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NEJ1_YEAST
ID   NEJ1_YEAST              Reviewed;         342 AA.
AC   Q06148; D6VYR3; Q0P6Z6; Q0P6Z7; Q0P707;
DT   12-DEC-2006, integrated into UniProtKB/Swiss-Prot.
DT   01-NOV-1996, sequence version 1.
DT   03-AUG-2022, entry version 133.
DE   RecName: Full=Non-homologous end-joining protein 1;
GN   Name=NEJ1; Synonyms=LIF2; OrderedLocusNames=YLR265C;
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], AND VARIANTS ILE-17; ILE-21; GLU-65;
RP   ALA-105; GLN-161; GLY-204; PHE-231; GLU-249; VAL-270 AND CYS-281.
RC   STRAIN=DBVPG1135, DBVPG1373, DBVPG1378, DBVPG1788, DBVPG1794, DBVPG1853,
RC   DBVPG3051, DBVPG6044, DBVPG6763, DBVPG6765, SK1, Y55, and YPS128;
RX   PubMed=16951060; DOI=10.1534/genetics.106.062166;
RA   Liti G., Barton D.B., Louis E.J.;
RT   "Sequence diversity, reproductive isolation and species concepts in
RT   Saccharomyces.";
RL   Genetics 174:839-850(2006).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 204508 / S288c;
RX   PubMed=9169871;
RA   Johnston M., Hillier L.W., Riles L., Albermann K., Andre B., Ansorge W.,
RA   Benes V., Brueckner M., Delius H., Dubois E., Duesterhoeft A.,
RA   Entian K.-D., Floeth M., Goffeau A., Hebling U., Heumann K.,
RA   Heuss-Neitzel D., Hilbert H., Hilger F., Kleine K., Koetter P., Louis E.J.,
RA   Messenguy F., Mewes H.-W., Miosga T., Moestl D., Mueller-Auer S.,
RA   Nentwich U., Obermaier B., Piravandi E., Pohl T.M., Portetelle D.,
RA   Purnelle B., Rechmann S., Rieger M., Rinke M., Rose M., Scharfe M.,
RA   Scherens B., Scholler P., Schwager C., Schwarz S., Underwood A.P.,
RA   Urrestarazu L.A., Vandenbol M., Verhasselt P., Vierendeels F., Voet M.,
RA   Volckaert G., Voss H., Wambutt R., Wedler E., Wedler H., Zimmermann F.K.,
RA   Zollner A., Hani J., Hoheisel J.D.;
RT   "The nucleotide sequence of Saccharomyces cerevisiae chromosome XII.";
RL   Nature 387:87-90(1997).
RN   [3]
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   [4]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC   STRAIN=ATCC 204508 / S288c;
RX   PubMed=17322287; DOI=10.1101/gr.6037607;
RA   Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F.,
RA   Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J.,
RA   Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J.,
RA   Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D.,
RA   LaBaer J.;
RT   "Approaching a complete repository of sequence-verified protein-encoding
RT   clones for Saccharomyces cerevisiae.";
RL   Genome Res. 17:536-543(2007).
RN   [5]
RP   FUNCTION, AND INDUCTION.
RX   PubMed=11676923; DOI=10.1016/s0960-9822(01)00488-2;
RA   Kegel A., Sjoestrand J.O.O., Aastroem S.U.;
RT   "Nej1p, a cell type-specific regulator of nonhomologous end joining in
RT   yeast.";
RL   Curr. Biol. 11:1611-1617(2001).
RN   [6]
RP   FUNCTION, INTERACTION WITH LIF1, AND INDUCTION.
RX   PubMed=11711435; DOI=10.1101/gad.206801;
RA   Frank-Vaillant M., Marcand S.;
RT   "NHEJ regulation by mating type is exercised through a novel protein,
RT   Lif2p, essential to the ligase IV pathway.";
RL   Genes Dev. 15:3005-3012(2001).
