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Protein

Replication factor A protein 1

Gene

RFA1

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

As part of the replication protein A (RPA/RP-A), a single-stranded DNA-binding heterotrimeric complex, may play an essential role in DNA replication, recombination and repair. Binds and stabilizes single-stranded DNA intermediates, preventing complementary DNA reannealing and recruiting different proteins involved in DNA metabolism. Binds to single-stranded sequences participating in DNA replication in addition to those mediating transcriptional repression (URS1) and activation (CAR1). Stimulates the activity of a cognate strand exchange protein (SEP1). It cooperates with T-AG and DNA topoisomerase I to unwind template DNA containing the simian virus 40 origin of DNA replication.

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
DNA bindingi197 – 28488OBAdd
BLAST
Zinc fingeri486 – 50823C4-typeSequence analysisAdd
BLAST

GO - Molecular functioni

  • double-stranded DNA binding Source: SGD
  • metal ion binding Source: UniProtKB-KW
  • sequence-specific DNA binding Source: SGD
  • single-stranded DNA binding Source: SGD

GO - Biological processi

  • DNA repair Source: CACAO
  • DNA replication Source: SGD
  • DNA topological change Source: SGD
  • DNA unwinding involved in DNA replication Source: SGD
  • double-strand break repair via homologous recombination Source: SGD
  • establishment of protein localization Source: SGD
  • heteroduplex formation Source: SGD
  • mitotic recombination Source: SGD
  • nucleotide-excision repair Source: SGD
  • protein ubiquitination Source: SGD
  • reciprocal meiotic recombination Source: SGD
  • sporulation Source: CACAO
  • telomere maintenance via recombination Source: SGD
  • telomere maintenance via telomerase Source: SGD
  • telomere maintenance via telomere lengthening Source: SGD
Complete GO annotation...

Keywords - Biological processi

DNA replication

Keywords - Ligandi

DNA-binding, Metal-binding, Zinc

Enzyme and pathway databases

BioCyciYEAST:G3O-28869-MONOMER.
ReactomeiR-SCE-110312. Translesion synthesis by REV1.
R-SCE-110314. Recognition of DNA damage by PCNA-containing replication complex.
R-SCE-110320. Translesion Synthesis by POLH.
R-SCE-3108214. SUMOylation of DNA damage response and repair proteins.
R-SCE-5651801. PCNA-Dependent Long Patch Base Excision Repair.
R-SCE-5655862. Translesion synthesis by POLK.
R-SCE-5656121. Translesion synthesis by POLI.
R-SCE-5656169. Termination of translesion DNA synthesis.
R-SCE-5696395. Formation of Incision Complex in GG-NER.
R-SCE-5696397. Gap-filling DNA repair synthesis and ligation in GG-NER.
R-SCE-5696400. Dual Incision in GG-NER.
R-SCE-6782135. Dual incision in TC-NER.
R-SCE-6782210. Gap-filling DNA repair synthesis and ligation in TC-NER.
R-SCE-68962. Activation of the pre-replicative complex.
R-SCE-69166. Removal of the Flap Intermediate.

Names & Taxonomyi

Protein namesi
Recommended name:
Replication factor A protein 1
Short name:
RF-A protein 1
Alternative name(s):
DNA-binding protein BUF2
Replication protein A 69 kDa DNA-binding subunit
Single-stranded DNA-binding protein
Gene namesi
Name:RFA1
Synonyms:BUF2, RPA1
Ordered Locus Names:YAR007C
ORF Names:FUN3
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome I

Organism-specific databases

EuPathDBiFungiDB:YAR007C.
SGDiS000000065. RFA1.

Subcellular locationi

GO - Cellular componenti

  • chromosome, telomeric region Source: SGD
  • condensed nuclear chromosome Source: SGD
  • cytoplasm Source: SGD
  • cytosol Source: SGD
  • DNA replication factor A complex Source: SGD
  • nucleus Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemovedCombined sources
Chaini2 – 621620Replication factor A protein 1PRO_0000097268Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei2 – 21N-acetylserineCombined sources
Modified residuei178 – 1781Phosphoserine; by ATM or ATRCombined sources

Post-translational modificationi

The N-terminus is blocked.

