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A0MTA1

- APEX1_DANRE

UniProt

A0MTA1 - APEX1_DANRE

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Protein

DNA-(apurinic or apyrimidinic site) lyase

Gene

apex1

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.PROSITE-ProRule annotation

Cofactori

Mg2+By similarity, Mn2+By similarityNote: Probably binds two magnesium or manganese ions per subunit.By similarity

Sites

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

GO - Molecular functioni

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

GO - Biological processi

  1. base-excision repair Source: RefGenome
  2. DNA catabolic process, endonucleolytic Source: GOC
  3. DNA catabolic process, exonucleolytic Source: GOC
  4. DNA demethylation Source: UniProtKB
  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 PROSITE-ProRule annotation. Nucleusnucleolus By similarity. Nucleus speckle PROSITE-ProRule annotation. Endoplasmic reticulum By similarity. Cytoplasm PROSITE-ProRule annotation. Mitochondrion By similarity

GO - Cellular componenti

  1. endoplasmic reticulum Source: UniProtKB-KW
  2. mitochondrion Source: UniProtKB-KW
  3. 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) lyasePRO_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

1
310
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi55 – 617Combined sources
Helixi65 – 706Combined sources
Helixi73 – 808Combined sources
Beta strandi83 – 886Combined sources
Helixi94 – 963Combined sources
Helixi99 – 1024Combined sources
Beta strandi108 – 1136Combined sources
Beta strandi124 – 1307Combined sources
Beta strandi133 – 1386Combined sources
Turni142 – 1465Combined sources
Beta strandi150 – 1545Combined sources
Beta strandi159 – 1646Combined sources
Helixi170 – 1723Combined sources
Helixi175 – 19521Combined sources
Beta strandi198 – 2036Combined sources
Helixi210 – 2123Combined sources
Helixi216 – 2194Combined sources
Helixi227 – 23812Combined sources
Beta strandi241 – 2433Combined sources
Helixi244 – 2485Combined sources
Helixi262 – 2643Combined sources
Helixi265 – 2684Combined sources
Beta strandi275 – 2806Combined sources
Helixi281 – 2866Combined sources
Beta strandi287 – 2926Combined sources
Beta strandi298 – 3014Combined sources
Beta strandi304 – 3085Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2O3CX-ray2.30A/B/C33-310[»]
ProteinModelPortaliA0MTA1.
SMRiA0MTA1. Positions 33-310.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiA0MTA1.

Family & Domainsi

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiCOG0708.
HOGENOMiHOG000034586.
HOVERGENiHBG050531.
InParanoidiA0MTA1.
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

        10         20         30         40         50
MPKRAKKNEE GVDGEADNGT AAAKKEKKGK EPEAPILYED PPEKLTSKDG
60 70 80 90 100
RAANMKITSW NVDGLRAWVK KNGLDWVRKE DPDILCLQET KCAEKALPAD
110 120 130 140 150
ITGMPEYPHK YWAGSEDKEG YSGVAMLCKT EPLNVTYGIG KEEHDKEGRV
160 170 180 190 200
ITAEFPDFFL VTAYVPNASR GLVRLDYRKT WDVDFRAYLC GLDARKPLVL
210 220 230 240 250
CGDLNVAHQE IDLKNPKGNR KNAGFTPEER EGFTQLLEAG FTDSFRELYP
260 270 280 290 300
DQAYAYTFWT YMMNARSKNV GWRLDYFVLS SALLPGLCDS KIRNTAMGSD
310
HCPITLFLAV
Length:310
Mass (Da):34,881
Last modified:December 12, 2006 - v1
Checksum:iF57493D443106F4B
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti16 – 161A → S in CAI11781. (PubMed:23594743)Curated
Sequence conflicti80 – 9314Missing in AAI64240. 1 PublicationCuratedAdd
BLAST
Sequence conflicti80 – 9314Missing in AAH97053. 1 PublicationCuratedAdd
BLAST
Sequence conflicti103 – 1031G → A in AAH55545. 1 PublicationCurated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
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:
PDBei
RCSB PDBi
PDBji
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...
MobiDBi 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 A0MTA1.
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: November 26, 2014
This is version 61 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