Reviewed, UniProtKB/Swiss-Prot P06777 (RAD1_YEAST)

Names and origin

Protein names

Recommended name:
    DNA repair protein RAD1

Gene names

Name:	RAD1
Ordered Locus Names:	YPL022W

Organism

Saccharomyces cerevisiae (Baker's yeast) [Complete proteome]

Taxonomic identifier

4932 [NCBI]

Taxonomic lineage

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

Protein attributes

Sequence length	1100 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	Involved in nucleotide excision repair of DNA damaged with UV light, bulky adducts, or cross-linking agents. Along with RAD10 forms an endonuclease that specifically degrades single-stranded DNA. Ref.4
Subunit structure	Component of the nucleotide excision repair factor 1 (NEF1) complex consisting of RAD1, RAD10 and RAD14. Interacts with SAW1. Ref.4 Ref.7 Ref.9
Subcellular location	Nucleus.
Miscellaneous	Present with 1400 molecules/cell in log phase SD medium. Ref.6
Sequence similarities	Belongs to the XPF family.
Sequence caution	The sequence AAA34929.1 differs from that shown. Reason: Frameshift at positions 923, 934 and 948.

Ontologies

Keywords
Biological process	DNA damage DNA repair
Cellular component	Nucleus
Ligand	DNA-binding
Molecular function	Endonuclease Hydrolase Nuclease
PTM	Phosphoprotein
Technical term	Complete proteome
Gene Ontology (GO)
Biological process	double-strand break repair via single-strand annealing, removal of nonhomologous ends Inferred from mutant phenotype. Source: SGD meiotic mismatch repair Inferred from mutant phenotype. Source: SGD nucleotide-excision repair, DNA incision, 5'-to lesion Inferred from direct assay. Source: SGD removal of nonhomologous ends Inferred from mutant phenotype. Source: SGD
Cellular component	nucleotide-excision repair factor 1 complex Ref.5 Inferred from physical interaction. Source: SGD
Molecular function	endonuclease activity Inferred from electronic annotation. Source: UniProtKB-KW protein binding Ref.5 Inferred from physical interaction. Source: IntAct single-stranded DNA binding Inferred from direct assay. Source: SGD
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
RAD10	P06838	1	EBI-14752,EBI-14637
RAD14	P28519	1	EBI-14752,EBI-14641
SAW1	P39735	1	EBI-14752,EBI-20627
SLX4	Q12098	1	EBI-14752,EBI-37788

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 1100	1100	DNA repair protein RAD1		PRO_0000198857
Regions
	Compositional bias	1 – 110	110	Asp/Glu-rich (acidic)
	Compositional bias	516 – 576	61	Arg/Lys-rich (basic)
	Compositional bias	595 – 689	95	Asp/Glu-rich (acidic)
	Compositional bias	1041 – 1100	60	Asp/Glu-rich (acidic)
Amino acid modifications
	Modified residue	1071	1	Phosphoserine Ref.8
	Modified residue	1072	1	Phosphothreonine Ref.8
Experimental info
	Sequence conflict	223	1	D → N in AAA34929. Ref.3
	Sequence conflict	883	1	C → Y in AAA34929. Ref.3
	Sequence conflict	886	1	M → I in AAA34929. Ref.3
	Sequence conflict	912	1	E → K in AAA34929. Ref.3
	Sequence conflict	924	1	V → I in AAA34929. Ref.3
	Sequence conflict	1016	1	G → R in AAA34929. Ref.3

