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Database: UniProt
Entry: P03877
LinkDB: P03877
Original site: P03877 
ID   SCE3_YEAST              Reviewed;         415 AA.
AC   P03877; A0A0A7P044; Q35790; Q9ZZX3;
DT   21-JUL-1986, integrated into UniProtKB/Swiss-Prot.
DT   29-APR-2008, sequence version 3.
DT   08-NOV-2023, entry version 166.
DE   RecName: Full=Intron-encoded DNA endonuclease aI3;
DE   AltName: Full=DNA endonuclease I-SceIII;
DE   Contains:
DE     RecName: Full=Truncated non-functional cytochrome oxidase 1;
DE   Contains:
DE     RecName: Full=DNA endonuclease aI3;
DE              EC=3.1.-.-;
DE     AltName: Full=Intron-encoded endonuclease I-SceIII;
DE   Flags: Precursor;
GN   Name=AI3; Synonyms=ENS3, I-SCEIII; OrderedLocusNames=Q0060;
OS   Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OG   Mitochondrion.
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 24657 / D273-10B;
RX   PubMed=6254986; DOI=10.1016/s0021-9258(19)70224-5;
RA   Bonitz S.G., Coruzzi G., Thalenfeld B.E., Tzagoloff A., Macino G.;
RT   "Assembly of the mitochondrial membrane system. Structure and nucleotide
RT   sequence of the gene coding for subunit 1 of yeast cytochrome oxidase.";
RL   J. Biol. Chem. 255:11927-11941(1980).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC   STRAIN=Capensis / YB4237;
RX   PubMed=8112577; DOI=10.1016/0378-1119(94)90516-9;
RA   Szczepanek T., Macadre C., Meunier B., Lazowska J.;
RT   "Two homologous introns from related Saccharomyces species differ in their
RT   mobility.";
RL   Gene 139:1-7(1994).
RN   [3]
RP   ERRATUM OF PUBMED:8112577.
RX   DOI=10.1016/0378-1119(94)90224-0;
RA   Szczepanek T., Macadre C., Meunier B., Lazowska J.;
RL   Gene 144:149-149(1994).
RN   [4]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 96604 / S288c / FY1679;
RX   PubMed=9872396; DOI=10.1016/s0014-5793(98)01467-7;
RA   Foury F., Roganti T., Lecrenier N., Purnelle B.;
RT   "The complete sequence of the mitochondrial genome of Saccharomyces
RT   cerevisiae.";
RL   FEBS Lett. 440:325-331(1998).
RN   [5]
RP   GENOME REANNOTATION.
RC   STRAIN=ATCC 96604 / S288c / FY1679;
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   [6]
RP   FUNCTION, ENDONUCLEASE ACTIVITY, COFACTOR, PH OPTIMUM, AND CLEAVAGE SITE
RP   SPECIFICITY.
RX   PubMed=8367285; DOI=10.1093/nar/21.16.3683;
RA   Schapira M., Desdouets C., Jacq C., Perea J.;
RT   "I-Sce III an intron-encoded DNA endonuclease from yeast mitochondria.
RT   Asymmetrical DNA binding properties and cleavage reaction.";
RL   Nucleic Acids Res. 21:3683-3689(1993).
RN   [7]
RP   FUNCTION, ENDONUCLEASE ACTIVITY, PROTEOLYTIC CLEAVAGE, AND INTRON HOMING.
RX   PubMed=7797552; DOI=10.1074/jbc.270.26.15563;
RA   Guo W.-W., Moran J.V., Hoffman P.W., Henke R.M., Butow R.A., Perlman P.S.;
RT   "The mobile group I intron 3 alpha of the yeast mitochondrial COXI gene
RT   encodes a 35-kDa processed protein that is an endonuclease but not a
RT   maturase.";
RL   J. Biol. Chem. 270:15563-15570(1995).
CC   -!- FUNCTION: Mitochondrial DNA endonuclease involved in intron homing. It
CC       introduces a specific double-strand break in the DNA of the COX1 gene
CC       and thus mediates the insertion of an intron, containing its own coding
CC       sequence (group I intron), into an intronless gene. Recognizes with
CC       high specificity and cleaves the sequence 5'-GGTTTTGGTAACTATTTATTAC-3'.
