P51173 (APEA_DICDI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
DNA-(apurinic or apyrimidinic site) lyase
EC=4.2.99.18

Alternative name(s):
Class II apurinic/apyrimidinic(AP)-endonuclease

Gene names

Name:	apeA
ORF Names:	DDB_G0277701

Organism

Dictyostelium discoideum (Slime mold) [Reference proteome]

Taxonomic identifier

44689 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Amoebozoa › Mycetozoa › Dictyosteliida › Dictyostelium

Protein attributes

Sequence length	361 AA.
Sequence status	Complete.
Protein existence	Evidence at transcript level

General annotation (Comments)

Catalytic activity	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.
Cofactor	Magnesium. Can also utilize manganese. Probably binds two magnesium or manganese ions per subunit By similarity.
Subcellular location	Nucleus Potential.
Induction	By DNA-damaging agents including UV, MNNG, gamma rays, bleomycin and streptozotocin.
Sequence similarities	Belongs to the DNA repair enzymes AP/ExoA family.

Ontologies

Keywords
Biological process	DNA damage DNA repair
Cellular component	Nucleus
Ligand	Magnesium Metal-binding
Molecular function	Lyase
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	base-excision repair Traceable author statement PubMed 2580557. Source: dictyBase
Cellular_component	nucleus Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	DNA binding Inferred from electronic annotation. Source: InterPro DNA-(apurinic or apyrimidinic site) lyase activity Inferred from electronic annotation. Source: EC endodeoxyribonuclease activity, producing 3'-phosphomonoesters Traceable author statement PubMed 2580557. Source: dictyBase metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 361	361	DNA-(apurinic or apyrimidinic site) lyase		PRO_0000200016
Regions
	Motif	41 – 44	4	Nuclear localization signal Potential
	Compositional bias	27 – 39	13	Poly-Glu
	Compositional bias	70 – 80	11	Poly-Glu
Sites
	Active site	211	1	By similarity
	Active site	252	1	Proton donor/acceptor By similarity
	Metal binding	139	1	Magnesium 1 By similarity
	Metal binding	252	1	Magnesium 2 By similarity
	Metal binding	254	1	Magnesium 2 By similarity
	Metal binding	350	1	Magnesium 1 By similarity
	Site	254	1	Transition state stabilizer By similarity
	Site	324	1	Important for catalytic activity By similarity
	Site	351	1	Interaction with DNA substrate By similarity
Experimental info
	Sequence conflict	126	1	Y → C in AAC47024. Ref.1
	Sequence conflict	203	1	D → V in AAC47024. Ref.1

Sequences

	Sequence		Length	Mass (Da)
	P51173 [UniParc]. Last modified December 4, 2007. Version 2. Checksum: BBD46E1CE3B5135A	FASTA	361	41,327
	10 20 30 40 50 60 MTSRTKKLKM DEEEILKKED GSETTSEEEK EEVEEEEEED KKRKLVKKTP AKKAPAKKAA 70 80 90 100 110 120 AKKKSKDEDE DEEEKEEEEE TNKTTASVSI AIDNLDEPKV EENQMKIISW NVAGFKSVLS 130 140 150 160 170 180 KGFTEYVEKE NPDVLCLQET KINPSNIKKD QMPKGYEYHF IEADQKGHHG TGVLTKKKPN 190 200 210 220 230 240 AITFGIGIAK HDNEGRVITL EYDQFYIVNT YIPNAGTRGL QRLDYRIKEW DVDFQAYLEK 250 260 270 280 290 300 LNATKPIIWC GDLNVAHTEI DLKNPKTNKK SAGFTIEERT SFSNFLEKGY VDSYRHFNPG 310 320 330 340 350 360 KEGSYTFWSY LGGGRSKNVG WRLDYFVVSK RLMDSIKISP FHRTSVMGSD HCPIGVVVDL N

References

	« Hide 'large scale' referencesShow 'large scale' references »
[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]	"Sequence and analysis of chromosome 2 of Dictyostelium discoideum." Gloeckner G., Eichinger L., Szafranski K., Pachebat J.A., Bankier A.T., Dear P.H., Lehmann R., Baumgart C., Parra G., Abril J.F., Guigo R., Kumpf K., Tunggal B., Cox E.C., Quail M.A., Platzer M., Rosenthal A., Noegel A.A. Nature 418:79-85(2002) [PubMed] [Europe PMC] [Abstract] 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.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	U31631 Genomic DNA. Translation: AAC47024.1. AAFI02000021 Genomic DNA. Translation: EAL68586.1.
PIR	S68268.
RefSeq	XP_642518.1. XM_637426.1.
3D structure databases
ProteinModelPortal	P51173.
ModBase	Search...
Protein-protein interaction databases
STRING	44689.DDB_0185018.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblProtists	DDB0185018; DDB0185018; DDB_G0277701.
GeneID	8621167.
KEGG	ddi:DDB_G0277701.
Organism-specific databases
dictyBase	DDB_G0277701. apeA.
Phylogenomic databases
eggNOG	COG0708.
KO	K10771.
OMA	GIRACLK.
ProtClustDB	CLSZ2453462.
Family and domain databases
InterPro	IPR020847. AP_endonuclease_F1_BS. IPR020848. AP_endonuclease_F1_CS. IPR005135. Endo/exonuclease/phosphatase. IPR004808. ExoDNase_III. [Graphical view]
PANTHER	PTHR22748. PTHR22748. 1 hit.
Pfam	PF03372. Exo_endo_phos. 1 hit. [Graphical view]
SUPFAM	SSF56219. Exo_endo_phos. 1 hit.
TIGRFAMs	TIGR00633. xth. 1 hit.
PROSITE	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]
ProtoNet	Search...

Entry information

Entry name

APEA_DICDI

Accession

Primary (citable) accession number: P51173
Secondary accession number(s): Q54Z97, Q75K06

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 1, 1996
Last sequence update:	December 4, 2007
Last modified:	May 1, 2013
This is version 89 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)