Sequences

	Sequence		Length	Mass (Da)
	P06777-1 [UniParc]. Last modified January 1, 1988. Version 1. Checksum: 06FDA601F3F59B10	FASTA	1,100	126,370
	10 20 30 40 50 60 MSQLFYQGDS DDELQEELTR QTTQASQSSK IKNEDEPDDS NHLNEVENED SKVLDDDAVL 70 80 90 100 110 120 YPLIPNEPDD IETSKPNIND IRPVDIQLTL PLPFQQKVVE NSLITEDALI IMGKGLGLLD 130 140 150 160 170 180 IVANLLHVLA TPTSINGQLK RALVLVLNAK PIDNVRIKEA LEELSWFSNT GKDDDDTAVE 190 200 210 220 230 240 SDDELFERPF NVVTADSLSI EKRRKLYISG GILSITSRIL IVDLLSGIVH PNRVTGMLVL 250 260 270 280 290 300 NADSLRHNSN ESFILEIYRS KNTWGFIKAF SEAPETFVME FSPLRTKMKE LRLKNVLLWP 310 320 330 340 350 360 RFRVEVSSCL NATNKTSHNK VIEVKVSLTN SMSQIQFGLM ECLKKCIAEL SRKNPELALD 370 380 390 400 410 420 WWNMENVLDI NFIRSIDSVM VPNWHRISYE SKQLVKDIRF LRHLLKMLVT SDAVDFFGEI 430 440 450 460 470 480 QLSLDANKPS VSRKYSESPW LLVDEAQLVI SYAKKRIFYK NEYTLEENPK WEQLIHILHD 490 500 510 520 530 540 ISHERMTNHL QGPTLVACSD NLTCLELAKV LNASNKKRGV RQVLLNKLKW YRKQREETKK 550 560 570 580 590 600 LVKEVQSQDT FPENATLNVS STFSKEQVTT KRRRTRGASQ VAAVEKLRNA GTNVDMEVVF 610 620 630 640 650 660 EDHKLSEEIK KGSGDDLDDG QEENAANDSK IFEIQEQENE ILIDDGDAEF DNGELEYVGD 670 680 690 700 710 720 LPQHITTHFN KDLWAEHCNE YEYVDRQDEI LISTFKSLND NCSLQEMMPS YIIMFEPDIS 730 740 750 760 770 780 FIRQIEVYKA IVKDLQPKVY FMYYGESIEE QSHLTAIKRE KDAFTKLIRE NANLSHHFET 790 800 810 820 830 840 NEDLSHYKNL AERKLKLSKL RKSNTRNAGG QQGFHNLTQD VVIVDTREFN ASLPGLLYRY 850 860 870 880 890 900 GIRVIPCMLT VGDYVITPDI CLERKSISDL IGSLQNNRLA NQCKKMLKYY AYPTLLIEFD 910 920 930 940 950 960 EGQSFSLEPF SERRNYKNKD ISTVHPISSK LSQDEIQLKL AKLVLRFPTL KIIWSSSPLQ 970 980 990 1000 1010 1020 TVNIILELKL GREQPDPSNA VILGTNKVRS DFNSTAKGLK DGDNESKFKR LLNVPGVSKI 1030 1040 1050 1060 1070 1080 DYFNLRKKIK SFNKLQKLSW NEINELINDE DLTDRIYYFL RTEKEEQEQE STDENLESPG 1090 1100 KTTDDNALHD HHNDVPEAPV

