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Non-homologous end-joining protein 1

 NEJ1_YEAST              Reviewed;         342 AA.
Q06148; D6VYR3; Q0P6Z6; Q0P6Z7; Q0P707;
12-DEC-2006, integrated into UniProtKB/Swiss-Prot.
01-NOV-1996, sequence version 1.
29-SEP-2021, entry version 130.
RecName: Full=Non-homologous end-joining protein 1;
Name=NEJ1; Synonyms=LIF2; OrderedLocusNames=YLR265C;
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
Saccharomycetales; Saccharomycetaceae; Saccharomyces.
NCBI_TaxID=559292;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND VARIANTS ILE-17; ILE-21; GLU-65;
ALA-105; GLN-161; GLY-204; PHE-231; GLU-249; VAL-270 AND CYS-281.
STRAIN=DBVPG1135, DBVPG1373, DBVPG1378, DBVPG1788, DBVPG1794, DBVPG1853,
DBVPG3051, DBVPG6044, DBVPG6763, DBVPG6765, SK1, Y55, and YPS128;
PubMed=16951060; DOI=10.1534/genetics.106.062166;
Liti G., Barton D.B., Louis E.J.;
"Sequence diversity, reproductive isolation and species concepts in
Saccharomyces.";
Genetics 174:839-850(2006).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 204508 / S288c;
PubMed=9169871;
Johnston M., Hillier L.W., Riles L., Albermann K., Andre B., Ansorge W.,
Benes V., Brueckner M., Delius H., Dubois E., Duesterhoeft A.,
Entian K.-D., Floeth M., Goffeau A., Hebling U., Heumann K.,
Heuss-Neitzel D., Hilbert H., Hilger F., Kleine K., Koetter P., Louis E.J.,
Messenguy F., Mewes H.-W., Miosga T., Moestl D., Mueller-Auer S.,
Nentwich U., Obermaier B., Piravandi E., Pohl T.M., Portetelle D.,
Purnelle B., Rechmann S., Rieger M., Rinke M., Rose M., Scharfe M.,
Scherens B., Scholler P., Schwager C., Schwarz S., Underwood A.P.,
Urrestarazu L.A., Vandenbol M., Verhasselt P., Vierendeels F., Voet M.,
Volckaert G., Voss H., Wambutt R., Wedler E., Wedler H., Zimmermann F.K.,
Zollner A., Hani J., Hoheisel J.D.;
"The nucleotide sequence of Saccharomyces cerevisiae chromosome XII.";
Nature 387:87-90(1997).
[3]
GENOME REANNOTATION.
STRAIN=ATCC 204508 / S288c;
PubMed=24374639; DOI=10.1534/g3.113.008995;
Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
"The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
G3 (Bethesda) 4:389-398(2014).
[4]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
STRAIN=ATCC 204508 / S288c;
PubMed=17322287; DOI=10.1101/gr.6037607;
Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F.,
Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J.,
Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J.,
Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D.,
LaBaer J.;
"Approaching a complete repository of sequence-verified protein-encoding
clones for Saccharomyces cerevisiae.";
Genome Res. 17:536-543(2007).
[5]
FUNCTION, AND INDUCTION.
PubMed=11676923; DOI=10.1016/s0960-9822(01)00488-2;
Kegel A., Sjoestrand J.O.O., Aastroem S.U.;
"Nej1p, a cell type-specific regulator of nonhomologous end joining in
yeast.";
Curr. Biol. 11:1611-1617(2001).
[6]
FUNCTION, INTERACTION WITH LIF1, AND INDUCTION.
PubMed=11711435; DOI=10.1101/gad.206801;
Frank-Vaillant M., Marcand S.;
"NHEJ regulation by mating type is exercised through a novel protein,
Lif2p, essential to the ligase IV pathway.";
Genes Dev. 15:3005-3012(2001).
[7]
FUNCTION, AND INDUCTION.
PubMed=11740566; DOI=10.1038/414666a;
Valencia M., Bentele M., Vaze M.B., Herrmann G., Kraus E., Lee S.E.,
Schaer P., Haber J.E.;
"NEJ1 controls non-homologous end joining in Saccharomyces cerevisiae.";
Nature 414:666-669(2001).
[8]
FUNCTION.
PubMed=11701889; DOI=10.1126/science.1065672;
Ooi S.L., Shoemaker D.D., Boeke J.D.;
"A DNA microarray-based genetic screen for nonhomologous end-joining
mutants in Saccharomyces cerevisiae.";
Science 294:2552-2556(2001).
