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Protein

DNA-(apurinic or apyrimidinic site) lyase 1

Gene

APN1

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

DNA repair enzyme that cleaves apurinic/apyrimidinic (AP) sites and removes 3'-blocking groups present at single strand breaks of damaged DNA. APN1 accounts for > 97% of both apurinic/ apyrimidinic (AP) lyase and DNA 3'-repair diesterase activities.

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

Zn2+Note: Binds 3 Zn2+ ions.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi83 – 831Zinc 1By similarity
Metal bindingi123 – 1231Zinc 1By similarity
Metal bindingi158 – 1581Zinc 1By similarity
Metal bindingi158 – 1581Zinc 2By similarity
Metal bindingi192 – 1921Zinc 2By similarity
Metal bindingi195 – 1951Zinc 3By similarity
Metal bindingi229 – 2291Zinc 2By similarity
Metal bindingi242 – 2421Zinc 3By similarity
Metal bindingi244 – 2441Zinc 3By similarity
Metal bindingi274 – 2741Zinc 2By similarity

GO - Molecular functioni

  1. 3'-tyrosyl-DNA phosphodiesterase activity Source: SGD
  2. DNA-(apurinic or apyrimidinic site) lyase activity Source: SGD
  3. DNA binding Source: InterPro
  4. double-stranded DNA 3'-5' exodeoxyribonuclease activity Source: SGD
  5. phosphoric diester hydrolase activity Source: SGD
  6. zinc ion binding Source: InterPro

GO - Biological processi

  1. base-excision repair Source: SGD
  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

Metal-binding, Zinc

Enzyme and pathway databases

BioCyciYEAST:G3O-31899-MONOMER.
BRENDAi4.2.99.18. 984.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA-(apurinic or apyrimidinic site) lyase 1 (EC:4.2.99.18)
Alternative name(s):
Apurinic-apyrimidinic endonuclease 1
Short name:
AP endonuclease 1
Gene namesi
Name:APN1
Ordered Locus Names:YKL114C
ORF Names:YKL513
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311 Componenti: Chromosome XI

Organism-specific databases

SGDiS000001597. APN1.

Subcellular locationi

GO - Cellular componenti

  1. mitochondrion Source: SGD
  2. nucleus Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11Removed1 Publication
Chaini2 – 367366DNA-(apurinic or apyrimidinic site) lyase 1PRO_0000190898Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei356 – 3561Phosphoserine1 Publication

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiP22936.
PaxDbiP22936.
PeptideAtlasiP22936.

Expressioni

Gene expression databases

GenevestigatoriP22936.

Interactioni

Subunit structurei

Monomer.

Protein-protein interaction databases

BioGridi34020. 83 interactions.
DIPiDIP-4106N.
IntActiP22936. 2 interactions.
MINTiMINT-537191.
STRINGi4932.YKL114C.

Structurei

3D structure databases

ProteinModelPortaliP22936.
SMRiP22936. Positions 18-296.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the AP endonuclease 2 family.Curated

Phylogenomic databases

eggNOGiCOG0648.
GeneTreeiENSGT00390000013698.
HOGENOMiHOG000224893.
InParanoidiP22936.
KOiK10771.
OMAiENWWKAV.
OrthoDBiEOG71VT48.