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Nucleotide sequence and functional analysis of the RAD1 gene of Saccharomyces cerevisiae." Reynolds P., Prakash L., Prakash S. Mol. Cell. Biol. 7:1012-1020(1987) [PubMed: 3550428] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"The nucleotide sequence of Saccharomyces cerevisiae chromosome XVI." Bussey H., Storms R.K., Ahmed A., Albermann K., Allen E., Ansorge W., Araujo R., Aparicio A., Barrell B.G., Badcock K., Benes V., Botstein D., Bowman S., Brueckner M., Carpenter J., Cherry J.M., Chung E., Churcher C.M. , Coster F., Davis K., Davis R.W., Dietrich F.S., Delius H., DiPaolo T., Dubois E., Duesterhoeft A., Duncan M., Floeth M., Fortin N., Friesen J.D., Fritz C., Goffeau A., Hall J., Hebling U., Heumann K., Hilbert H., Hillier L.W., Hunicke-Smith S., Hyman R.W., Johnston M., Kalman S., Kleine K., Komp C., Kurdi O., Lashkari D., Lew H., Lin A., Lin D., Louis E.J., Marathe R., Messenguy F., Mewes H.-W., Mirtipati S., Moestl D., Mueller-Auer S., Namath A., Nentwich U., Oefner P., Pearson D., Petel F.X., Pohl T.M., Purnelle B., Rajandream M.A., Rechmann S., Rieger M., Riles L., Roberts D., Schaefer M., Scharfe M., Scherens B., Schramm S., Schroeder M., Sdicu A.-M., Tettelin H., Urrestarazu L.A., Ushinsky S., Vierendeels F., Vissers S., Voss H., Walsh S.V., Wambutt R., Wang Y., Wedler E., Wedler H., Winnett E., Zhong W.-W., Zollner A., Vo D.H., Hani J. Nature 387:103-105(1997) [PubMed: 9169875] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204511 / S288c / AB972.
[3]	"Molecular cloning and nucleotide sequence analysis of the Saccharomyces cerevisiae RAD1 gene." Yang E., Friedberg E.C. Mol. Cell. Biol. 4:2161-2169(1984) [PubMed: 6095044] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-1035.
[4]	"Yeast DNA repair and recombination proteins Rad1 and Rad10 constitute a single-stranded-DNA endonuclease." Tomkinson A.E., Bardwell A.J., Bardwell L., Tappe N.J., Friedberg E.C. Nature 362:860-862(1993) [PubMed: 8479526] [Abstract] Cited for: FUNCTION, INTERACTION WITH RAD10.
[5]	"Nucleotide excision repair in yeast is mediated by sequential assembly of repair factors and not by a pre-assembled repairosome." Guzder S.N., Sung P., Prakash L., Prakash S. J. Biol. Chem. 271:8903-8910(1996) [PubMed: 8621533] [Abstract] Cited for: IDENTIFICATION IN THE NEF1 COMPLEX.
[6]	"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: 14562106] [Abstract] Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[7]	"Examining protein protein interactions using endogenously tagged yeast arrays: the cross-and-capture system." Suter B., Fetchko M.J., Imhof R., Graham C.I., Stoffel-Studer I., Zbinden C., Raghavan M., Lopez L., Beneti L., Hort J., Fillingham J., Greenblatt J.F., Giaever G., Nislow C., Stagljar I. Genome Res. 17:1774-1782(2007) [PubMed: 17989249] [Abstract] Cited for: INTERACTION WITH SAW1.
[8]	"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: 17563356] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-1071 AND THR-1072, MASS SPECTROMETRY.
[9]	"Microarray-based genetic screen defines SAW1, a gene required for Rad1/Rad10-dependent processing of recombination intermediates." Li F., Dong J., Pan X., Oum J.-H., Boeke J.D., Lee S.E. Mol. Cell 30:325-335(2008) [PubMed: 18471978] [Abstract] Cited for: INTERACTION WITH SAW1.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBLGenBankDDBJ	M15435 Genomic DNA. Translation: AAA34934.1. U36624 Genomic DNA. Translation: AAB68165.1. K02070 Genomic DNA. Translation: AAA34929.1. Frameshift.
PIR	DDBYD1. A26129.
RefSeq	NP_015303.1.
3D structure databases
ModBase	Search...
Protein-protein interaction databases
DIP	DIP:2424N.
IntAct	P06777. 36 interactions.
STRING	P06777.
Proteomic databases
PeptideAtlas	P06777.
PRIDE	P06777.
Genome annotation databases
Ensembl	YPL022W; YPL022W; YPL022W; Saccharomyces cerevisiae. [Genome view]
GeneID	856085.
KEGG	sce:YPL022W.
NMPDR	fig|4932.3.peg.6437.
Organism-specific databases
CYGD	YPL022w.
SGD	S000005943. RAD1.
Phylogenomic databases
HOGENOM	P06777.
OMA	FMYYGES
OrthoDB	EOG9M0GJ1
Gene expression databases
ArrayExpress	P06777.
Genevestigator	P06777.
GermOnline	YPL022W. Saccharomyces cerevisiae.
Family and domain databases
InterPro	IPR020819. DNA_repair_nuc_XPF/helicase. IPR006166. ERCC4_domain. IPR006167. Rad1. IPR011335. Restrict_endonuc_II-like_core. [Graphical view]
Gene3D	G3DSA:3.40.50.10130. DNA_repair_nuc_XPF/helicase. 1 hit.
Pfam	PF02732. ERCC4. 1 hit. [Graphical view]
SMART	SM00891. ERCC4. 1 hit. [Graphical view]
TIGRFAMs	TIGR00596. rad1. 1 hit.
ProtoNet	Search...
Other Resources
NextBio	981101.

Entry information

Entry name

RAD1_YEAST

Accession

Primary (citable) accession number: P06777

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 1, 1988
Last sequence update:	January 1, 1988
Last modified:	November 24, 2009
This is version 89 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

FPAP (Fungal Proteome Annotation Project)