APTX_YEAST
ID APTX_YEAST Reviewed; 217 AA.
AC Q08702; D6W2V9; Q05189;
DT 01-FEB-2005, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 150.
DE RecName: Full=Aprataxin-like protein;
DE EC=3.6.1.71 {ECO:0000269|PubMed:16964241, ECO:0000269|PubMed:24362567};
DE EC=3.6.1.72 {ECO:0000250|UniProtKB:O74859};
DE AltName: Full=Hit family protein 3;
GN Name=HNT3; OrderedLocusNames=YOR258W;
OS Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX NCBI_TaxID=559292;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 204510 / AB320;
RX PubMed=3526331; DOI=10.1073/pnas.83.15.5512;
RA Baum P., Furlong C., Byers B.;
RT "Yeast gene required for spindle pole body duplication: homology of its
RT product with Ca2+-binding proteins.";
RL Proc. Natl. Acad. Sci. U.S.A. 83:5512-5516(1986).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 96604 / S288c / FY1679;
RX PubMed=9153759;
RX DOI=10.1002/(sici)1097-0061(199704)13:5<483::aid-yea105>3.0.co;2-u;
RA Poirey R., Jauniaux J.-C.;
RT "Sequencing analysis of a 36.8 kb fragment of yeast chromosome XV reveals
RT 26 open reading frames including SEC63, CDC31, SUG2, GCD1, RBL2, PNT1, PAC1
RT and VPH1.";
RL Yeast 13:483-487(1997).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169874;
RA Dujon B., Albermann K., Aldea M., Alexandraki D., Ansorge W., Arino J.,
RA Benes V., Bohn C., Bolotin-Fukuhara M., Bordonne R., Boyer J., Camasses A.,
RA Casamayor A., Casas C., Cheret G., Cziepluch C., Daignan-Fornier B.,
RA Dang V.-D., de Haan M., Delius H., Durand P., Fairhead C., Feldmann H.,
RA Gaillon L., Galisson F., Gamo F.-J., Gancedo C., Goffeau A., Goulding S.E.,
RA Grivell L.A., Habbig B., Hand N.J., Hani J., Hattenhorst U., Hebling U.,
RA Hernando Y., Herrero E., Heumann K., Hiesel R., Hilger F., Hofmann B.,
RA Hollenberg C.P., Hughes B., Jauniaux J.-C., Kalogeropoulos A.,
RA Katsoulou C., Kordes E., Lafuente M.J., Landt O., Louis E.J., Maarse A.C.,
RA Madania A., Mannhaupt G., Marck C., Martin R.P., Mewes H.-W., Michaux G.,
RA Paces V., Parle-McDermott A.G., Pearson B.M., Perrin A., Pettersson B.,
RA Poch O., Pohl T.M., Poirey R., Portetelle D., Pujol A., Purnelle B.,
RA Ramezani Rad M., Rechmann S., Schwager C., Schweizer M., Sor F., Sterky F.,
RA Tarassov I.A., Teodoru C., Tettelin H., Thierry A., Tobiasch E.,
RA Tzermia M., Uhlen M., Unseld M., Valens M., Vandenbol M., Vetter I.,
RA Vlcek C., Voet M., Volckaert G., Voss H., Wambutt R., Wedler H.,
RA Wiemann S., Winsor B., Wolfe K.H., Zollner A., Zumstein E., Kleine K.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome XV.";
RL Nature 387:98-102(1997).
RN [4]
RP GENOME REANNOTATION.
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=24374639; DOI=10.1534/g3.113.008995;
RA Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
RT "The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
RL G3 (Bethesda) 4:389-398(2014).
RN [5]
RP SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
RX PubMed=14562095; DOI=10.1038/nature02026;
RA Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W.,
RA Weissman J.S., O'Shea E.K.;
RT "Global analysis of protein localization in budding yeast.";
RL Nature 425:686-691(2003).
RN [6]
RP LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
RX PubMed=14562106; DOI=10.1038/nature02046;
RA Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N.,
RA O'Shea E.K., Weissman J.S.;
RT "Global analysis of protein expression in yeast.";
RL Nature 425:737-741(2003).
RN [7]
RP IDENTIFICATION.
RX PubMed=16547001; DOI=10.1074/jbc.m507946200;
RA Kijas A.W., Harris J.L., Harris J.M., Lavin M.F.;
RT "Aprataxin forms a discrete branch in the HIT (histidine triad) superfamily
RT of proteins with both DNA/RNA binding and nucleotide hydrolase
RT activities.";
RL J. Biol. Chem. 281:13939-13948(2006).
