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Protein

DNA-(apurinic or apyrimidinic site) lyase

Gene

apex1

Organism
Danio rerio (Zebrafish) (Brachydanio rerio)
Status
Reviewed-Annotation score: 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 act as an 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)DescriptionActionsGraphical viewLength
Metal bindingi63Magnesium 1By similarity1
Metal bindingi89Magnesium 1By similarity1
Active sitei164By similarity1
Active sitei203Proton donor/acceptorBy similarity1
Metal bindingi203Magnesium 2By similarity1
Metal bindingi205Magnesium 2By similarity1
Sitei205Transition state stabilizerBy similarity1
Sitei275Important for catalytic activityBy similarity1
Metal bindingi300Magnesium 1By similarity1

GO - Molecular functioni

GO - Biological processi

  • base-excision repair Source: GO_Central
  • DNA demethylation Source: UniProtKB
  • heart contraction Source: ZFIN
  • heart looping Source: ZFIN
  • negative regulation of apoptotic process Source: ZFIN
  • 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
Proteomesi
  • UP000000437 Componenti: 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

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Endoplasmic reticulum, Mitochondrion, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi58T → C: Confers redox activity. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00004025751 – 310DNA-(apurinic or apyrimidinic site) lyaseAdd BLAST310

Proteomic databases

PaxDbiA0MTA1.
PeptideAtlasiA0MTA1.
PRIDEiA0MTA1.

Expressioni

Developmental stagei

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

Interactioni

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei301Interaction with DNA substrateBy similarity1

Protein-protein interaction databases

STRINGi7955.ENSDARP00000067373.

Structurei

Secondary structure

1310
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi55 – 61Combined sources7
Helixi65 – 70Combined sources6
Helixi73 – 80Combined sources8
Beta strandi83 – 88Combined sources6
Helixi94 – 96Combined sources3
Helixi99 – 102Combined sources4
Beta strandi108 – 113Combined sources6
Beta strandi124 – 130Combined sources7
Beta strandi133 – 138Combined sources6
Turni142 – 146Combined sources5
Beta strandi150 – 154Combined sources5
Beta strandi159 – 164Combined sources6
Helixi170 – 172Combined sources3
Helixi175 – 195Combined sources21
Beta strandi198 – 203Combined sources6
Helixi210 – 212Combined sources3
Helixi216 – 219Combined sources4
Helixi227 – 238Combined sources12
Beta strandi241 – 243Combined sources3
Helixi244 – 248Combined sources5
Helixi262 – 264Combined sources3
Helixi265 – 268Combined sources4
Beta strandi275 – 280Combined sources6
Helixi281 – 286Combined sources6
Beta strandi287 – 292Combined sources6
Beta strandi298 – 301Combined sources4
Beta strandi304 – 308Combined sources5

3D structure databases

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

Miscellaneous databases

EvolutionaryTraceiA0MTA1.

Family & Domainsi

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiKOG1294. Eukaryota.
COG0708. LUCA.
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)DescriptionActionsGraphical viewLength
Sequence conflicti16A → S in CAI11781 (PubMed:23594743).Curated1
Sequence conflicti80 – 93Missing in AAI64240 (Ref. 3) CuratedAdd BLAST14
Sequence conflicti80 – 93Missing in AAH97053 (Ref. 3) CuratedAdd BLAST14
Sequence conflicti103G → A in AAH55545 (Ref. 3) Curated1

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.
UniGeneiDr.20170.

Genome annotation databases

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.
UniGeneiDr.20170.

3D structure databases

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

Protein-protein interaction databases

STRINGi7955.ENSDARP00000067373.

Proteomic databases

PaxDbiA0MTA1.
PeptideAtlasiA0MTA1.
PRIDEiA0MTA1.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

KEGGidre:406730.

Organism-specific databases

CTDi328.
ZFINiZDB-GENE-040426-2761. apex1.

Phylogenomic databases

eggNOGiKOG1294. Eukaryota.
COG0708. LUCA.
HOGENOMiHOG000034586.
HOVERGENiHBG050531.
InParanoidiA0MTA1.
KOiK10771.
PhylomeDBiA0MTA1.
TreeFamiTF315048.

Miscellaneous databases

EvolutionaryTraceiA0MTA1.
PROiA0MTA1.

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]
ProtoNetiSearch...

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 2, 2016
This is version 73 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

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 one 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.