Family and domain databases

Gene3Di3.20.20.150. 1 hit.
HAMAPiMF_00152. Nfo.
InterProiIPR001719. AP_endonuc_2.
IPR018246. AP_endonuc_F2_Zn_BS.
IPR013022. Xyl_isomerase-like_TIM-brl.
[Graphical view]
PANTHERiPTHR21445. PTHR21445. 1 hit.
PfamiPF01261. AP_endonuc_2. 1 hit.
[Graphical view]
SMARTiSM00518. AP2Ec. 1 hit.
[Graphical view]
SUPFAMiSSF51658. SSF51658. 1 hit.
TIGRFAMsiTIGR00587. nfo. 1 hit.
PROSITEiPS00729. AP_NUCLEASE_F2_1. 1 hit.
PS00730. AP_NUCLEASE_F2_2. 1 hit.
PS00731. AP_NUCLEASE_F2_3. 1 hit.
PS51432. AP_NUCLEASE_F2_4. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P22936-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MPSTPSFVRS AVSKYKFGAH MSGAGGISNS VTNAFNTGCN SFAMFLKSPR
60 70 80 90 100
KWVSPQYTQE EIDKFKKNCA TYNYNPLTDV LPHGQYFINL ANPDREKAEK
110 120 130 140 150
SYESFMDDLN RCEQLGIGLY NLHPGSTLKG DHQLQLKQLA SYLNKAIKET
160 170 180 190 200
KFVKIVLENM AGTGNLVGSS LVDLKEVIGM IEDKSRIGVC IDTCHTFAAG
210 220 230 240 250
YDISTTETFN NFWKEFNDVI GFKYLSAVHL NDSKAPLGAN RDLHERLGQG
260 270 280 290 300
YLGIDVFRMI AHSEYLQGIP IVLETPYEND EGYGNEIKLM EWLESKSESE
310 320 330 340 350
LLEDKEYKEK NDTLQKLGAK SRKEQLDKFE VKQKKRAGGT KRKKATAEPS
360
DNDILSQMTK KRKTKKE
Length:367
Mass (Da):41,439
Last modified:January 22, 2007 - v4
Checksum:i76C14935B760A6D1
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti239 – 2391A → S in AAA34429 (PubMed:1693433).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M33667 Genomic DNA. Translation: AAA34429.1.
S93804 Genomic DNA. Translation: AAB22003.1.
Z28114 Genomic DNA. Translation: CAA81954.1.
BK006944 Genomic DNA. Translation: DAA09044.1.
PIRiS29871.
RefSeqiNP_012808.1. NM_001179680.1.

Genome annotation databases

EnsemblFungiiYKL114C; YKL114C; YKL114C.
GeneIDi853746.
KEGGisce:YKL114C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M33667 Genomic DNA. Translation: AAA34429.1.
S93804 Genomic DNA. Translation: AAB22003.1.
Z28114 Genomic DNA. Translation: CAA81954.1.
BK006944 Genomic DNA. Translation: DAA09044.1.
PIRiS29871.
RefSeqiNP_012808.1. NM_001179680.1.

3D structure databases

ProteinModelPortaliP22936.
SMRiP22936. Positions 18-296.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi34020. 83 interactions.
DIPiDIP-4106N.
IntActiP22936. 2 interactions.
MINTiMINT-537191.
STRINGi4932.YKL114C.

Proteomic databases

MaxQBiP22936.
PaxDbiP22936.
PeptideAtlasiP22936.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYKL114C; YKL114C; YKL114C.
GeneIDi853746.
KEGGisce:YKL114C.

Organism-specific databases

SGDiS000001597. APN1.

Phylogenomic databases

eggNOGiCOG0648.
GeneTreeiENSGT00390000013698.
HOGENOMiHOG000224893.
InParanoidiP22936.
KOiK10771.
OMAiENWWKAV.
OrthoDBiEOG71VT48.

Enzyme and pathway databases

BioCyciYEAST:G3O-31899-MONOMER.
BRENDAi4.2.99.18. 984.

Miscellaneous databases

NextBioi974804.
PROiP22936.

Gene expression databases

GenevestigatoriP22936.