CC       {ECO:0000269|PubMed:7797552, ECO:0000269|PubMed:8367285}.
CC   -!- COFACTOR:
CC       Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC         Evidence={ECO:0000269|PubMed:8367285};
CC   -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC       pH dependence:
CC         Optimum pH is 8.0. {ECO:0000269|PubMed:8367285};
CC   -!- SUBCELLULAR LOCATION: Mitochondrion. Membrane {ECO:0000305}; Multi-pass
CC       membrane protein {ECO:0000305}.
CC   -!- PTM: The mature protein may arise from proteolytic cleavage of an in-
CC       frame translation of some COX1 exons plus the intron containing the aI3
CC       open reading frame. {ECO:0000269|PubMed:7797552,
CC       ECO:0000269|PubMed:8367285}.
CC   -!- MISCELLANEOUS: Strain Capensis / YB4237 has two stop codons in position
CC       276 and 407, which disrupt the gene coding for this protein.
CC       Consequently, the corresponding intron containing its coding sequence
CC       is not mobile.
CC   -!- SIMILARITY: In the C-terminal section; belongs to the LAGLIDADG
CC       endonuclease family. {ECO:0000305}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=AAA17560.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC       Sequence=AAA17560.1; Type=Erroneous termination; Note=Truncated C-terminus.; Evidence={ECO:0000305};
CC       Sequence=CAA24061.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC       Sequence=CAA24062.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR   EMBL; V00694; CAA24062.1; ALT_SEQ; Genomic_DNA.
DR   EMBL; V00694; CAA24061.1; ALT_SEQ; Genomic_DNA.
DR   EMBL; U00801; AAA17560.1; ALT_SEQ; Unassigned_DNA.
DR   EMBL; KP263414; AIZ98884.1; -; Genomic_DNA.
DR   PIR; A04510; QXBY33.
DR   PIR; S78646; S78646.
DR   RefSeq; NP_009308.2; NC_001224.1.
DR   AlphaFoldDB; P03877; -.
DR   SMR; P03877; -.
DR   BioGRID; 34787; 2.
DR   STRING; 4932.Q0060; -.
DR   PaxDb; 4932-Q0060; -.
DR   PeptideAtlas; P03877; -.
DR   EnsemblFungi; Q0060_mRNA; Q0060; Q0060.
DR   GeneID; 854595; -.
DR   KEGG; sce:Q0060; -.
DR   AGR; SGD:S000007263; -.
DR   SGD; S000007263; AI3.
DR   VEuPathDB; FungiDB:Q0060; -.
DR   eggNOG; KOG4769; Eukaryota.
DR   HOGENOM; CLU_559205_0_0_1; -.
DR   InParanoid; P03877; -.
DR   OMA; YIMSAIA; -.
DR   OrthoDB; 2322030at2759; -.
DR   BioCyc; YEAST:G3O-34374-MONOMER; -.
DR   BioGRID-ORCS; 854595; 0 hits in 10 CRISPR screens.
DR   PRO; PR:P03877; -.
DR   Proteomes; UP000002311; Mitochondrion.
DR   RNAct; P03877; Protein.
DR   GO; GO:0005751; C:mitochondrial respiratory chain complex IV; IBA:GO_Central.
DR   GO; GO:0005739; C:mitochondrion; TAS:SGD.
DR   GO; GO:0004129; F:cytochrome-c oxidase activity; IEA:InterPro.
DR   GO; GO:0004519; F:endonuclease activity; IDA:SGD.
DR   GO; GO:0020037; F:heme binding; IEA:InterPro.
DR   GO; GO:0015990; P:electron transport coupled proton transport; IBA:GO_Central.
DR   GO; GO:0006314; P:intron homing; IEA:UniProtKB-KW.
DR   GO; GO:0006123; P:mitochondrial electron transport, cytochrome c to oxygen; IBA:GO_Central.
DR   GO; GO:0006397; P:mRNA processing; IEA:UniProtKB-KW.
DR   GO; GO:0008380; P:RNA splicing; IEA:UniProtKB-KW.
DR   Gene3D; 1.20.210.10; Cytochrome c oxidase-like, subunit I domain; 1.
DR   Gene3D; 3.10.28.10; Homing endonucleases; 2.
