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A0MTA1

- APEX1_DANRE

UniProt

A0MTA1 - APEX1_DANRE

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Protein
DNA-(apurinic or apyrimidinic site) lyase
Gene
apex1, apex1a, apex1b, si:ch211-214j24.12, zgc:66204
Organism
Danio rerio (Zebrafish) (Brachydanio rerio)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

Functioni

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.2 Publications

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.

Cofactori

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

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi63 – 631Magnesium 1 By similarity
Metal bindingi89 – 891Magnesium 1 By similarity
Active sitei164 – 1641 By similarity
Active sitei203 – 2031Proton donor/acceptor By similarity
Metal bindingi203 – 2031Magnesium 2 By similarity
Metal bindingi205 – 2051Magnesium 2 By similarity
Sitei205 – 2051Transition state stabilizer By similarity
Sitei275 – 2751Important for catalytic activity By similarity
Metal bindingi300 – 3001Magnesium 1 By similarity
Sitei301 – 3011Interaction with DNA substrate By similarity

GO - Molecular functioni

  1. DNA binding Source: UniProtKB-KW
  2. DNA-(apurinic or apyrimidinic site) lyase activity Source: RefGenome
  3. RNA binding Source: UniProtKB-KW
  4. double-stranded DNA 3'-5' exodeoxyribonuclease activity Source: RefGenome
  5. metal ion binding Source: UniProtKB-KW
Complete GO annotation...

GO - Biological processi

  1. DNA catabolic process, endonucleolytic Source: GOC
  2. DNA catabolic process, exonucleolytic Source: GOC
  3. DNA demethylation Source: UniProtKB
  4. base-excision repair Source: RefGenome
  5. heart contraction Source: ZFIN
  6. heart looping Source: ZFIN
  7. negative regulation of apoptotic process Source: ZFIN
  8. positive regulation of gene expression Source: ZFIN
Complete GO annotation...

Keywords - Molecular functioni

Endonuclease, Hydrolase, Lyase, Nuclease

Keywords - Biological processi

DNA damage, DNA repair

Keywords - Ligandi

DNA-binding, Magnesium, Metal-binding, RNA-binding

Names & Taxonomyi

Protein namesi
Recommended 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 namesi
Name:apex1
Synonyms:apex1a, apex1b
ORF Names:si:ch211-214j24.12, zgc:66204
OrganismiDanio rerio (Zebrafish) (Brachydanio rerio)
Taxonomic identifieri7955 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiActinopterygiiNeopterygiiTeleosteiOstariophysiCypriniformesCyprinidaeDanio
ProteomesiUP000000437: Unplaced

Organism-specific databases

ZFINiZDB-GENE-040426-2761. apex1.

Subcellular locationi

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

GO - Cellular componenti

  1. endoplasmic reticulum Source: UniProtKB-SubCell
  2. mitochondrion Source: UniProtKB-SubCell
  3. nuclear speck Source: UniProtKB-SubCell
  4. nucleolus Source: UniProtKB-SubCell
  5. nucleus Source: RefGenome
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Endoplasmic reticulum, Mitochondrion, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi58 – 581T → C: Confers redox activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 310310DNA-(apurinic or apyrimidinic site) lyase
PRO_0000402575Add
BLAST

Proteomic databases

PRIDEiA0MTA1.

Expressioni

Developmental stagei

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

Gene expression databases

BgeeiA0MTA1.

Interactioni

Protein-protein interaction databases

STRINGi7955.ENSDARP00000067373.

Structurei

Secondary structure

Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi55 – 617
Helixi65 – 706
Helixi73 – 808
Beta strandi83 – 886
Helixi94 – 963
Helixi99 – 1024
Beta strandi108 – 1136
Beta strandi124 – 1307
Beta strandi133 – 1386
Turni142 – 1465
Beta strandi150 – 1545
Beta strandi159 – 1646
Helixi170 – 1723
Helixi175 – 19521
Beta strandi198 – 2036
Helixi210 – 2123
Helixi216 – 2194
Helixi227 – 23812
Beta strandi241 – 2433
Helixi244 – 2485
Helixi262 – 2643
Helixi265 – 2684
Beta strandi275 – 2806
Helixi281 – 2866
Beta strandi287 – 2926
Beta strandi298 – 3014
Beta strandi304 – 3085

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2O3CX-ray2.30A/B/C33-310[»]
ProteinModelPortaliA0MTA1.
SMRiA0MTA1. Positions 33-310.

Miscellaneous databases

EvolutionaryTraceiA0MTA1.

