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Protein

DNA-(apurinic or apyrimidinic site) lyase

Gene

apeA

Organism
Dictyostelium discoideum (Slime mold)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at transcript leveli

Functioni

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 bindingi139Magnesium 1By similarity1
Active sitei211By similarity1
Active sitei252Proton donor/acceptorBy similarity1
Metal bindingi252Magnesium 2By similarity1
Metal bindingi254Magnesium 2By similarity1
Sitei254Transition state stabilizerBy similarity1
Sitei324Important for catalytic activityBy similarity1
Metal bindingi350Magnesium 1By similarity1

GO - Molecular functioni

GO - Biological processi

  • base-excision repair Source: dictyBase
Complete GO annotation...

Keywords - Molecular functioni

Lyase

Keywords - Biological processi

DNA damage, DNA repair

Keywords - Ligandi

Magnesium, Metal-binding

Enzyme and pathway databases

ReactomeiR-DDI-110357. Displacement of DNA glycosylase by APEX1.
R-DDI-110362. POLB-Dependent Long Patch Base Excision Repair.
R-DDI-110373. Resolution of AP sites via the multiple-nucleotide patch replacement pathway.
R-DDI-73930. Abasic sugar-phosphate removal via the single-nucleotide replacement pathway.
R-DDI-73933. Resolution of Abasic Sites (AP sites).

Names & Taxonomyi

Protein namesi
Recommended name:
DNA-(apurinic or apyrimidinic site) lyase (EC:4.2.99.18)
Alternative name(s):
Class II apurinic/apyrimidinic(AP)-endonuclease
Gene namesi
Name:apeA
ORF Names:DDB_G0277701
OrganismiDictyostelium discoideum (Slime mold)
Taxonomic identifieri44689 [NCBI]
Taxonomic lineageiEukaryotaAmoebozoaMycetozoaDictyosteliidaDictyostelium
Proteomesi
  • UP000002195 Componentsi: Chromosome 2, Unassembled WGS sequence

Organism-specific databases

dictyBaseiDDB_G0277701. apeA.

Subcellular locationi

  • Nucleus PROSITE-ProRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002000161 – 361DNA-(apurinic or apyrimidinic site) lyaseAdd BLAST361

Proteomic databases

PaxDbiP51173.

Expressioni

Inductioni

By DNA-damaging agents including UV, MNNG, gamma rays, bleomycin and streptozotocin.

Interactioni

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei351Interaction with DNA substrateBy similarity1

Protein-protein interaction databases

STRINGi44689.DDB0185018.

Structurei

3D structure databases

ProteinModelPortaliP51173.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi41 – 44Nuclear localization signalSequence analysis4

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi27 – 39Poly-GluAdd BLAST13
Compositional biasi70 – 80Poly-GluAdd BLAST11

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiKOG1294. Eukaryota.
COG0708. LUCA.
InParanoidiP51173.
KOiK10771.
OMAiYTPNSQQ.
PhylomeDBiP51173.

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.
PS00727. AP_NUCLEASE_F1_2. 1 hit.
PS00728. AP_NUCLEASE_F1_3. 1 hit.
PS51435. AP_NUCLEASE_F1_4. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P51173-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTSRTKKLKM DEEEILKKED GSETTSEEEK EEVEEEEEED KKRKLVKKTP
60 70 80 90 100
AKKAPAKKAA AKKKSKDEDE DEEEKEEEEE TNKTTASVSI AIDNLDEPKV
110 120 130 140 150
EENQMKIISW NVAGFKSVLS KGFTEYVEKE NPDVLCLQET KINPSNIKKD
160 170 180 190 200
QMPKGYEYHF IEADQKGHHG TGVLTKKKPN AITFGIGIAK HDNEGRVITL
210 220 230 240 250
EYDQFYIVNT YIPNAGTRGL QRLDYRIKEW DVDFQAYLEK LNATKPIIWC
260 270 280 290 300
GDLNVAHTEI DLKNPKTNKK SAGFTIEERT SFSNFLEKGY VDSYRHFNPG
310 320 330 340 350
KEGSYTFWSY LGGGRSKNVG WRLDYFVVSK RLMDSIKISP FHRTSVMGSD
360
HCPIGVVVDL N
Length:361
Mass (Da):41,327
Last modified:December 4, 2007 - v2
Checksum:iBBD46E1CE3B5135A
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti126Y → C in AAC47024 (PubMed:8657579).Curated1
Sequence conflicti203D → V in AAC47024 (PubMed:8657579).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U31631 Genomic DNA. Translation: AAC47024.1.
AAFI02000021 Genomic DNA. Translation: EAL68586.1.
PIRiS68268.
RefSeqiXP_642518.1. XM_637426.1.

Genome annotation databases

EnsemblProtistsiEAL68586; EAL68586; DDB_G0277701.
GeneIDi8621167.
KEGGiddi:DDB_G0277701.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U31631 Genomic DNA. Translation: AAC47024.1.
AAFI02000021 Genomic DNA. Translation: EAL68586.1.
PIRiS68268.
RefSeqiXP_642518.1. XM_637426.1.

3D structure databases

ProteinModelPortaliP51173.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi44689.DDB0185018.

Proteomic databases

PaxDbiP51173.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblProtistsiEAL68586; EAL68586; DDB_G0277701.
GeneIDi8621167.
KEGGiddi:DDB_G0277701.

Organism-specific databases

dictyBaseiDDB_G0277701. apeA.

Phylogenomic databases

eggNOGiKOG1294. Eukaryota.
COG0708. LUCA.
InParanoidiP51173.
KOiK10771.
OMAiYTPNSQQ.
PhylomeDBiP51173.

Enzyme and pathway databases

ReactomeiR-DDI-110357. Displacement of DNA glycosylase by APEX1.
R-DDI-110362. POLB-Dependent Long Patch Base Excision Repair.
R-DDI-110373. Resolution of AP sites via the multiple-nucleotide patch replacement pathway.
R-DDI-73930. Abasic sugar-phosphate removal via the single-nucleotide replacement pathway.
R-DDI-73933. Resolution of Abasic Sites (AP sites).

Miscellaneous databases

PROiP51173.

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.
PS00727. AP_NUCLEASE_F1_2. 1 hit.
PS00728. AP_NUCLEASE_F1_3. 1 hit.
PS51435. AP_NUCLEASE_F1_4. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiAPEA_DICDI
AccessioniPrimary (citable) accession number: P51173
Secondary accession number(s): Q54Z97, Q75K06
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: December 4, 2007
Last modified: November 2, 2016
This is version 111 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Dictyostelium discoideum
    Dictyostelium discoideum: entries, gene names and cross-references to dictyBase
  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.