DR   InterPro; IPR023616; Cyt_c_oxase-like_su1_dom.
DR   InterPro; IPR036927; Cyt_c_oxase-like_su1_sf.
DR   InterPro; IPR000883; Cyt_C_Oxase_1.
DR   InterPro; IPR027434; Homing_endonucl.
DR   InterPro; IPR004860; LAGLIDADG_2.
DR   PANTHER; PTHR36181; INTRON-ENCODED ENDONUCLEASE AI3-RELATED; 1.
DR   PANTHER; PTHR36181:SF6; LAGLIDADG ENDONUCLEASE; 1.
DR   Pfam; PF00115; COX1; 1.
DR   Pfam; PF00961; LAGLIDADG_1; 2.
DR   PRINTS; PR01165; CYCOXIDASEI.
DR   SUPFAM; SSF81442; Cytochrome c oxidase subunit I-like; 1.
DR   SUPFAM; SSF55608; Homing endonucleases; 2.
DR   PROSITE; PS50855; COX1; 1.
PE   1: Evidence at protein level;
KW   Endonuclease; Hydrolase; Intron homing; Membrane; Mitochondrion;
KW   mRNA processing; mRNA splicing; Nuclease; Reference proteome;
KW   Transmembrane; Transmembrane helix.
FT   CHAIN           1..?
FT                   /note="Truncated non-functional cytochrome oxidase 1"
FT                   /id="PRO_0000045049"
FT   CHAIN           ?..415
FT                   /note="DNA endonuclease aI3"
FT                   /id="PRO_0000045050"
FT   TRANSMEM        16..36
FT                   /note="Helical"
FT                   /evidence="ECO:0000255"
FT   TRANSMEM        57..77
FT                   /note="Helical"
FT                   /evidence="ECO:0000255"
FT   REGION          1..81
FT                   /note="COX1 exons 1 to 3 encoded"
FT   REGION          82..415
FT                   /note="COX1 intron 3 encoded"
FT   VARIANT         55
FT                   /note="F -> Y (in strain: Capensis / YB4237)"
FT   VARIANT         60
FT                   /note="V -> A (in strain: Capensis / YB4237)"
FT   VARIANT         71
FT                   /note="V -> W (in strain: Capensis / YB4237)"
FT   VARIANT         76
FT                   /note="I -> M (in strain: Capensis / YB4237)"
FT   VARIANT         399
FT                   /note="R -> M (in strain: Capensis / YB4237)"
FT   CONFLICT        122
FT                   /note="T -> S (in Ref. 1; CAA24062)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        176
FT                   /note="T -> P (in Ref. 1; CAA24062)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        200
FT                   /note="E -> G (in Ref. 1; CAA24062)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        217..218
FT                   /note="TI -> NQ (in Ref. 1; CAA24062)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        247..248
FT                   /note="GM -> IL (in Ref. 1; CAA24062)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        269
FT                   /note="A -> T (in Ref. 1; CAA24062)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        284
FT                   /note="N -> I (in Ref. 1; CAA24062)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        380
FT                   /note="K -> N (in Ref. 1; CAA24062)"
FT                   /evidence="ECO:0000305"
SQ   SEQUENCE   415 AA;  47917 MW;  D86BD856933C8548 CRC64;
     MVQRWLYSTN AKDIAVLYFM LAIFSGMAGT AMSLIIRLEL AAPGSQYLHG NSQLFNVLVV
     GHAVLMIFFL VMPALIGGFG NQKRYESNNN NNQVMENKEY NLKLNYDKLG PYLAGLIEGD
     GTITVQNSSS MKKSKYRPLI VVVFKLEDLE LANYLCNLTK CGKVYKKINR NYVLWTIHDL
     KGVYTLLNII NGYMRTPKYE AFVRGAEFMN NYINSTTITH NKLKNMDNIK IKPLDTSDIG
     SNAWLAGMTD ADGNFSINLM NGKNRSSRAM PYYCLELRQN YQKNSNNNNI NFSYFYIMSA
     IATYFNVNLY SRERNLNLLV STNNTYKTYY SYKVMVANTY KNIKVMEYFN KYSLLSSKHL
     DFLDWSKLVI LINNEGQSMK TNGSWELGMN LRKDYNKTRT TFTWSHLKNT YLENK
//
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