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0708.
HOGENOMiHOG000034586.
HOVERGENiHBG050531.
InParanoidiQ7SXL6.
KOiK10771.
PhylomeDBiA0MTA1.
TreeFamiTF315048.

Family and domain databases

Gene3Di3.60.10.10. 1 hit.
InterProiIPR004808. AP_endonuc_1.
IPR020847. AP_endonuclease_F1_BS.
IPR020848. AP_endonuclease_F1_CS.
IPR005135. Endo/exonuclease/phosphatase.
[Graphical view]
PANTHERiPTHR22748. PTHR22748. 1 hit.
PfamiPF03372. Exo_endo_phos. 1 hit.
[Graphical view]
SUPFAMiSSF56219. SSF56219. 1 hit.
TIGRFAMsiTIGR00633. xth. 1 hit.
PROSITEiPS00726. AP_NUCLEASE_F1_1. 1 hit.
PS00728. AP_NUCLEASE_F1_3. 1 hit.
PS51435. AP_NUCLEASE_F1_4. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

A0MTA1-1 [UniParc]FASTAAdd to Basket

« Hide

MPKRAKKNEE GVDGEADNGT AAAKKEKKGK EPEAPILYED PPEKLTSKDG    50
RAANMKITSW NVDGLRAWVK KNGLDWVRKE DPDILCLQET KCAEKALPAD 100
ITGMPEYPHK YWAGSEDKEG YSGVAMLCKT EPLNVTYGIG KEEHDKEGRV 150
ITAEFPDFFL VTAYVPNASR GLVRLDYRKT WDVDFRAYLC GLDARKPLVL 200
CGDLNVAHQE IDLKNPKGNR KNAGFTPEER EGFTQLLEAG FTDSFRELYP 250
DQAYAYTFWT YMMNARSKNV GWRLDYFVLS SALLPGLCDS KIRNTAMGSD 300
HCPITLFLAV 310
Length:310
Mass (Da):34,881
Last modified:December 12, 2006 - v1
Checksum:iF57493D443106F4B
GO

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti16 – 161A → S in CAI11781. 1 Publication
Sequence conflicti80 – 9314Missing in AAI64240. 1 Publication
Add
BLAST
Sequence conflicti80 – 9314Missing in AAH97053. 1 Publication
Add
BLAST
Sequence conflicti103 – 1031G → A in AAH55545. 1 Publication

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
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.
RefSeqiNP_998586.1. NM_213421.1.
UniGeneiDr.20170.

Genome annotation databases

GeneIDi406730.
KEGGidre:406730.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
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 .
RefSeqi NP_998586.1. NM_213421.1.
UniGenei Dr.20170.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
2O3C X-ray 2.30 A/B/C 33-310 [» ]
ProteinModelPortali A0MTA1.
SMRi A0MTA1. Positions 33-310.
ModBasei Search...

Protein-protein interaction databases

STRINGi 7955.ENSDARP00000067373.

Proteomic databases

PRIDEi A0MTA1.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

GeneIDi 406730.
KEGGi dre:406730.

Organism-specific databases

CTDi 328.
ZFINi ZDB-GENE-040426-2761. apex1.

Phylogenomic databases

eggNOGi COG0708.
HOGENOMi HOG000034586.
HOVERGENi HBG050531.
InParanoidi Q7SXL6.
KOi K10771.
PhylomeDBi A0MTA1.
TreeFami TF315048.

Miscellaneous databases

EvolutionaryTracei A0MTA1.
NextBioi 20818249.
PROi A0MTA1.

Gene expression databases

Bgeei A0MTA1.

Family and domain databases

Gene3Di 3.60.10.10. 1 hit.
InterProi IPR004808. AP_endonuc_1.
IPR020847. AP_endonuclease_F1_BS.
IPR020848. AP_endonuclease_F1_CS.
IPR005135. Endo/exonuclease/phosphatase.
[Graphical view ]
PANTHERi PTHR22748. PTHR22748. 1 hit.
Pfami PF03372. Exo_endo_phos. 1 hit.
[Graphical view ]
SUPFAMi SSF56219. SSF56219. 1 hit.
TIGRFAMsi TIGR00633. xth. 1 hit.
PROSITEi PS00726. AP_NUCLEASE_F1_1. 1 hit.
PS00728. AP_NUCLEASE_F1_3. 1 hit.
PS51435. AP_NUCLEASE_F1_4. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  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.
    , 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.

Entry informationi

Entry nameiAPEX1_DANRE
AccessioniPrimary (citable) accession number: A0MTA1
Secondary accession number(s): Q4V955, Q5RHZ7, Q7SXL6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 11, 2011
Last sequence update: December 12, 2006
Last modified: September 3, 2014
This is version 58 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

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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