Skip Header

You are using a version of Internet Explorer that may not display all features of this website. Please upgrade to a modern browser.
Contribute Send feedback
Read comments (?) or add your own

A0MTA1 (APEX1_DANRE) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 57. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | 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

EC=3.1.-.-
EC=4.2.99.18
Alternative name(s):
APEX nuclease
Short name=APEN
Apurinic-apyrimidinic endonuclease 1
Short name=AP endonuclease 1
Short name=zAP1
Gene names
Name:apex1
Synonyms:apex1a, apex1b
ORF Names:si:ch211-214j24.12, zgc:66204
OrganismDanio rerio (Zebrafish) (Brachydanio rerio) [Reference proteome]
Taxonomic identifier7955 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiActinopterygiiNeopterygiiTeleosteiOstariophysiCypriniformesCyprinidaeDanio

Protein attributes

Sequence length310 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Function as a 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. May also play a role in the epigenetic regulation of gene expression by participating in DNA demethylation. Required for passage through the midblastula transition MBT. May also acts as a endoribonuclease involved in the control of single-stranded RNA metabolism. Has no redox activity. Binds DNA and RNA. Ref.1 Ref.4

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.

Subcellular location

Nucleus By similarity. Nucleusnucleolus By similarity. Nucleus speckle By similarity. Endoplasmic reticulum By similarity. Cytoplasm By similarity. Mitochondrion By similarity.

Developmental stage

Expressed in unfertilized eggs and embryos at two stages (at protein level). Expressed throughout embryogenesis. Ref.1

Sequence similarities

Belongs to the DNA repair enzymes AP/ExoA family.

Ontologies

Keywords
   Biological processDNA damage
DNA repair
   Cellular componentCytoplasm
Endoplasmic reticulum
Mitochondrion
Nucleus
   LigandDNA-binding
Magnesium
Metal-binding
RNA-binding
   Molecular functionEndonuclease
Hydrolase
Lyase
Nuclease
   Technical term3D-structure
Complete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processDNA demethylation

Inferred from sequence or structural similarity. Source: UniProtKB

DNA repair

Inferred from electronic annotation. Source: UniProtKB-KW

heart contraction

Inferred from mutant phenotype Ref.1. Source: ZFIN

heart looping

Inferred from mutant phenotype Ref.1. Source: ZFIN

negative regulation of apoptotic process

Inferred from mutant phenotype Ref.1. Source: ZFIN

positive regulation of gene expression

Inferred from mutant phenotype PubMed 21172930. Source: ZFIN

   Cellular_componentendoplasmic reticulum

Inferred from electronic annotation. Source: UniProtKB-SubCell

mitochondrion

Inferred from electronic annotation. Source: UniProtKB-SubCell

nuclear speck

Inferred from electronic annotation. Source: UniProtKB-SubCell

nucleolus

Inferred from electronic annotation. Source: UniProtKB-SubCell

   Molecular_functionDNA binding

Inferred from electronic annotation. Source: UniProtKB-KW

DNA-(apurinic or apyrimidinic site) lyase activity

Inferred from electronic annotation. Source: UniProtKB-EC

RNA binding

Inferred from electronic annotation. Source: UniProtKB-KW

metal ion binding

Inferred from electronic annotation. Source: UniProtKB-KW

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 310310DNA-(apurinic or apyrimidinic site) lyase
PRO_0000402575

Sites

Active site1641 By similarity
Active site2031Proton donor/acceptor By similarity
Metal binding631Magnesium 1 By similarity
Metal binding891Magnesium 1 By similarity
Metal binding2031Magnesium 2 By similarity
Metal binding2051Magnesium 2 By similarity
Metal binding3001Magnesium 1 By similarity
Site2051Transition state stabilizer By similarity
Site2751Important for catalytic activity By similarity
Site3011Interaction with DNA substrate By similarity

Experimental info

Mutagenesis581T → C: Confers redox activity. Ref.4
Sequence conflict161A → S in CAI11781. Ref.2
Sequence conflict80 – 9314Missing in AAI64240. Ref.3
Sequence conflict80 – 9314Missing in AAH97053. Ref.3
Sequence conflict1031G → A in AAH55545. Ref.3

Secondary structure

................................................... 310
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
A0MTA1 [UniParc].

Last modified December 12, 2006. Version 1.
Checksum: F57493D443106F4B

FASTA31034,881
        10         20         30         40         50         60 
MPKRAKKNEE GVDGEADNGT AAAKKEKKGK EPEAPILYED PPEKLTSKDG RAANMKITSW 

        70         80         90        100        110        120 
NVDGLRAWVK KNGLDWVRKE DPDILCLQET KCAEKALPAD ITGMPEYPHK YWAGSEDKEG 

       130        140        150        160        170        180 
YSGVAMLCKT EPLNVTYGIG KEEHDKEGRV ITAEFPDFFL VTAYVPNASR GLVRLDYRKT 

       190        200        210        220        230        240 
WDVDFRAYLC GLDARKPLVL CGDLNVAHQE IDLKNPKGNR KNAGFTPEER EGFTQLLEAG 

       250        260        270        280        290        300 
FTDSFRELYP DQAYAYTFWT YMMNARSKNV GWRLDYFVLS SALLPGLCDS KIRNTAMGSD 

