Ligase-interacting factor 1 - Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)

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P53150 (LIF1_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified April 3, 2013. Version 92. History...

Clusters with 100%, 90%, 50% identity |

Documents (3) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
Ligase-interacting factor 1

Gene names

Name:	LIF1
Ordered Locus Names:	YGL090W

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

Eukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces ›

Protein attributes

Sequence length	421 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Stabilizes DNL4. Involved in non-homologous repair of DNA double-strand breaks. Ref.1
Subunit structure	Interacts with the BRCT domain of DNL4 and with NEJ1. The DNL4-LIF1 complex interacts with POL4. Ref.1 Ref.6 Ref.7
Subcellular location	Cytoplasm. Nucleus Ref.8.
Miscellaneous	Present with 876 molecules/cell in log phase SD medium.

Ontologies

Keywords
Biological process	DNA damage DNA repair
Cellular component	Cytoplasm Nucleus
PTM	Phosphoprotein
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	DNA recombination Inferred from electronic annotation. Source: InterPro double-strand break repair via nonhomologous end joining Inferred from direct assay PubMed 15342630. Source: SGD
Cellular_component	DNA ligase IV complex Inferred from physical interaction PubMed 17567543. Source: SGD cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	DNA binding Inferred from electronic annotation. Source: InterPro chromatin binding Inferred from direct assay PubMed 10679327. Source: SGD
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
DNL4	Q08387	3	EBI-23865,EBI-5983

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 421

421

Ligase-interacting factor 1

PRO_0000084419

Amino acid modifications

Modified residue

261

Phosphoserine Ref.10

Experimental info

Sequence conflict

S → G in AAU09724. Ref.5

Secondary structure

421

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

P53150 [UniParc].

Last modified October 1, 1996. Version 1.
Checksum: 5BEDC72059E9996F
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FASTA

421

48,259

        10         20         30         40         50         60 
MSQLTEFISC IPVVNEEQNE EDERGLCKIQ IEDGAMLETL DENSLSGLRI EKMLVSEGTG 

        70         80         90        100        110        120 
IFSKSSFGIN DLRIFTGENI DEESKKYVWY ELLKMLTGHK VYIASLDEKV VFTKWTCRMQ 

       130        140        150        160        170        180 
DDEVWKVVME LESSAIIRKI AELTLHPVKK GEIDLFEMAD KLYKDICCVN DSYRNIKESD 

       190        200        210        220        230        240 
SSNRNRVEQL ARERELLDKL LETRDERTRA MMVTLLNEKK KKIRELHEIL RQNNIKLSDD 

       250        260        270        280        290        300 
DVLDSALINT EVQKPISELN SPGKRMKRRK TVVEPQNLQK KLKDTSRRRA NRKISNQSVI 

       310        320        330        340        350        360 
KMEDDDFDDF QFFGLSKRPI ITAKDKLSEK YDDITSFGDD TQSISFESDS SSDVQKHLVS 

       370        380        390        400        410        420 
LEDNGIQISA GRSDEDYGDI SGSESETDAS AGEKKSSNHS EQSGNDREPC LQTESETDIE 


