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P51173

- APEA_DICDI

UniProt

P51173 - APEA_DICDI

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Protein

DNA-(apurinic or apyrimidinic site) lyase

Gene

apeA

Organism
Dictyostelium discoideum (Slime mold)
Status
Reviewed - Annotation score: 4 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

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

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi139 – 1391Magnesium 1By similarity
Active sitei211 – 2111By similarity
Active sitei252 – 2521Proton donor/acceptorBy similarity
Metal bindingi252 – 2521Magnesium 2By similarity
Metal bindingi254 – 2541Magnesium 2By similarity
Sitei254 – 2541Transition state stabilizerBy similarity
Sitei324 – 3241Important for catalytic activityBy similarity
Metal bindingi350 – 3501Magnesium 1By similarity
Sitei351 – 3511Interaction with DNA substrateBy similarity

GO - Molecular functioni

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

GO - Biological processi

  1. base-excision repair Source: dictyBase
  2. DNA catabolic process, endonucleolytic Source: GOC
  3. DNA catabolic process, exonucleolytic Source: GOC
Complete GO annotation...

Keywords - Molecular functioni

Lyase

Keywords - Biological processi

DNA damage, DNA repair

Keywords - Ligandi

Magnesium, Metal-binding

Enzyme and pathway databases

ReactomeiREACT_202785. Displacement of DNA glycosylase by APE1.
REACT_215768. Base-free sugar-phosphate removal via the single-nucleotide replacement pathway.
REACT_223018. Removal of DNA patch containing abasic residue.

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
ProteomesiUP000002195: Chromosome 2, UP000002195: Unassembled WGS sequence

Organism-specific databases

dictyBaseiDDB_G0277701. apeA.

Subcellular locationi

Nucleus PROSITE-ProRule annotation

GO - Cellular componenti

  1. nucleus Source: RefGenome
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 361361DNA-(apurinic or apyrimidinic site) lyasePRO_0000200016Add
BLAST

Expressioni

Inductioni

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

Interactioni

Protein-protein interaction databases

STRINGi44689.DDB_0185018.

Structurei

3D structure databases

ProteinModelPortaliP51173.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi41 – 444Nuclear localization signalSequence Analysis

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi27 – 3913Poly-GluAdd
BLAST
Compositional biasi70 – 8011Poly-GluAdd
BLAST

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiCOG0708.
InParanoidiP51173.
KOiK10771.
OMAiGWRIDYY.
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)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti126 – 1261Y → C in AAC47024. (PubMed:8657579)Curated
Sequence conflicti203 – 2031D → V in AAC47024. (PubMed:8657579)Curated

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
U31631 Genomic DNA. Translation: AAC47024.1.
AAFI02000021 Genomic DNA. Translation: EAL68586.1.
PIRiS68268.
RefSeqiXP_642518.1. XM_637426.1.

Genome annotation databases

EnsemblProtistsiDDB0185018; DDB0185018; DDB_G0277701.
GeneIDi8621167.
KEGGiddi:DDB_G0277701.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
U31631 Genomic DNA. Translation: AAC47024.1 .
AAFI02000021 Genomic DNA. Translation: EAL68586.1 .
PIRi S68268.
RefSeqi XP_642518.1. XM_637426.1.

3D structure databases

ProteinModelPortali P51173.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 44689.DDB_0185018.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblProtistsi DDB0185018 ; DDB0185018 ; DDB_G0277701 .
GeneIDi 8621167.
KEGGi ddi:DDB_G0277701.

Organism-specific databases

dictyBasei DDB_G0277701. apeA.

Phylogenomic databases

eggNOGi COG0708.
InParanoidi P51173.
KOi K10771.
OMAi GWRIDYY.
PhylomeDBi P51173.

Enzyme and pathway databases

Reactomei REACT_202785. Displacement of DNA glycosylase by APE1.
REACT_215768. Base-free sugar-phosphate removal via the single-nucleotide replacement pathway.
REACT_223018. Removal of DNA patch containing abasic residue.

Miscellaneous databases

PROi P51173.

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.
PS00727. AP_NUCLEASE_F1_2. 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. "Apurinic/apyrimidinic (AP) endonuclease from Dictyostelium discoideum: cloning, nucleotide sequence and induction by sublethal levels of DNA damaging agents."
    Freeland T.M., Guyer R.B., Ling A.Z., Deering R.A.
    Nucleic Acids Res. 24:1950-1953(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: AX4.
  3. "The genome of the social amoeba Dictyostelium discoideum."
    Eichinger L., Pachebat J.A., Gloeckner G., Rajandream M.A., Sucgang R., Berriman M., Song J., Olsen R., Szafranski K., Xu Q., Tunggal B., Kummerfeld S., Madera M., Konfortov B.A., Rivero F., Bankier A.T., Lehmann R., Hamlin N.
    , Davies R., Gaudet P., Fey P., Pilcher K., Chen G., Saunders D., Sodergren E.J., Davis P., Kerhornou A., Nie X., Hall N., Anjard C., Hemphill L., Bason N., Farbrother P., Desany B., Just E., Morio T., Rost R., Churcher C.M., Cooper J., Haydock S., van Driessche N., Cronin A., Goodhead I., Muzny D.M., Mourier T., Pain A., Lu M., Harper D., Lindsay R., Hauser H., James K.D., Quiles M., Madan Babu M., Saito T., Buchrieser C., Wardroper A., Felder M., Thangavelu M., Johnson D., Knights A., Loulseged H., Mungall K.L., Oliver K., Price C., Quail M.A., Urushihara H., Hernandez J., Rabbinowitsch E., Steffen D., Sanders M., Ma J., Kohara Y., Sharp S., Simmonds M.N., Spiegler S., Tivey A., Sugano S., White B., Walker D., Woodward J.R., Winckler T., Tanaka Y., Shaulsky G., Schleicher M., Weinstock G.M., Rosenthal A., Cox E.C., Chisholm R.L., Gibbs R.A., Loomis W.F., Platzer M., Kay R.R., Williams J.G., Dear P.H., Noegel A.A., Barrell B.G., Kuspa A.
    Nature 435:43-57(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: AX4.

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: October 29, 2014
This is version 97 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

External Data

Dasty 3