RN   [7]
RP   FUNCTION, AND INDUCTION.
RX   PubMed=11740566; DOI=10.1038/414666a;
RA   Valencia M., Bentele M., Vaze M.B., Herrmann G., Kraus E., Lee S.E.,
RA   Schaer P., Haber J.E.;
RT   "NEJ1 controls non-homologous end joining in Saccharomyces cerevisiae.";
RL   Nature 414:666-669(2001).
RN   [8]
RP   FUNCTION.
RX   PubMed=11701889; DOI=10.1126/science.1065672;
RA   Ooi S.L., Shoemaker D.D., Boeke J.D.;
RT   "A DNA microarray-based genetic screen for nonhomologous end-joining
RT   mutants in Saccharomyces cerevisiae.";
RL   Science 294:2552-2556(2001).
RN   [9]
RP   FUNCTION.
RX   PubMed=12399380; DOI=10.1093/genetics/162.2.677;
RA   Wilson T.E.;
RT   "A genomics-based screen for yeast mutants with an altered
RT   recombination/end-joining repair ratio.";
RL   Genetics 162:677-688(2002).
RN   [10]
RP   FUNCTION.
RX   PubMed=12769859; DOI=10.1016/s1097-2765(03)00177-1;
RA   Liti G., Louis E.J.;
RT   "NEJ1 prevents NHEJ-dependent telomere fusions in yeast without
RT   telomerase.";
RL   Mol. Cell 11:1373-1378(2003).
RN   [11]
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   [12]
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   [13]
RP   INTERACTION WITH LIF1.
RX   PubMed=16314503; DOI=10.1128/mcb.25.24.10782-10790.2005;
RA   Palmbos P.L., Daley J.M., Wilson T.E.;
RT   "Mutations of the Yku80 C terminus and Xrs2 FHA domain specifically block
RT   yeast nonhomologous end joining.";
RL   Mol. Cell. Biol. 25:10782-10790(2005).
CC   -!- FUNCTION: Involved in non-homologous end joining (NHEJ). Facilitates
CC       the transport of LIF1 into the nucleus, where it can interact with DNA
CC       ligase DNL4 to repair double-strand breaks (DSB). Mediates mating-type
CC       regulation of NHEJ. Prevents chromosome circularisation by NHEJ in
CC       absence of telomerase. {ECO:0000269|PubMed:11676923,
CC       ECO:0000269|PubMed:11701889, ECO:0000269|PubMed:11711435,
CC       ECO:0000269|PubMed:11740566, ECO:0000269|PubMed:12399380,
CC       ECO:0000269|PubMed:12769859}.
CC   -!- INTERACTION:
CC       Q06148; P53150: LIF1; NbExp=4; IntAct=EBI-34047, EBI-23865;
CC       Q06148; P12954: SRS2; NbExp=3; IntAct=EBI-34047, EBI-18110;
CC   -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:14562095}. Nucleus
CC       membrane {ECO:0000269|PubMed:14562095}; Multi-pass membrane protein
CC       {ECO:0000269|PubMed:14562095}.
CC   -!- INDUCTION: Repressed in diploid cells. {ECO:0000269|PubMed:11676923,
CC       ECO:0000269|PubMed:11711435, ECO:0000269|PubMed:11740566}.
CC   -!- MISCELLANEOUS: Present with 377 molecules/cell in log phase SD medium.
CC       {ECO:0000269|PubMed:14562106}.
CC   -!- SIMILARITY: Belongs to the XRCC4-XLF family. XLF subfamily.
CC       {ECO:0000305}.
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DR   EMBL; AM296374; CAL35943.1; -; Genomic_DNA.
DR   EMBL; AM296375; CAL35942.1; -; Genomic_DNA.
DR   EMBL; AM296376; CAL35941.1; -; Genomic_DNA.
DR   EMBL; AM296377; CAL35940.1; -; Genomic_DNA.