[9]
FUNCTION.
PubMed=12399380;
Wilson T.E.;
"A genomics-based screen for yeast mutants with an altered
recombination/end-joining repair ratio.";
Genetics 162:677-688(2002).
[10]
FUNCTION.
PubMed=12769859; DOI=10.1016/s1097-2765(03)00177-1;
Liti G., Louis E.J.;
"NEJ1 prevents NHEJ-dependent telomere fusions in yeast without
telomerase.";
Mol. Cell 11:1373-1378(2003).
[11]
SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
PubMed=14562095; DOI=10.1038/nature02026;
Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W.,
Weissman J.S., O'Shea E.K.;
"Global analysis of protein localization in budding yeast.";
Nature 425:686-691(2003).
[12]
LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
PubMed=14562106; DOI=10.1038/nature02046;
Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N.,
O'Shea E.K., Weissman J.S.;
"Global analysis of protein expression in yeast.";
Nature 425:737-741(2003).
[13]
INTERACTION WITH LIF1.
PubMed=16314503; DOI=10.1128/mcb.25.24.10782-10790.2005;
Palmbos P.L., Daley J.M., Wilson T.E.;
"Mutations of the Yku80 C terminus and Xrs2 FHA domain specifically block
yeast nonhomologous end joining.";
Mol. Cell. Biol. 25:10782-10790(2005).
-!- FUNCTION: Involved in non-homologous end joining (NHEJ). Facilitates
the transport of LIF1 into the nucleus, where it can interact with DNA
ligase DNL4 to repair double-strand breaks (DSB). Mediates mating-type
regulation of NHEJ. Prevents chromosome circularisation by NHEJ in
absence of telomerase. {ECO:0000269|PubMed:11676923,
ECO:0000269|PubMed:11701889, ECO:0000269|PubMed:11711435,
ECO:0000269|PubMed:11740566, ECO:0000269|PubMed:12399380,
ECO:0000269|PubMed:12769859}.
-!- INTERACTION:
Q06148; P53150: LIF1; NbExp=4; IntAct=EBI-34047, EBI-23865;
Q06148; P12954: SRS2; NbExp=3; IntAct=EBI-34047, EBI-18110;
-!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:14562095}. Nucleus
membrane {ECO:0000269|PubMed:14562095}; Multi-pass membrane protein
{ECO:0000269|PubMed:14562095}.
-!- INDUCTION: Repressed in diploid cells. {ECO:0000269|PubMed:11676923,
ECO:0000269|PubMed:11711435, ECO:0000269|PubMed:11740566}.
-!- MISCELLANEOUS: Present with 377 molecules/cell in log phase SD medium.
{ECO:0000269|PubMed:14562106}.
-!- SIMILARITY: Belongs to the XRCC4-XLF family. XLF subfamily.
{ECO:0000305}.
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EMBL; AM296374; CAL35943.1; -; Genomic_DNA.
EMBL; AM296375; CAL35942.1; -; Genomic_DNA.
EMBL; AM296376; CAL35941.1; -; Genomic_DNA.
EMBL; AM296377; CAL35940.1; -; Genomic_DNA.
EMBL; AM296378; CAL35939.1; -; Genomic_DNA.
EMBL; AM296379; CAL35938.1; -; Genomic_DNA.
EMBL; AM296380; CAL35937.1; -; Genomic_DNA.
EMBL; AM296381; CAL35936.1; -; Genomic_DNA.
EMBL; AM296382; CAL36078.1; -; Genomic_DNA.
EMBL; AM296383; CAL35935.1; -; Genomic_DNA.
EMBL; AM296384; CAL35934.1; -; Genomic_DNA.
EMBL; AM296385; CAL35933.1; -; Genomic_DNA.
EMBL; AM296386; CAL35932.1; -; Genomic_DNA.
EMBL; U17244; AAB67382.1; -; Genomic_DNA.
EMBL; AY557954; AAS56280.1; -; Genomic_DNA.
EMBL; BK006945; DAA09579.1; -; Genomic_DNA.
PIR; S51402; S51402.
RefSeq; NP_013367.1; NM_001182152.1.
SMR; Q06148; -.
BioGRID; 31533; 107.
DIP; DIP-4776N; -.
IntAct; Q06148; 3.
