LIF1_YEAST
ID LIF1_YEAST Reviewed; 421 AA.
AC P53150; D6VU55; E9P953;
DT 01-OCT-1996, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-1996, sequence version 1.
DT 03-AUG-2022, entry version 151.
DE RecName: Full=Ligase-interacting factor 1;
GN Name=LIF1; OrderedLocusNames=YGL090W;
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], FUNCTION, AND INTERACTION WITH DNL4.
RX PubMed=9670033; DOI=10.1093/emboj/17.14.4188;
RA Herrmann G., Lindahl T., Schar P.;
RT "Saccharomyces cerevisiae LIF1: a function involved in DNA double-strand
RT break repair related to mammalian XRCC4.";
RL EMBO J. 17:4188-4198(1998).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9290212;
RX DOI=10.1002/(sici)1097-0061(19970915)13:11<1077::aid-yea152>3.0.co;2-y;
RA Rieger M., Brueckner M., Schaefer M., Mueller-Auer S.;
RT "Sequence analysis of 203 kilobases from Saccharomyces cerevisiae
RT chromosome VII.";
RL Yeast 13:1077-1090(1997).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169869;
RA Tettelin H., Agostoni-Carbone M.L., Albermann K., Albers M., Arroyo J.,
RA Backes U., Barreiros T., Bertani I., Bjourson A.J., Brueckner M.,
RA Bruschi C.V., Carignani G., Castagnoli L., Cerdan E., Clemente M.L.,
RA Coblenz A., Coglievina M., Coissac E., Defoor E., Del Bino S., Delius H.,
RA Delneri D., de Wergifosse P., Dujon B., Durand P., Entian K.-D., Eraso P.,
RA Escribano V., Fabiani L., Fartmann B., Feroli F., Feuermann M.,
RA Frontali L., Garcia-Gonzalez M., Garcia-Saez M.I., Goffeau A.,
RA Guerreiro P., Hani J., Hansen M., Hebling U., Hernandez K., Heumann K.,
RA Hilger F., Hofmann B., Indge K.J., James C.M., Klima R., Koetter P.,
RA Kramer B., Kramer W., Lauquin G., Leuther H., Louis E.J., Maillier E.,
RA Marconi A., Martegani E., Mazon M.J., Mazzoni C., McReynolds A.D.K.,
RA Melchioretto P., Mewes H.-W., Minenkova O., Mueller-Auer S., Nawrocki A.,
RA Netter P., Neu R., Nombela C., Oliver S.G., Panzeri L., Paoluzi S.,
RA Plevani P., Portetelle D., Portillo F., Potier S., Purnelle B., Rieger M.,
RA Riles L., Rinaldi T., Robben J., Rodrigues-Pousada C.,
RA Rodriguez-Belmonte E., Rodriguez-Torres A.M., Rose M., Ruzzi M.,
RA Saliola M., Sanchez-Perez M., Schaefer B., Schaefer M., Scharfe M.,
RA Schmidheini T., Schreer A., Skala J., Souciet J.-L., Steensma H.Y.,
RA Talla E., Thierry A., Vandenbol M., van der Aart Q.J.M., Van Dyck L.,
RA Vanoni M., Verhasselt P., Voet M., Volckaert G., Wambutt R., Watson M.D.,
RA Weber N., Wedler E., Wedler H., Wipfli P., Wolf K., Wright L.F.,
RA Zaccaria P., Zimmermann M., Zollner A., Kleine K.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome VII.";
RL Nature 387:81-84(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 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 [6]
RP INTERACTION WITH NEJ1.
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 INTERACTION OF THE DNL4-LIF1 COMPLEX WITH POL4.
RX PubMed=12235149; DOI=10.1074/jbc.m206861200;
RA Tseng H.-M., Tomkinson A.E.;
RT "A physical and functional interaction between yeast Pol4 and Dnl4-Lif1
RT links DNA synthesis and ligation in nonhomologous end joining.";
RL J. Biol. Chem. 277:45630-45637(2002).
RN [8]
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 [9]
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 [10]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=19779198; DOI=10.1126/science.1172867;
RA Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.;
RT "Global analysis of Cdk1 substrate phosphorylation sites provides insights
RT into evolution.";
RL Science 325:1682-1686(2009).
RN [11]
RP X-RAY CRYSTALLOGRAPHY (3.92 ANGSTROMS) OF 1-246 IN COMPLEX WITH THE TANDEM
RP BRCT DOMAINS OF DNL4.
