Reviewed, UniProtKB/Swiss-Prot P22936 (APN1_YEAST)

Names and origin

Protein names

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 names

Name:	APN1
Ordered Locus Names:	YKL114C
ORF Names:	YKL513

Organism

Saccharomyces cerevisiae (Baker's yeast) [Complete proteome]

Taxonomic identifier

4932 [NCBI]

Taxonomic lineage

Eukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces

Protein attributes

Sequence length	367 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	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 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	Binds 3 zinc ions.
Subunit structure	Monomer.
Subcellular location	Nucleus.
Miscellaneous	Present with 7250 molecules/cell in log phase SD medium. Ref.6
Sequence similarities	Belongs to the AP endonuclease 2 family.

Ontologies

Keywords
Biological process	DNA damage DNA repair
Cellular component	Nucleus
Ligand	Metal-binding Zinc
Molecular function	Lyase
PTM	Phosphoprotein
Technical term	Complete proteome Direct protein sequencing
Gene Ontology (GO)
Biological process	base-excision repair Inferred from direct assay. Source: SGD
Cellular component	mitochondrion Inferred from direct assay. Source: SGD nucleus Inferred from direct assay. Source: SGD
Molecular function	3'-tyrosyl-DNA phosphodiesterase activity Inferred from direct assay. Source: SGD DNA binding Inferred from electronic annotation. Source: InterPro DNA-(apurinic or apyrimidinic site) lyase activity Ref.1 Inferred from direct assay. Source: SGD double-stranded DNA specific 3'-5' exodeoxyribonuclease activity Inferred from direct assay. Source: SGD endonuclease activity Inferred from electronic annotation. Source: InterPro zinc 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
	Initiator methionine	1	1	Removed Ref.4
	Chain	2 – 367	366	DNA-(apurinic or apyrimidinic site) lyase 1		PRO_0000190898
Sites
	Metal binding	83	1	Zinc 1 By similarity
	Metal binding	123	1	Zinc 1 By similarity
	Metal binding	158	1	Zinc 1 By similarity
	Metal binding	158	1	Zinc 2 By similarity
	Metal binding	192	1	Zinc 2 By similarity
	Metal binding	195	1	Zinc 3 By similarity
	Metal binding	229	1	Zinc 2 By similarity
	Metal binding	242	1	Zinc 3 By similarity
	Metal binding	244	1	Zinc 3 By similarity
	Metal binding	274	1	Zinc 2 By similarity
Amino acid modifications
	Modified residue	4	1	Phosphothreonine Ref.7
Experimental info
	Sequence conflict	239	1	A → S in AAA34429. Ref.1

Sequences

	Sequence		Length	Mass (Da)
	P22936-1 [UniParc]. Last modified January 23, 2007. Version 4. Checksum: 76C14935B760A6D1	FASTA	367	41,439
	10 20 30 40 50 60 MPSTPSFVRS AVSKYKFGAH MSGAGGISNS VTNAFNTGCN SFAMFLKSPR KWVSPQYTQE 70 80 90 100 110 120 EIDKFKKNCA TYNYNPLTDV LPHGQYFINL ANPDREKAEK SYESFMDDLN RCEQLGIGLY 130 140 150 160 170 180 NLHPGSTLKG DHQLQLKQLA SYLNKAIKET KFVKIVLENM AGTGNLVGSS LVDLKEVIGM 190 200 210 220 230 240 IEDKSRIGVC IDTCHTFAAG YDISTTETFN NFWKEFNDVI GFKYLSAVHL NDSKAPLGAN 250 260 270 280 290 300 RDLHERLGQG YLGIDVFRMI AHSEYLQGIP IVLETPYEND EGYGNEIKLM EWLESKSESE 310 320 330 340 350 360 LLEDKEYKEK NDTLQKLGAK SRKEQLDKFE VKQKKRAGGT KRKKATAEPS DNDILSQMTK KRKTKKE

References

	« Hide 'large scale' referencesShow 'large scale' references »
[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(1990) [PubMed: 1693433] [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(1992) [PubMed: 1561835] [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(1994) [PubMed: 8196765] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 96604 / S288c / FY1679.
[4]	"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(1988) [PubMed: 3056935] [Abstract] Cited for: CHARACTERIZATION, PROTEIN SEQUENCE OF 2-26.
[5]	"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(1991) [PubMed: 1720775] [Abstract] Cited for: METAL-BINDING STUDIES.
[6]	"Global analysis of protein expression in yeast." Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S. Nature 425:737-741(2003) [PubMed: 14562106] [Abstract] Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[7]	"A multidimensional chromatography technology for in-depth phosphoproteome analysis." Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H. Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed: 18407956] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-4, MASS SPECTROMETRY.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBLGenBankDDBJ	M33667 Genomic DNA. Translation: AAA34429.1. S93804 Genomic DNA. Translation: AAB22003.1. Z28114 Genomic DNA. Translation: CAA81954.1.
PIR	S29871.
RefSeq	NP_012808.1.
3D structure databases
HSSP	HSSP built from PDB template 1QUM based on UniProtKB P12638.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP:4106N.
IntAct	P22936. 4 interactions.
STRING	P22936.
Proteomic databases
PeptideAtlas	P22936.
Genome annotation databases
Ensembl	YKL114C; YKL114C; YKL114C; Saccharomyces cerevisiae. [Genome view]
GeneID	853746.
GenomeReviews	Gene locus YKL114C in contig Y13137_GR.
KEGG	sce:YKL114C.
NMPDR	fig|4932.3.peg.3789.
Organism-specific databases
CYGD	YKL114c.
SGD	S000001597. APN1.
Phylogenomic databases
HOGENOM	P22936.
OMA	FAMFLKS.
Enzyme and pathway databases
BRENDA	4.2.99.18. 250.
Gene expression databases
ArrayExpress	P22936.
Genevestigator	P22936.
GermOnline	YKL114C. Saccharomyces cerevisiae.
Family and domain databases
InterPro	IPR001719. AP_endonuc_F2. IPR018246. AP_endonuc_F2_Zn_BS. IPR013022. Xyl_isomerase-like_TIM-brl. IPR012307. Xyl_isomerase_TIM-brl. [Graphical view]
Gene3D	G3DSA:3.20.20.150. Xyl_isomerase-like_TIM-brl. 1 hit.
PANTHER	PTHR21445. AP_endnuclease2. 1 hit.
Pfam	PF01261. AP_endonuc_2. 1 hit. [Graphical view]
SMART	SM00518. AP2Ec. 1 hit. [Graphical view]
TIGRFAMs	TIGR00587. nfo. 1 hit.
PROSITE	PS00729. 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]
ProtoNet	Search...
Other Resources
NextBio	974804.

Entry information

Entry name

APN1_YEAST

Accession

Primary (citable) accession number: P22936

Entry history

Integrated into UniProtKB/Swiss-Prot:	August 1, 1991
Last sequence update:	January 23, 2007
Last modified:	November 3, 2009
This is version 91 of the entry and version 4 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

FPAP (Fungal Proteome Annotation Project)