Reviewed, UniProtKB/Swiss-Prot P23196 (APEX1_BOVIN)

Names and origin

Protein names

Recommended name:
    DNA-(apurinic or apyrimidinic site) lyase
    EC=4.2.99.18
Alternative name(s):
    Apurinic-apyrimidinic endonuclease 1
      Short name=AP endonuclease 1
    APEX nuclease
      Short name=APEN

Gene names

Name:	APEX1
Synonyms:	APE, APEX, BAP1

Organism

Bos taurus (Bovine)

Taxonomic identifier

9913 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Laurasiatheria › Cetartiodactyla › Ruminantia › Pecora › Bovidae › Bovinae › Bos

Protein attributes

Sequence length	318 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	Repairs oxidative DNA damages in vitro. May have a role in protection against cell lethality and suppression of mutations. Removes the blocking groups from the 3'-termini of the DNA strand breaks generated by ionizing radiations and bleomycin.
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.
Subunit structure	Monomer. Component of the SET complex, which also contains SET, ANP32A, HMGB2 and NME1 By similarity.
Subcellular location	Nucleus.
Tissue specificity	Thymus.
Induction	By several DNA damaging agents.
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
PTM	Acetylation Phosphoprotein
Technical term	3D-structure Direct protein sequencing
Gene Ontology (GO)
Biological process	DNA repair Inferred from electronic annotation. Source: UniProtKB-KW cell redox homeostasis Inferred from sequence or structural similarity. Source: AgBase regulation of DNA binding Inferred from sequence or structural similarity. Source: AgBase
Cellular component	nucleus Inferred from sequence or structural similarity. Source: AgBase perinuclear region of cytoplasm Inferred from sequence or structural similarity. Source: AgBase
Molecular function	DNA binding Inferred from sequence or structural similarity. Source: AgBase DNA-(apurinic or apyrimidinic site) lyase activity Inferred from electronic annotation. Source: EC endonuclease activity Inferred from electronic annotation. Source: InterPro magnesium ion binding Inferred from electronic annotation. Source: UniProtKB-KW oxidoreductase activity Inferred from sequence or structural similarity. Source: AgBase phosphoric diester hydrolase activity Inferred from sequence or structural similarity. Source: AgBase transcription coactivator activity Inferred from sequence or structural similarity. Source: AgBase
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

1

1

Removed Ref.1 Ref.3

Chain

2 – 318

317

DNA-(apurinic or apyrimidinic site) lyase

PRO_0000200009

Sites

Active site

309

1

Proton acceptor By similarity

Metal binding

68

1

Magnesium or manganese By similarity

Metal binding

96

1

Magnesium or manganese By similarity

Metal binding

210

1

Magnesium or manganese By similarity

Metal binding

212

1

Magnesium or manganese By similarity

Metal binding

308

1

Magnesium or manganese By similarity

Metal binding

309

1

Magnesium or manganese By similarity

Amino acid modifications

Modified residue

197

1

N6-acetyllysine By similarity

Modified residue

262

1

Phosphotyrosine By similarity

Experimental info

Sequence conflict

21 – 22

2

PE → LP AA sequence Ref.3

Sequence conflict

291

1

V → L in AAI22611. Ref.2

Secondary structure

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318

Helix Strand Turn

Details...