RN [8]
RP FUNCTION, AND CATALYTIC ACTIVITY.
RX PubMed=16964241; DOI=10.1038/nature05164;
RA Ahel I., Rass U., El-Khamisy S.F., Katyal S., Clements P.M., McKinnon P.J.,
RA Caldecott K.W., West S.C.;
RT "The neurodegenerative disease protein aprataxin resolves abortive DNA
RT ligation intermediates.";
RL Nature 443:713-716(2006).
RN [9]
RP FUNCTION, AND CATALYTIC ACTIVITY.
RX PubMed=24362567; DOI=10.1038/nature12824;
RA Tumbale P., Williams J.S., Schellenberg M.J., Kunkel T.A., Williams R.S.;
RT "Aprataxin resolves adenylated RNA-DNA junctions to maintain genome
RT integrity.";
RL Nature 506:111-115(2014).
CC -!- FUNCTION: DNA-binding protein involved in single-strand DNA break
CC repair, double-strand DNA break repair and base excision repair.
CC Resolves abortive DNA ligation intermediates formed either at base
CC excision sites, or when DNA ligases attempt to repair non-ligatable
CC breaks induced by reactive oxygen species. Catalyzes the release of
CC adenylate groups covalently linked to 5'-phosphate termini, resulting
CC in the production of 5'-phosphate termini that can be efficiently
CC rejoined (PubMed:16964241, PubMed:24362567). Likewise, catalyzes the
CC release of 3'-linked guanosine (DNAppG) and inosine (DNAppI) from DNA,
CC but has higher specific activity with 5'-linked adenosine (AppDNA) (By
CC similarity). {ECO:0000250|UniProtKB:O74859,
CC ECO:0000269|PubMed:16964241, ECO:0000269|PubMed:24362567}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a 5'-end adenosine-5'-diphospho-5'-(2'-deoxyribonucleoside)-
CC DNA + H2O = a 5'-end 5'-monophospho-2'-deoxyribonucleoside-DNA + AMP
CC + 2 H(+); Xref=Rhea:RHEA:52128, Rhea:RHEA-COMP:13180, Rhea:RHEA-
CC COMP:13181, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:136412,
CC ChEBI:CHEBI:136413, ChEBI:CHEBI:456215; EC=3.6.1.71;
CC Evidence={ECO:0000269|PubMed:16964241, ECO:0000269|PubMed:24362567};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a 5'-end adenosine-5'-diphospho-5'-ribonucleoside-2'-
CC deoxyribonucleotide-DNA + H2O = a 5'-end 5'-monophospho-
CC ribonucleoside-2'-deoxyribonucleotide-DNA + AMP + 2 H(+);
CC Xref=Rhea:RHEA:52132, Rhea:RHEA-COMP:13182, Rhea:RHEA-COMP:13183,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:136414,
CC ChEBI:CHEBI:136415, ChEBI:CHEBI:456215; EC=3.6.1.71;
CC Evidence={ECO:0000269|PubMed:16964241, ECO:0000269|PubMed:24362567};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a 3'-end 2'-deoxyribonucleotide-3'-diphospho-5'-guanosine-DNA
CC + H2O = a 3'-end 2'-deoxyribonucleotide 3'-phosphate-DNA + GMP + 2
CC H(+); Xref=Rhea:RHEA:52140, Rhea:RHEA-COMP:13186, Rhea:RHEA-
CC COMP:13187, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:58115,
CC ChEBI:CHEBI:136419, ChEBI:CHEBI:136420; EC=3.6.1.72;
CC Evidence={ECO:0000250|UniProtKB:O74859};
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:14562095}. Cytoplasm
CC {ECO:0000269|PubMed:14562095}.
CC -!- DOMAIN: The HIT domain is required for enzymatic activity.
CC {ECO:0000250}.
CC -!- MISCELLANEOUS: Present with 396 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
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DR EMBL; M14078; AAA66894.1; -; Genomic_DNA.
DR EMBL; Z75166; CAA99480.1; -; Genomic_DNA.
DR EMBL; BK006948; DAA11025.1; -; Genomic_DNA.
DR PIR; S67155; S67155.
DR RefSeq; NP_014901.1; NM_001183677.1.
DR AlphaFoldDB; Q08702; -.
DR SMR; Q08702; -.
DR BioGRID; 34648; 25.
DR DIP; DIP-5388N; -.
DR IntAct; Q08702; 2.
DR STRING; 4932.YOR258W; -.
DR MaxQB; Q08702; -.
DR PaxDb; Q08702; -.
