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P51173

- APEA_DICDI

UniProt

P51173 - APEA_DICDI

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Protein

DNA-(apurinic or apyrimidinic site) lyase

Gene
apeA, DDB_G0277701
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.

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 bindingi139 – 1391Magnesium 1 By similarity
Active sitei211 – 2111 By similarity
Active sitei252 – 2521Proton donor/acceptor By similarity
Metal bindingi252 – 2521Magnesium 2 By similarity
Metal bindingi254 – 2541Magnesium 2 By similarity
Sitei254 – 2541Transition state stabilizer By similarity
Sitei324 – 3241Important for catalytic activity By similarity
Metal bindingi350 – 3501Magnesium 1 By similarity
Sitei351 – 3511Interaction with DNA substrate By 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 Reviewed prediction

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.

Family & Domainsi

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi41 – 444Nuclear localization signal Reviewed prediction

Compositional bias

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

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0708.
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

MTSRTKKLKM DEEEILKKED GSETTSEEEK EEVEEEEEED KKRKLVKKTP    50
AKKAPAKKAA AKKKSKDEDE DEEEKEEEEE TNKTTASVSI AIDNLDEPKV 100
EENQMKIISW NVAGFKSVLS KGFTEYVEKE NPDVLCLQET KINPSNIKKD 150
QMPKGYEYHF IEADQKGHHG TGVLTKKKPN AITFGIGIAK HDNEGRVITL 200
EYDQFYIVNT YIPNAGTRGL QRLDYRIKEW DVDFQAYLEK LNATKPIIWC 250
GDLNVAHTEI DLKNPKTNKK SAGFTIEERT SFSNFLEKGY VDSYRHFNPG 300
KEGSYTFWSY LGGGRSKNVG WRLDYFVVSK RLMDSIKISP FHRTSVMGSD 350
HCPIGVVVDL N 361
Length:361
Mass (Da):41,327
Last modified:December 4, 2007 - v2
Checksum:iBBD46E1CE3B5135A
GO

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti126 – 1261Y → C in AAC47024. 1 Publication
Sequence conflicti203 – 2031D → V in AAC47024. 1 Publication

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.
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: September 3, 2014
This is version 95 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