       310 
HCPITLFLAV 

« Hide

References

« Hide 'large scale' references
[1]"DNA repair protein involved in heart and blood development."
Wang Y., Shupenko C.C., Melo L.F., Strauss P.R.
Mol. Cell. Biol. 26:9083-9093(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA], FUNCTION, DEVELOPMENTAL STAGE.
Tissue: Embryo.
[2]"The zebrafish reference genome sequence and its relationship to the human genome."
Howe K., Clark M.D., Torroja C.F., Torrance J., Berthelot C., Muffato M., Collins J.E., Humphray S., McLaren K., Matthews L., McLaren S., Sealy I., Caccamo M., Churcher C., Scott C., Barrett J.C., Koch R., Rauch G.J. expand/collapse author list , White S., Chow W., Kilian B., Quintais L.T., Guerra-Assuncao J.A., Zhou Y., Gu Y., Yen J., Vogel J.H., Eyre T., Redmond S., Banerjee R., Chi J., Fu B., Langley E., Maguire S.F., Laird G.K., Lloyd D., Kenyon E., Donaldson S., Sehra H., Almeida-King J., Loveland J., Trevanion S., Jones M., Quail M., Willey D., Hunt A., Burton J., Sims S., McLay K., Plumb B., Davis J., Clee C., Oliver K., Clark R., Riddle C., Eliott D., Threadgold G., Harden G., Ware D., Mortimer B., Kerry G., Heath P., Phillimore B., Tracey A., Corby N., Dunn M., Johnson C., Wood J., Clark S., Pelan S., Griffiths G., Smith M., Glithero R., Howden P., Barker N., Stevens C., Harley J., Holt K., Panagiotidis G., Lovell J., Beasley H., Henderson C., Gordon D., Auger K., Wright D., Collins J., Raisen C., Dyer L., Leung K., Robertson L., Ambridge K., Leongamornlert D., McGuire S., Gilderthorp R., Griffiths C., Manthravadi D., Nichol S., Barker G., Whitehead S., Kay M., Brown J., Murnane C., Gray E., Humphries M., Sycamore N., Barker D., Saunders D., Wallis J., Babbage A., Hammond S., Mashreghi-Mohammadi M., Barr L., Martin S., Wray P., Ellington A., Matthews N., Ellwood M., Woodmansey R., Clark G., Cooper J., Tromans A., Grafham D., Skuce C., Pandian R., Andrews R., Harrison E., Kimberley A., Garnett J., Fosker N., Hall R., Garner P., Kelly D., Bird C., Palmer S., Gehring I., Berger A., Dooley C.M., Ersan-Urun Z., Eser C., Geiger H., Geisler M., Karotki L., Kirn A., Konantz J., Konantz M., Oberlander M., Rudolph-Geiger S., Teucke M., Osoegawa K., Zhu B., Rapp A., Widaa S., Langford C., Yang F., Carter N.P., Harrow J., Ning Z., Herrero J., Searle S.M., Enright A., Geisler R., Plasterk R.H., Lee C., Westerfield M., de Jong P.J., Zon L.I., Postlethwait J.H., Nusslein-Volhard C., Hubbard T.J., Roest Crollius H., Rogers J., Stemple D.L.
Nature 496:498-503(2013) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: Tuebingen.
[3]NIH - Zebrafish Gene Collection (ZGC) project
Submitted (AUG-2003) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
Tissue: Olfactory epithelium.
[4]"Evolution of the redox function in mammalian apurinic/apyrimidinic endonuclease."
Georgiadis M.M., Luo M., Gaur R.K., Delaplane S., Li X., Kelley M.R.
Mutat. Res. 643:54-63(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF 33-310, FUNCTION, MUTAGENESIS OF THR-58.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
EF041101 mRNA. Translation: ABK35081.1.
EF041102 mRNA. Translation: ABK35082.1.
EF041103 Genomic DNA. Translation: ABK35083.1.
EF041104 Genomic DNA. Translation: ABK35084.1.
BX323558 Genomic DNA. Translation: CAI11781.1.
BC055545 mRNA. Translation: AAH55545.1.
BC097053 mRNA. Translation: AAH97053.1.
BC164240 mRNA. Translation: AAI64240.1.
RefSeqNP_998586.1. NM_213421.1.
UniGeneDr.20170.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2O3CX-ray2.30A/B/C33-310[»]
ProteinModelPortalA0MTA1.
SMRA0MTA1. Positions 33-310.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING7955.ENSDARP00000067373.

Proteomic databases

PRIDEA0MTA1.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

GeneID406730.
KEGGdre:406730.

Organism-specific databases

CTD328.
ZFINZDB-GENE-040426-2761. apex1.

Phylogenomic databases

eggNOGCOG0708.
HOGENOMHOG000034586.
HOVERGENHBG050531.
InParanoidQ7SXL6.
KOK10771.
PhylomeDBA0MTA1.
TreeFamTF315048.

Gene expression databases

BgeeA0MTA1.

Family and domain databases

Gene3D3.60.10.10. 1 hit.
InterProIPR004808. AP_endonuc_1.
IPR020847. AP_endonuclease_F1_BS.
IPR020848. AP_endonuclease_F1_CS.
IPR005135. Endo/exonuclease/phosphatase.
[Graphical view]
PANTHERPTHR22748. PTHR22748. 1 hit.
PfamPF03372. Exo_endo_phos. 1 hit.
[Graphical view]
SUPFAMSSF56219. SSF56219. 1 hit.
TIGRFAMsTIGR00633. xth. 1 hit.
PROSITEPS00726. AP_NUCLEASE_F1_1. 1 hit.
PS00728. AP_NUCLEASE_F1_3. 1 hit.
PS51435. AP_NUCLEASE_F1_4. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceA0MTA1.
NextBio20818249.
PROA0MTA1.

Entry information

Entry nameAPEX1_DANRE
AccessionPrimary (citable) accession number: A0MTA1
Secondary accession number(s): Q4V955, Q5RHZ7, Q7SXL6
Entry history
Integrated into UniProtKB/Swiss-Prot: January 11, 2011
Last sequence update: December 12, 2006
Last modified: April 16, 2014
This is version 57 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

PDB cross-references

Index of Protein Data Bank (PDB) cross-references