Beta strand

54 – 56

3

Beta strand

61 – 67

7

Helix

71 – 76

6

Helix

79 – 86

8

Beta strand

89 – 94

6

Helix

105 – 108

4

Helix

111 – 113

3

Beta strand

115 – 119

5

Beta strand

121 – 123

3

Beta strand

130 – 136

7

Beta strand

139 – 144

6

Helix

148 – 150

3

Beta strand

151 – 153

3

Beta strand

156 – 160

5

Beta strand

165 – 170

6

Helix

181 – 201

21

Beta strand

204 – 209

6

Helix

216 – 218

3

Turn

222 – 227

6

Helix

233 – 245

13

Helix

251 – 255

5

Turn

268 – 271

4

Helix

272 – 275

4

Beta strand

282 – 286

5

Helix

288 – 293

6

Beta strand

294 – 299

6

Beta strand

305 – 308

4

Beta strand

311 – 315

5

Sequences

	Sequence		Length	Mass (Da)
	P23196-1 [UniParc]. Last modified January 23, 2007. Version 2. Checksum: 40C733FBA2EA738D	FASTA	318	35,570
	10 20 30 40 50 60 MPKRGKKGAV VEDAEEPKTE PEAKKSKAGA KKNEKEAVGE GAVLYEDPPD QKTSPSGKSA 70 80 90 100 110 120 TLKICSWNVD GLRAWIKKKG LDWVKEEAPD ILCLQETKCS ENKLPVELQE LSGLSHQYWS 130 140 150 160 170 180 APSDKEGYSG VGLLSRQCPL KVSYGIGEEE HDQEGRVIVA EYDAFVLVTA YVPNAGRGLV 190 200 210 220 230 240 RLEYRQRWDE AFRKFLKGLA SRKPLVLCGD LNVAHEEIDL RNPKGNKKNA GFTPQERQGF 250 260 270 280 290 300 GELLQAVPLT DSFRHLYPNT AYAYTFWTYM MNARSKNVGW RLDYFLLSQS VLPALCDSKI 310 RSKALGSDHC PITLYLAL

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Isolation of cDNA clones encoding an enzyme from bovine cells that repairs oxidative DNA damage in vitro: homology with bacterial repair enzymes." Robson C.N., Milne A.M., Pappin D.J.C., Hickson I.D. Nucleic Acids Res. 19:1087-1092(1991) [PubMed: 1708495] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA], PROTEIN SEQUENCE OF 2-19. Tissue: Thymus.
[2]	NIH - Mammalian Gene Collection (MGC) project Submitted (AUG-2006) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Strain: Hereford. Tissue: Basal ganglia.
[3]	"Purification and amino-terminal amino acid sequence of an apurinic/apyrimidinic endonuclease from calf thymus." Henner W.D., Kiker N.P., Jorgensen T.J., Munck J.-N. Nucleic Acids Res. 15:5529-5544(1987) [PubMed: 2441359] [Abstract] Cited for: PROTEIN SEQUENCE OF 2-23. Tissue: Thymus.
[4]	"Three-dimensional structure prediction of bovine AP lyase, BAP1: prediction of interaction with DNA and alterations as a result of Arg176->Ala, Asp282->Ala, and His308->Asn mutations." Khurshid R., Salim A., Abbasi A. Biochem. Biophys. Res. Commun. 326:711-717(2005) [PubMed: 15607727] [Abstract] Cited for: 3D-STRUCTURE MODELING OF 40-318.

Cross-references

Sequence databases

EMBLGenBankDDBJ

X56685 mRNA. Translation: CAA40014.1.
BC122610 mRNA. Translation: AAI22611.1.

IPI

IPI00715890.

PIR

S26830.

RefSeq

NP_788782.2.

UniGene

Bt.1302

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1LYR	model	-	A	40-318	[»]
1XZR	model	-	A	40-318	[»]
1XZS	model	-	A	40-318	[»]
1XZT	model	-	A	40-318	[»]

SMR

P23196. Positions 44-318.

ModBase

Search...

Protein-protein interaction databases

STRING

P23196.

Genome annotation databases

Ensembl

ENSBTAT00000003559; ENSBTAP00000003559; ENSBTAG00000002745; Bos taurus. [Genome view]

GeneID

281630.

KEGG

bta:281630.

Organism-specific databases

CTD

281630.

Phylogenomic databases

HOVERGEN

P23196.

Enzyme and pathway databases

BRENDA

4.2.99.18. 251.

Family and domain databases

InterPro

IPR000097. AP_endonuclease_F1.
IPR005135. Endo/exonuclease/phosphatase.
IPR004808. exoDNase_III.
[Graphical view]

PANTHER

PTHR22748. ExoIII_xth. 1 hit.

Pfam

PF03372. Exo_endo_phos. 1 hit.
[Graphical view]

TIGRFAMs

TIGR00195. exoDNase_III. 1 hit.
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

APEX1_BOVIN

Accession

Primary (citable) accession number: P23196
Secondary accession number(s): Q0IIJ5

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1991
Last sequence update:	January 23, 2007
Last modified:	October 13, 2009
This is version 94 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HPI (Human Proteome Initiative)