RX PubMed=16388993; DOI=10.1016/j.dnarep.2005.11.004;
RA Dore A.S., Furnham N., Davies O.R., Sibanda B.L., Chirgadze D.Y.,
RA Jackson S.P., Pellegrini L., Blundell T.L.;
RT "Structure of an Xrcc4-DNA ligase IV yeast ortholog complex reveals a novel
RT BRCT interaction mode.";
RL DNA Repair 5:362-368(2006).
CC -!- FUNCTION: Stabilizes DNL4. Involved in non-homologous repair of DNA
CC double-strand breaks. {ECO:0000269|PubMed:9670033}.
CC -!- SUBUNIT: Interacts with the BRCT domain of DNL4 and with NEJ1. The
CC DNL4-LIF1 complex interacts with POL4. {ECO:0000269|PubMed:11711435,
CC ECO:0000269|PubMed:12235149, ECO:0000269|PubMed:16388993,
CC ECO:0000269|PubMed:9670033}.
CC -!- INTERACTION:
CC P53150; Q08387: DNL4; NbExp=3; IntAct=EBI-23865, EBI-5983;
CC P53150; Q06148: NEJ1; NbExp=4; IntAct=EBI-23865, EBI-34047;
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:14562095}. Nucleus
CC {ECO:0000269|PubMed:14562095}.
CC -!- MISCELLANEOUS: Present with 876 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; Z72612; CAA96796.1; -; Genomic_DNA.
DR EMBL; AY723807; AAU09724.1; -; Genomic_DNA.
DR EMBL; BK006941; DAA08016.1; -; Genomic_DNA.
DR PIR; S64097; S64097.
DR RefSeq; NP_011425.1; NM_001180955.1.
DR PDB; 1Z56; X-ray; 3.92 A; A/B=1-246.
DR PDBsum; 1Z56; -.
DR AlphaFoldDB; P53150; -.
DR SMR; P53150; -.
DR BioGRID; 33161; 81.
DR ComplexPortal; CPX-1665; DNA ligase IV complex.
DR DIP; DIP-5477N; -.
DR IntAct; P53150; 10.
DR MINT; P53150; -.
DR STRING; 4932.YGL090W; -.
DR iPTMnet; P53150; -.
DR MaxQB; P53150; -.
DR PaxDb; P53150; -.
DR PRIDE; P53150; -.
DR EnsemblFungi; YGL090W_mRNA; YGL090W; YGL090W.
DR GeneID; 852790; -.
DR KEGG; sce:YGL090W; -.
DR SGD; S000003058; LIF1.
DR VEuPathDB; FungiDB:YGL090W; -.
DR eggNOG; ENOG502S010; Eukaryota.
DR HOGENOM; CLU_053373_0_0_1; -.
DR InParanoid; P53150; -.
DR OMA; EFICCVP; -.
DR BioCyc; YEAST:G3O-30590-MON; -.
DR EvolutionaryTrace; P53150; -.
DR PRO; PR:P53150; -.
DR Proteomes; UP000002311; Chromosome VII.
DR RNAct; P53150; protein.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0032807; C:DNA ligase IV complex; IPI:SGD.
DR GO; GO:0005634; C:nucleus; IDA:SGD.
DR GO; GO:0003682; F:chromatin binding; IDA:SGD.
DR GO; GO:0006303; P:double-strand break repair via nonhomologous end joining; IDA:SGD.
DR Gene3D; 1.20.5.370; -; 1.
DR InterPro; IPR014751; XRCC4-like_C.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; DNA damage; DNA repair; Nucleus;
KW Reference proteome.
FT CHAIN 1..421
FT /note="Ligase-interacting factor 1"
FT /id="PRO_0000084419"
FT REGION 365..421
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 388..402
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT CONFLICT 44
FT /note="S -> G (in Ref. 5; AAU09724)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 421 AA; 48259 MW; 5BEDC72059E9996F CRC64;
MSQLTEFISC IPVVNEEQNE EDERGLCKIQ IEDGAMLETL DENSLSGLRI EKMLVSEGTG
IFSKSSFGIN DLRIFTGENI DEESKKYVWY ELLKMLTGHK VYIASLDEKV VFTKWTCRMQ
DDEVWKVVME LESSAIIRKI AELTLHPVKK GEIDLFEMAD KLYKDICCVN DSYRNIKESD
SSNRNRVEQL ARERELLDKL LETRDERTRA MMVTLLNEKK KKIRELHEIL RQNNIKLSDD
DVLDSALINT EVQKPISELN SPGKRMKRRK TVVEPQNLQK KLKDTSRRRA NRKISNQSVI
KMEDDDFDDF QFFGLSKRPI ITAKDKLSEK YDDITSFGDD TQSISFESDS SSDVQKHLVS
LEDNGIQISA GRSDEDYGDI SGSESETDAS AGEKKSSNHS EQSGNDREPC LQTESETDIE
T