MINT; Q06148; -.
STRING; 4932.YLR265C; -.
CarbonylDB; Q06148; -.
iPTMnet; Q06148; -.
MaxQB; Q06148; -.
PaxDb; Q06148; -.
PRIDE; Q06148; -.
EnsemblFungi; YLR265C_mRNA; YLR265C; YLR265C.
GeneID; 850970; -.
KEGG; sce:YLR265C; -.
SGD; S000004255; NEJ1.
VEuPathDB; FungiDB:YLR265C; -.
HOGENOM; CLU_799750_0_0_1; -.
InParanoid; Q06148; -.
OMA; KFQHQEF; -.
PRO; PR:Q06148; -.
Proteomes; UP000002311; Chromosome XII.
RNAct; Q06148; protein.
GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
GO; GO:0032807; C:DNA ligase IV complex; IPI:SGD.
GO; GO:0016021; C:integral component of membrane; IEA:UniProtKB-KW.
GO; GO:0070419; C:nonhomologous end joining complex; IBA:GO_Central.
GO; GO:0031965; C:nuclear membrane; IEA:UniProtKB-SubCell.
GO; GO:0005634; C:nucleus; IDA:SGD.
GO; GO:0045027; F:DNA end binding; IDA:SGD.
GO; GO:0006303; P:double-strand break repair via nonhomologous end joining; IMP:SGD.
GO; GO:0045002; P:double-strand break repair via single-strand annealing; IMP:SGD.
GO; GO:0035825; P:homologous recombination; IMP:SGD.
InterPro; IPR015381; XLF_fam.
Pfam; PF09302; XLF; 1.
1: Evidence at protein level;
Cytoplasm; DNA damage; DNA repair; Membrane; Nucleus; Reference proteome;
Transmembrane; Transmembrane helix.
CHAIN 1..342
/note="Non-homologous end-joining protein 1"
/id="PRO_0000268689"
TRANSMEM 27..47
/note="Helical"
/evidence="ECO:0000255"
TRANSMEM 129..149
/note="Helical"
/evidence="ECO:0000255"
REGION 270..342
/note="Disordered"
/evidence="ECO:0000256|SAM:MobiDB-lite"
COMPBIAS 278..294
/note="Basic and acidic residues"
/evidence="ECO:0000256|SAM:MobiDB-lite"
COMPBIAS 295..325
/note="Polar residues"
/evidence="ECO:0000256|SAM:MobiDB-lite"
VARIANT 17
/note="V -> I (in strain: DBVPG1135, DBVPG1373, DBVPG1378,
DBVPG1788, DBVPG1794, DBVPG1853, DBVPG3051, DBVPG6044,
DBVPG6763, DBVPG6765, SK1, Y55 and YPS128)"
/evidence="ECO:0000269|PubMed:16951060"
VARIANT 21
/note="N -> I (in strain: DBVPG1135, DBVPG1373, DBVPG1378,
DBVPG1788, DBVPG1794, DBVPG1853, DBVPG3051, DBVPG6763,
DBVPG6765 and SK1)"
/evidence="ECO:0000269|PubMed:16951060"
VARIANT 65
/note="Q -> E (in strain: YPS128)"
/evidence="ECO:0000269|PubMed:16951060"
VARIANT 105
/note="V -> A (in strain: YPS128)"
/evidence="ECO:0000269|PubMed:16951060"
VARIANT 161
/note="E -> Q (in strain: DBVPG1135, DBVPG1373, DBVPG1378,
DBVPG1788, DBVPG1794, DBVPG1853, DBVPG3051, DBVPG6763,
DBVPG6765 and SK1)"
/evidence="ECO:0000269|PubMed:16951060"
VARIANT 204
/note="D -> G (in strain: DBVPG6044 and Y55)"
/evidence="ECO:0000269|PubMed:16951060"
VARIANT 231
/note="L -> F (in strain: DBVPG1135, DBVPG1373, DBVPG1378,
DBVPG1788, DBVPG1794, DBVPG1853, DBVPG3051, DBVPG6763,
DBVPG6765 and SK1)"
/evidence="ECO:0000269|PubMed:16951060"
VARIANT 249
/note="K -> E (in strain: DBVPG1135, DBVPG1373, DBVPG1378,
DBVPG1788, DBVPG1794, DBVPG1853, DBVPG3051, DBVPG6763,
DBVPG6765 and SK1)"
/evidence="ECO:0000269|PubMed:16951060"
VARIANT 270
/note="A -> V (in strain: DBVPG1135, DBVPG1373, DBVPG1378,
DBVPG1788, DBVPG1794, DBVPG1853, DBVPG3051, DBVPG6763,
DBVPG6765 and SK1)"
/evidence="ECO:0000269|PubMed:16951060"
VARIANT 281
/note="R -> C (in strain: DBVPG1135, DBVPG1373, DBVPG1378,