DR PRIDE; Q08702; -.
DR EnsemblFungi; YOR258W_mRNA; YOR258W; YOR258W.
DR GeneID; 854432; -.
DR KEGG; sce:YOR258W; -.
DR SGD; S000005784; HNT3.
DR VEuPathDB; FungiDB:YOR258W; -.
DR eggNOG; KOG0562; Eukaryota.
DR GeneTree; ENSGT00940000156806; -.
DR HOGENOM; CLU_066882_3_1_1; -.
DR InParanoid; Q08702; -.
DR OMA; HPFDAFE; -.
DR BioCyc; YEAST:G3O-33749-MON; -.
DR BRENDA; 3.1.11.7; 984.
DR BRENDA; 3.6.1.71; 984.
DR PRO; PR:Q08702; -.
DR Proteomes; UP000002311; Chromosome XV.
DR RNAct; Q08702; protein.
DR GO; GO:0005737; C:cytoplasm; HDA:SGD.
DR GO; GO:0005634; C:nucleus; HDA:SGD.
DR GO; GO:0033699; F:DNA 5'-adenosine monophosphate hydrolase activity; IDA:UniProtKB.
DR GO; GO:0120108; F:DNA-3'-diphospho-5'-guanosine diphosphatase; IEA:UniProtKB-EC.
DR GO; GO:0003725; F:double-stranded RNA binding; IBA:GO_Central.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0030983; F:mismatched DNA binding; IBA:GO_Central.
DR GO; GO:1990165; F:single-strand break-containing DNA binding; IBA:GO_Central.
DR GO; GO:0003697; F:single-stranded DNA binding; IBA:GO_Central.
DR GO; GO:0006974; P:cellular response to DNA damage stimulus; IMP:SGD.
DR GO; GO:0006302; P:double-strand break repair; IBA:GO_Central.
DR GO; GO:0000012; P:single strand break repair; IBA:GO_Central.
DR Gene3D; 3.30.428.10; -; 1.
DR InterPro; IPR026963; Aprataxin-like.
DR InterPro; IPR011146; HIT-like.
DR InterPro; IPR036265; HIT-like_sf.
DR InterPro; IPR032566; Znf-C2HE.
DR PANTHER; PTHR12486:SF4; PTHR12486:SF4; 1.
DR Pfam; PF01230; HIT; 1.
DR Pfam; PF16278; zf-C2HE; 1.
DR SUPFAM; SSF54197; SSF54197; 1.
PE 1: Evidence at protein level;
KW Cytoplasm; DNA damage; DNA repair; DNA-binding; Hydrolase; Metal-binding;
KW Nucleus; Reference proteome; Zinc.
FT CHAIN 1..217
FT /note="Aprataxin-like protein"
FT /id="PRO_0000109802"
FT DOMAIN 6..139
FT /note="HIT"
FT REGION 34..38
FT /note="Interaction with DNA"
FT /evidence="ECO:0000250|UniProtKB:O74859"
FT REGION 121..132
FT /note="Interaction with DNA"
FT /evidence="ECO:0000250|UniProtKB:O74859"
FT REGION 144..148
FT /note="Interaction with DNA"
FT /evidence="ECO:0000250|UniProtKB:O74859"
FT ACT_SITE 130
FT /note="Nucleophile"
FT /evidence="ECO:0000250|UniProtKB:O74859"
FT BINDING 188
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250|UniProtKB:O74859"
FT BINDING 191
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250|UniProtKB:O74859"
FT BINDING 205
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250|UniProtKB:O74859"
FT BINDING 209
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250|UniProtKB:O74859"
FT SITE 10
FT /note="Interaction with DNA"
FT /evidence="ECO:0000250|UniProtKB:O74859"
FT CONFLICT 80
FT /note="I -> S (in Ref. 1; AAA66894)"
FT /evidence="ECO:0000305"
FT CONFLICT 157
FT /note="F -> N (in Ref. 1; AAA66894)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 217 AA; 25757 MW; 8BA406AEDF17FA29 CRC64;
MSWRYALKNY VTSPETVNDD TVTYFDDKVS IIRDSFPKSE CHLLILPRTM QLSRSHPTKV
IDAKFKNEFE SYVNSAIDHI FRHFQEKFRI KKSDDDKDPC WDDILKDKNK FVRNFVQVGI
HSVPSMANLH IHVISKDFHS VRLKNKKHYN SFNTGFFISW DDLPLNGKNL GTDKEIETTY
LKEHDLLCCY CQRNFSNKFS LLKKHLELEF NSHFELK