Family and domain databases

Gene3Di3.20.20.150. 1 hit.
HAMAPiMF_00152. Nfo.
InterProiIPR001719. AP_endonuc_2.
IPR018246. AP_endonuc_F2_Zn_BS.
IPR013022. Xyl_isomerase-like_TIM-brl.
[Graphical view]
PANTHERiPTHR21445. PTHR21445. 1 hit.
PfamiPF01261. AP_endonuc_2. 1 hit.
[Graphical view]
SMARTiSM00518. AP2Ec. 1 hit.
[Graphical view]
SUPFAMiSSF51658. SSF51658. 1 hit.
TIGRFAMsiTIGR00587. nfo. 1 hit.
PROSITEiPS00729. AP_NUCLEASE_F2_1. 1 hit.
PS00730. AP_NUCLEASE_F2_2. 1 hit.
PS00731. AP_NUCLEASE_F2_3. 1 hit.
PS51432. AP_NUCLEASE_F2_4. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Yeast structural gene (APN1) for the major apurinic endonuclease: homology to Escherichia coli endonuclease IV."
    Popoff S.C., Spira A.I., Johnson A.W., Demple B.
    Proc. Natl. Acad. Sci. U.S.A. 87:4193-4197(1989) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "Sequence of a 10.7 kb segment of yeast chromosome XI identifies the APN1 and the BAF1 loci and reveals one tRNA gene and several new open reading frames including homologs to RAD2 and kinases."
    Jacquier A., Legrain P., Dujon B.
    Yeast 8:121-132(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  3. "Complete DNA sequence of yeast chromosome XI."
    Dujon B., Alexandraki D., Andre B., Ansorge W., Baladron V., Ballesta J.P.G., Banrevi A., Bolle P.-A., Bolotin-Fukuhara M., Bossier P., Bou G., Boyer J., Buitrago M.J., Cheret G., Colleaux L., Daignan-Fornier B., del Rey F., Dion C.
    , Domdey H., Duesterhoeft A., Duesterhus S., Entian K.-D., Erfle H., Esteban P.F., Feldmann H., Fernandes L., Fobo G.M., Fritz C., Fukuhara H., Gabel C., Gaillon L., Garcia-Cantalejo J.M., Garcia-Ramirez J.J., Gent M.E., Ghazvini M., Goffeau A., Gonzalez A., Grothues D., Guerreiro P., Hegemann J.H., Hewitt N., Hilger F., Hollenberg C.P., Horaitis O., Indge K.J., Jacquier A., James C.M., Jauniaux J.-C., Jimenez A., Keuchel H., Kirchrath L., Kleine K., Koetter P., Legrain P., Liebl S., Louis E.J., Maia e Silva A., Marck C., Monnier A.-L., Moestl D., Mueller S., Obermaier B., Oliver S.G., Pallier C., Pascolo S., Pfeiffer F., Philippsen P., Planta R.J., Pohl F.M., Pohl T.M., Poehlmann R., Portetelle D., Purnelle B., Puzos V., Ramezani Rad M., Rasmussen S.W., Remacha M.A., Revuelta J.L., Richard G.-F., Rieger M., Rodrigues-Pousada C., Rose M., Rupp T., Santos M.A., Schwager C., Sensen C., Skala J., Soares H., Sor F., Stegemann J., Tettelin H., Thierry A., Tzermia M., Urrestarazu L.A., van Dyck L., van Vliet-Reedijk J.C., Valens M., Vandenbol M., Vilela C., Vissers S., von Wettstein D., Voss H., Wiemann S., Xu G., Zimmermann J., Haasemann M., Becker I., Mewes H.-W.
    Nature 369:371-378(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  4. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  5. "Yeast DNA diesterase for 3'-fragments of deoxyribose: purification and physical properties of a repair enzyme for oxidative DNA damage."
    Johnson A.W., Demple B.
    J. Biol. Chem. 263:18009-18016(1987) [PubMed] [Europe PMC] [Abstract]
    Cited for: CHARACTERIZATION, PROTEIN SEQUENCE OF 2-26.
  6. "Metalloenzymes in DNA repair. Escherichia coli endonuclease IV and Saccharomyces cerevisiae Apn1."
    Levin J.D., Shapiro R., Demple B.
    J. Biol. Chem. 266:22893-22898(1990) [PubMed] [Europe PMC] [Abstract]
    Cited for: METAL-BINDING STUDIES.
  7. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  8. "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution."
    Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.
    Science 325:1682-1686(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-356, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

Entry informationi

Entry nameiAPN1_YEAST
AccessioniPrimary (citable) accession number: P22936
Secondary accession number(s): D6VXH4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 31, 1991
Last sequence update: January 22, 2007
Last modified: January 6, 2015
This is version 134 of the entry and version 4 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 7250 molecules/cell in log phase SD medium.1 Publication

Keywords - Technical termi

Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  3. Yeast chromosome XI
    Yeast (Saccharomyces cerevisiae) chromosome XI: entries and gene names

External Data

Dasty 3

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 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.