DBVPG1788, DBVPG1794, DBVPG1853, DBVPG3051, DBVPG6763,
DBVPG6765 and SK1)"
/evidence="ECO:0000269|PubMed:16951060"
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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WP1676: Non-homologous end-joining
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WP1222: Non-homologous end joining
WP1324: Non-homologous end joining
WP1371: G Protein Signaling Pathways
WP753: Non-homologous end joining
WP1097: Non-homologous end joining
WP1201: Non-homologous end joining
WP1242: Non-homologous end joining
WP438: Non-homologous end joining
WP2199: Seed Development
WP1208: Non-homologous end joining
WP1570: Non-homologous end joining
WP1277: Non-homologous end joining
WP1692: Protein export
WP426: Urea cycle and metabolism of amino groups
WP1351: Apoptosis
WP1036: Homologous recombination
WP1644: DNA replication
WP79: Tryptophan metabolism
WP1411: Cell Division: First embryonic mitosis

Related Genes :
[ligD PA2138] Multifunctional non-homologous end joining protein LigD (NHEJ DNA polymerase) [Includes: 3'-phosphoesterase (3'-ribonuclease/3'-phosphatase); DNA ligase D (LigD) (EC 6.5.1.1) (Polydeoxyribonucleotide synthase [ATP]); DNA repair polymerase (Pol) (Polymerase/primase)]
[NEJ1 LIF2 YLR265C] Non-homologous end-joining protein 1
[NHEJ1 XLF] Non-homologous end-joining factor 1 (Protein cernunnos) (XRCC4-like factor)
[Nhej1 Xlf] Non-homologous end-joining factor 1 (Protein cernunnos) (XRCC4-like factor)
[ligD MSMEG_5570 MSMEI_5419] Multifunctional non-homologous end joining protein LigD (NHEJ DNA polymerase) [Includes: DNA repair polymerase (Pol) (Polymerase/primase); 3'-phosphoesterase (3'-ribonuclease/3'-phosphatase) (PE); DNA ligase (Lig) (EC 6.5.1.1) (Polydeoxyribonucleotide synthase [ATP])]
[ligD Rv0938 MTCY08D9.01c MTCY10D7.36c] Multifunctional non-homologous end joining DNA repair protein LigD (NHEJ DNA repair protein D) (Mt-Lig) (NHEJ DNA polymerase) [Includes: DNA repair polymerase (Pol) (Polymerase/primase); 3'-phosphoesterase (3'-ribonuclease/3'-phosphatase) (PE); DNA ligase (Lig) (EC 6.5.1.1) (Polydeoxyribonucleotide synthase [ATP])]
[IFFO1 IFFO] Non-homologous end joining factor IFFO1 (NHEJ factor IFFO1) (Intermediate filament family orphan 1) (Tumor antigen HOM-TES-103)
[CYREN C7orf49 MRI] Cell cycle regulator of non-homologous end joining (Cell cycle regulator of NHEJ) (Modulator of retrovirus infection homolog)
[ligd ykoU BSU13400] Bifunctional non-homologous end joining protein LigD (NHEJ DNA polymerase) [Includes: DNA ligase (Lig) (EC 6.5.1.1) (Polydeoxyribonucleotide synthase [ATP]); DNA repair polymerase (Pol) (Polymerase/primase)]
[Cyren Mri] Cell cycle regulator of non-homologous end joining (Cell cycle regulator of NHEJ) (Modulator of retrovirus infection homolog)
[ligD BQ2027_MB0963] Multifunctional non-homologous end joining protein LigD (NHEJ DNA polymerase) [Includes: DNA repair polymerase (Pol) (Polymerase/primase); 3'-phosphoesterase (3'-ribonuclease/3'-phosphatase) (PE); DNA ligase (Lig) (EC 6.5.1.1) (Polydeoxyribonucleotide synthase [ATP])]
[Iffo1 Iffo] Non-homologous end joining factor IFFO1 (NHEJ factor IFFO1) (Intermediate filament family orphan 1)