DR   EMBL; AM296378; CAL35939.1; -; Genomic_DNA.
DR   EMBL; AM296379; CAL35938.1; -; Genomic_DNA.
DR   EMBL; AM296380; CAL35937.1; -; Genomic_DNA.
DR   EMBL; AM296381; CAL35936.1; -; Genomic_DNA.
DR   EMBL; AM296382; CAL36078.1; -; Genomic_DNA.
DR   EMBL; AM296383; CAL35935.1; -; Genomic_DNA.
DR   EMBL; AM296384; CAL35934.1; -; Genomic_DNA.
DR   EMBL; AM296385; CAL35933.1; -; Genomic_DNA.
DR   EMBL; AM296386; CAL35932.1; -; Genomic_DNA.
DR   EMBL; U17244; AAB67382.1; -; Genomic_DNA.
DR   EMBL; AY557954; AAS56280.1; -; Genomic_DNA.
DR   EMBL; BK006945; DAA09579.1; -; Genomic_DNA.
DR   PIR; S51402; S51402.
DR   RefSeq; NP_013367.1; NM_001182152.1.
DR   AlphaFoldDB; Q06148; -.
DR   BioGRID; 31533; 107.
DR   DIP; DIP-4776N; -.
DR   IntAct; Q06148; 3.
DR   MINT; Q06148; -.
DR   STRING; 4932.YLR265C; -.
DR   CarbonylDB; Q06148; -.
DR   iPTMnet; Q06148; -.
DR   MaxQB; Q06148; -.
DR   PaxDb; Q06148; -.
DR   PRIDE; Q06148; -.
DR   EnsemblFungi; YLR265C_mRNA; YLR265C; YLR265C.
DR   GeneID; 850970; -.
DR   KEGG; sce:YLR265C; -.
DR   SGD; S000004255; NEJ1.
DR   VEuPathDB; FungiDB:YLR265C; -.
DR   HOGENOM; CLU_799750_0_0_1; -.
DR   InParanoid; Q06148; -.
DR   OMA; KFQHQEF; -.
DR   BioCyc; YEAST:G3O-32365-MON; -.
DR   PRO; PR:Q06148; -.
DR   Proteomes; UP000002311; Chromosome XII.
DR   RNAct; Q06148; protein.
DR   GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR   GO; GO:0032807; C:DNA ligase IV complex; IPI:SGD.
DR   GO; GO:0016021; C:integral component of membrane; IEA:UniProtKB-KW.
DR   GO; GO:0070419; C:nonhomologous end joining complex; IBA:GO_Central.
DR   GO; GO:0031965; C:nuclear membrane; IEA:UniProtKB-SubCell.
DR   GO; GO:0005634; C:nucleus; IDA:SGD.
DR   GO; GO:0045027; F:DNA end binding; IDA:SGD.
DR   GO; GO:0006303; P:double-strand break repair via nonhomologous end joining; IMP:SGD.
DR   GO; GO:0045002; P:double-strand break repair via single-strand annealing; IMP:SGD.
DR   GO; GO:0035825; P:homologous recombination; IMP:SGD.
DR   InterPro; IPR015381; XLF_N.
DR   Pfam; PF09302; XLF; 1.
PE   1: Evidence at protein level;
KW   Cytoplasm; DNA damage; DNA repair; Membrane; Nucleus; Reference proteome;
KW   Transmembrane; Transmembrane helix.