T

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Saccharomyces cerevisiae LIF1: a function involved in DNA double-strand break repair related to mammalian XRCC4." Herrmann G., Lindahl T., Schar P. EMBO J. 17:4188-4198(1998) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, INTERACTION WITH DNL4.
[2]	"Sequence analysis of 203 kilobases from Saccharomyces cerevisiae chromosome VII." Rieger M., Brueckner M., Schaefer M., Mueller-Auer S. Yeast 13:1077-1090(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[3]	"The nucleotide sequence of Saccharomyces cerevisiae chromosome VII." Tettelin H., Agostoni-Carbone M.L., Albermann K., Albers M., Arroyo J., Backes U., Barreiros T., Bertani I., Bjourson A.J., Brueckner M., Bruschi C.V., Carignani G., Castagnoli L., Cerdan E., Clemente M.L., Coblenz A., Coglievina M., Coissac E. Kleine K. Nature 387:81-84(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 96604 / S288c / FY1679.
[4]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[5]	"Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae." 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. LaBaer J. Genome Res. 17:536-543(2007) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[6]	"NHEJ regulation by mating type is exercised through a novel protein, Lif2p, essential to the ligase IV pathway." Frank-Vaillant M., Marcand S. Genes Dev. 15:3005-3012(2001) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH NEJ1.
[7]	"A physical and functional interaction between yeast Pol4 and Dnl4-Lif1 links DNA synthesis and ligation in nonhomologous end joining." Tseng H.-M., Tomkinson A.E. J. Biol. Chem. 277:45630-45637(2002) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION OF THE DNL4-LIF1 COMPLEX WITH POL4.
[8]	"Global analysis of protein localization in budding yeast." Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W., Weissman J.S., O'Shea E.K. Nature 425:686-691(2003) [PubMed] [Europe PMC] [Abstract] Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
[9]	"Global analysis of protein expression in yeast." Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S. Nature 425:737-741(2003) [PubMed] [Europe PMC] [Abstract] Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[10]	"Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases." Smolka M.B., Albuquerque C.P., Chen S.H., Zhou H. Proc. Natl. Acad. Sci. U.S.A. 104:10364-10369(2007) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-261, MASS SPECTROMETRY.
[11]	"Structure of an Xrcc4-DNA ligase IV yeast ortholog complex reveals a novel BRCT interaction mode." Dore A.S., Furnham N., Davies O.R., Sibanda B.L., Chirgadze D.Y., Jackson S.P., Pellegrini L., Blundell T.L. DNA Repair 5:362-368(2006) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.92 ANGSTROMS) OF 1-246 IN COMPLEX WITH THE TANDEM BRCT DOMAINS OF DNL4.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

Z72612 Genomic DNA. Translation: CAA96796.1.
AY723807 Genomic DNA. Translation: AAU09724.1.
BK006941 Genomic DNA. Translation: DAA08016.1.

PIR

S64097.

RefSeq

NP_011425.1. NM_001180955.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1Z56	X-ray	3.92	A/B	1-246	[»]

ProteinModelPortal

P53150.

SMR

P53150. Positions 159-235.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-5477N.

IntAct

P53150. 9 interactions.

MINT

MINT-492607.

STRING

4932.YGL090W.

Proteomic databases

PaxDb

P53150.

PeptideAtlas

P53150.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YGL090W; YGL090W; YGL090W.

GeneID

852790.

KEGG

sce:YGL090W.

Organism-specific databases

CYGD

YGL090w.

SGD

S000003058. LIF1.

Phylogenomic databases

eggNOG

NOG72265.

K10982.

OrthoDB

EOG4JDMHG.

Gene expression databases

Genevestigator

P53150.

GermOnline

YGL090W. Saccharomyces cerevisiae.

Family and domain databases

Gene3D

1.20.5.370. 1 hit.

InterPro

IPR015381. XLF/Cernunnos.
IPR014751. XRCC4_C.
[Graphical view]

Pfam

PF09302. XLF. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P53150.

NextBio

972288.

Entry information

Entry name

LIF1_YEAST

Accession

Primary (citable) accession number: P53150
Secondary accession number(s): D6VU55, E9P953

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 1, 1996
Last sequence update:	October 1, 1996
Last modified:	April 3, 2013
This is version 92 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program

Relevant documents

Yeast

Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD

Yeast chromosome VII

Yeast (Saccharomyces cerevisiae) chromosome VII: entries and gene names

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

Names·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Binary interactions

With

Entry

#Exp.

IntAct

Notes

Sequence annotation (Features)

Molecule processing

Amino acid modifications

Experimental info

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Gene expression databases

Family and domain databases

Other

Entry information

Relevant documents