[ligD MT0965] Multifunctional non-homologous end joining DNA repair protein LigD (NHEJ DNA repair protein D) (Mt-Lig) (NHEJ DNA polymerase) [Includes: DNA repair polymerase (Pol) (Polymerase/primase); 3'-phosphoesterase (3'-ribonuclease/3'-phosphatase) (PE); DNA ligase (Lig) (EC 6.5.1.1) (Polydeoxyribonucleotide synthase [ATP])]
[Nhej1 Xlf] Non-homologous end-joining factor 1 (Protein cernunnos) (XRCC4-like factor)
[mku Rv0937c] Non-homologous end joining protein Ku (Mt-Ku)
[xlf1 mug104 nej1 SPCC24B10.14c] Xrcc4-like factor 1 (Meiotically up-regulated gene 104 protein) (Non-homologous end-joining protein 1)
[ku PA2150] Non-homologous end joining protein Ku
[] Core protein precursor (EC 2.7.7.48) (EC 3.4.21.98) (EC 3.6.1.15) (EC 3.6.4.13) (Envelope glycoprotein E1) (Envelope glycoprotein E2) (Genome polyprotein) (Gp32) (Hepacivirin) (Mature core protein) (NS1) (NS3 helicase) (NS3 protease) (NS3P) (NS5B) (Non-structural protein 4A) (Non-structural protein 4B) (Non-structural protein 5A) (Protease NS2) (RNA-directed RNA polymerase) (Serine protease/helicase NS3) (Viroporin p7) (Viroporin p70) (gp35) (gp68) (gp70) (p21) (p23) (p27) (p56/58) (p68) (p8)
[ku MSMEG_5580 MSMEI_5431] Non-homologous end joining protein Ku
[ku ykoV BSU13410] Non-homologous end joining protein Ku
[nhej1 xlf zgc:85657] Non-homologous end-joining factor 1 (Protein cernunnos) (XRCC4-like factor)
[CYREN MRI] Cell cycle regulator of non-homologous end joining (Cell cycle regulator of NHEJ) (Modulator of retrovirus infection)
[PSMD14 POH1] 26S proteasome non-ATPase regulatory subunit 14 (EC 3.4.19.-) (26S proteasome regulatory subunit RPN11) (26S proteasome-associated PAD1 homolog 1)
[Ddit3 Chop Chop10 Gadd153] DNA damage-inducible transcript 3 protein (DDIT-3) (C/EBP zeta) (C/EBP-homologous protein) (CHOP) (C/EBP-homologous protein 10) (CHOP-10) (CCAAT/enhancer-binding protein homologous protein) (Growth arrest and DNA-damage-inducible protein GADD153)
[Tesc Chp3] Calcineurin B homologous protein 3 (Tescalcin) (TE-1) (TSC)
[DDIT3 CHOP CHOP10 GADD153] DNA damage-inducible transcript 3 protein (DDIT-3) (C/EBP zeta) (C/EBP-homologous protein) (CHOP) (C/EBP-homologous protein 10) (CHOP-10) (CCAAT/enhancer-binding protein homologous protein) (Growth arrest and DNA damage-inducible protein GADD153)
[Nlrp1b Nalp1b] NACHT, LRR and PYD domains-containing protein 1b allele 1 (EC 3.4.-.-) [Cleaved into: NACHT, LRR and PYD domains-containing protein 1b, C-terminus (Nlrp1b1-CT); NACHT, LRR and PYD domains-containing protein 1b, N-terminus (Nlrp1b1-NT)]
[AIFM2 AMID PRG3] Ferroptosis suppressor protein 1 (FSP1) (EC 1.6.5.-) (Apoptosis-inducing factor homologous mitochondrion-associated inducer of death) (AMID) (p53-responsive gene 3 protein)
[PAIR2 ASY1 Os09g0506800 LOC_Os09g32930 OSNPB_090506800] Meiosis-specific protein PAIR2 (OsASY1) (Protein HOMOLOGOUS PAIRING ABERRATION IN RICE MEIOSIS 2)
[SPPL3 IMP2 PSL4] Signal peptide peptidase-like 3 (SPP-like 3) (EC 3.4.23.-) (Intramembrane protease 2) (IMP-2) (Presenilin homologous protein 1) (PSH1) (Presenilin-like protein 4)

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