FT   CHAIN           1..342
FT                   /note="Non-homologous end-joining protein 1"
FT                   /id="PRO_0000268689"
FT   TRANSMEM        27..47
FT                   /note="Helical"
FT                   /evidence="ECO:0000255"
FT   TRANSMEM        129..149
FT                   /note="Helical"
FT                   /evidence="ECO:0000255"
FT   REGION          270..342
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        278..294
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        295..325
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   VARIANT         17
FT                   /note="V -> I (in strain: DBVPG1135, DBVPG1373, DBVPG1378,
FT                   DBVPG1788, DBVPG1794, DBVPG1853, DBVPG3051, DBVPG6044,
FT                   DBVPG6763, DBVPG6765, SK1, Y55 and YPS128)"
FT                   /evidence="ECO:0000269|PubMed:16951060"
FT   VARIANT         21
FT                   /note="N -> I (in strain: DBVPG1135, DBVPG1373, DBVPG1378,
FT                   DBVPG1788, DBVPG1794, DBVPG1853, DBVPG3051, DBVPG6763,
FT                   DBVPG6765 and SK1)"
FT                   /evidence="ECO:0000269|PubMed:16951060"
FT   VARIANT         65
FT                   /note="Q -> E (in strain: YPS128)"
FT                   /evidence="ECO:0000269|PubMed:16951060"
FT   VARIANT         105
FT                   /note="V -> A (in strain: YPS128)"
FT                   /evidence="ECO:0000269|PubMed:16951060"
FT   VARIANT         161
FT                   /note="E -> Q (in strain: DBVPG1135, DBVPG1373, DBVPG1378,
FT                   DBVPG1788, DBVPG1794, DBVPG1853, DBVPG3051, DBVPG6763,
FT                   DBVPG6765 and SK1)"
FT                   /evidence="ECO:0000269|PubMed:16951060"
FT   VARIANT         204
FT                   /note="D -> G (in strain: DBVPG6044 and Y55)"
FT                   /evidence="ECO:0000269|PubMed:16951060"
FT   VARIANT         231
FT                   /note="L -> F (in strain: DBVPG1135, DBVPG1373, DBVPG1378,
FT                   DBVPG1788, DBVPG1794, DBVPG1853, DBVPG3051, DBVPG6763,
FT                   DBVPG6765 and SK1)"
FT                   /evidence="ECO:0000269|PubMed:16951060"
FT   VARIANT         249
FT                   /note="K -> E (in strain: DBVPG1135, DBVPG1373, DBVPG1378,
FT                   DBVPG1788, DBVPG1794, DBVPG1853, DBVPG3051, DBVPG6763,
FT                   DBVPG6765 and SK1)"
FT                   /evidence="ECO:0000269|PubMed:16951060"
FT   VARIANT         270
FT                   /note="A -> V (in strain: DBVPG1135, DBVPG1373, DBVPG1378,
FT                   DBVPG1788, DBVPG1794, DBVPG1853, DBVPG3051, DBVPG6763,
FT                   DBVPG6765 and SK1)"
FT                   /evidence="ECO:0000269|PubMed:16951060"
FT   VARIANT         281
FT                   /note="R -> C (in strain: DBVPG1135, DBVPG1373, DBVPG1378,
FT                   DBVPG1788, DBVPG1794, DBVPG1853, DBVPG3051, DBVPG6763,
FT                   DBVPG6765 and SK1)"
FT                   /evidence="ECO:0000269|PubMed:16951060"
SQ   SEQUENCE   342 AA;  39116 MW;  5E09B5F851CF03B9 CRC64;
     MDSELKGQQL SDAEWCVKKI NGEGNCLLLF LPMSSPTTIV MIVLVSLERL VPYVFKLSQT
     QLSQQCQSQG FTDSISLNLI KLKLMDILQA PQEINQIGLV DSNLVFSFDV SADITVSINS
     VPSHVTKDMF YMILQSLCML LLKLVNLSTQ YHYVQRDILN EKQKCLDFLL ISLRDLDGGS
     KVISQWAPEN SKNYESLQQC TDDDIIKKLL HKGKFQHQEF LADSLKTLLS LRNKFQDVSR
     FEESGELNKK ERVRFPAVNH FYNDDFELQA DPTNEARPNS RGKIKPKTDF KPKSRESSTS
     SQLRLENFSE SEATPEKTKS SSSLVEEYPQ KKRKFGKVRI KN
 
 
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