonuclease Exonuclease Hydrolase Lyase Nuclease
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	DNA recombination Inferred from electronic annotation. Source: UniProtKB-KW DNA repair Inferred from electronic annotation. Source: UniProtKB-KW cell cycle Inferred from electronic annotation. Source: UniProtKB-KW nucleic acid phosphodiester bond hydrolysis Inferred from electronic annotation. Source: GOC
Cellular_component	mitochondrion Inferred from electronic annotation. Source: UniProtKB-SubCell nucleus Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	DNA binding Inferred from electronic annotation. Source: UniProtKB-KW DNA-(apurinic or apyrimidinic site) lyase activity Inferred from electronic annotation. Source: EC endonuclease activity Inferred from electronic annotation. Source: UniProtKB-KW exonuclease activity Inferred from electronic annotation. Source: UniProtKB-KW zinc ion binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 514

514

DNA-(apurinic or apyrimidinic site) lyase 2

PRO_0000200013

Regions

Region

390 – 397

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

Sites

Active site

156

By similarity

Active site

197

Proton donor/acceptor By similarity

Metal binding

Magnesium 1 By similarity

Metal binding

Magnesium 1 By similarity

Metal binding

197

Magnesium 2 By similarity

Metal binding

199

Magnesium 2 By similarity

Metal binding

303

Magnesium 1 By similarity

Site

199

Transition state stabilizer By similarity

Site

277

Important for catalytic activity By similarity

Site

304

Interaction with DNA substrate By similarity

Experimental info

Sequence conflict

369

K → Q in AAX46554. Ref.1

Sequences

Sequence

Length

Mass (Da)

Tools

Q5E9N9 [UniParc].

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

FASTA

514

56,938

        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

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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.
IPI	IPI00696158.
RefSeq	NP_001015577.1. NM_001015577.1.
UniGene	Bt.1184.
3D structure databases
ProteinModelPortal	Q5E9N9.
ModBase	Search...
Proteomic databases
PRIDE	Q5E9N9.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
GeneID	511790.
KEGG	bta:511790.
Organism-specific databases
CTD	27301.
Phylogenomic databases
eggNOG	COG0708.
HOGENOM	HOG000231386.
HOVERGEN	HBG054715.
InParanoid	Q5E9N9.
KO	K10772.
OrthoDB	EOG4NS3BQ.
Enzyme and pathway databases
BioCyc	CATTLE:511790-MONOMER.
Family and domain databases
Gene3D	3.60.10.10. 1 hit.
InterPro	IPR020847. AP_endonuclease_F1_BS. IPR005135. Endo/exonuclease/phosphatase. IPR004808. ExoDNase_III. IPR010666. Znf_GRF. [Graphical view]
PANTHER	PTHR22748. PTHR22748. 1 hit.
Pfam	PF03372. Exo_endo_phos. 1 hit. PF06839. zf-GRF. 1 hit. [Graphical view]
SUPFAM	SSF56219. Exo_endo_phos. 1 hit.
TIGRFAMs	TIGR00633. xth. 1 hit.
PROSITE	PS00726. AP_NUCLEASE_F1_1. 1 hit. PS00727. AP_NUCLEASE_F1_2. False negative. PS00728. AP_NUCLEASE_F1_3. False negative. PS51435. AP_NUCLEASE_F1_4. 1 hit. [Graphical view]
ProtoNet	Search...
Other
NextBio	20870098.

Entry information

Entry name

APEX2_BOVIN

Accession

Primary (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:	May 29, 2013
This is version 57 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Regions

Sites

Experimental info

Sequences

References

Cross-references

Sequence databases

3D structure databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Family and domain databases

Other

Entry information

Relevant documents