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

MaxQBiP22336.

PTM databases

iPTMnetiP22336.

Interactioni

Subunit structurei

Component of the heterotrimeric canonical replication protein A complex (RPA). Interacts with POB3.1 Publication

Binary interactionsi

WithEntry#Exp.IntActNotes
POB3Q046363EBI-14971,EBI-27863
RFA2P267544EBI-14971,EBI-14976
SGS1P351875EBI-14971,EBI-17059
YKU80Q044372EBI-14971,EBI-8224

Protein-protein interaction databases

BioGridi31793. 196 interactions.
DIPiDIP-2512N.
IntActiP22336. 33 interactions.
MINTiMINT-476157.

Structurei

Secondary structure

1
621
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi187 – 1893Combined sources
Turni192 – 1943Combined sources
Beta strandi198 – 21316Combined sources
Beta strandi218 – 22811Combined sources
Beta strandi231 – 2377Combined sources
Helixi239 – 24810Combined sources
Beta strandi251 – 2599Combined sources
Beta strandi261 – 2644Combined sources
Turni267 – 2693Combined sources
Beta strandi270 – 2745Combined sources
Beta strandi276 – 2805Combined sources
Beta strandi285 – 2895Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1YNXNMR-A181-294[»]
ProteinModelPortaliP22336.
SMRiP22336. Positions 181-615.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP22336.

Family & Domainsi

Sequence similaritiesi

Contains 1 OB DNA-binding domain.Curated

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri486 – 50823C4-typeSequence analysisAdd
BLAST

Keywords - Domaini

Zinc-finger

Phylogenomic databases

GeneTreeiENSGT00390000012403.
HOGENOMiHOG000162322.
InParanoidiP22336.
KOiK07466.
OMAiNDVGPRR.
OrthoDBiEOG71P2KR.

Family and domain databases

Gene3Di2.40.50.140. 4 hits.
InterProiIPR012340. NA-bd_OB-fold.
IPR004365. NA-bd_OB_tRNA.
IPR013955. Rep_factor-A_C.
IPR007199. Rep_factor-A_N.
IPR031657. REPA_OB_2.
IPR004591. Rfa1.
[Graphical view]
PfamiPF04057. Rep-A_N. 1 hit.
PF08646. Rep_fac-A_C. 1 hit.
PF16900. REPA_OB_2. 1 hit.
PF01336. tRNA_anti-codon. 1 hit.
[Graphical view]
SUPFAMiSSF50249. SSF50249. 4 hits.
TIGRFAMsiTIGR00617. rpa1. 1 hit.

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P22336-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSSVQLSRGD FHSIFTNKQR YDNPTGGVYQ VYNTRKSDGA NSNRKNLIMI
60 70 80 90 100
SDGIYHMKAL LRNQAASKFQ SMELQRGDII RVIIAEPAIV RERKKYVLLV
110 120 130 140 150
DDFELVQSRA DMVNQTSTFL DNYFSEHPNE TLKDEDITDS GNVANQTNAS
160 170 180 190 200
NAGVPDMLHS NSNLNANERK FANENPNSQK TRPIFAIEQL SPYQNVWTIK
210 220 230 240 250
ARVSYKGEIK TWHNQRGDGK LFNVNFLDTS GEIRATAFND FATKFNEILQ
260 270 280 290 300
EGKVYYVSKA KLQPAKPQFT NLTHPYELNL DRDTVIEECF DESNVPKTHF
310 320 330 340 350
NFIKLDAIQN QEVNSNVDVL GIIQTINPHF ELTSRAGKKF DRRDITIVDD
360 370 380 390 400
SGFSISVGLW NQQALDFNLP EGSVAAIKGV RVTDFGGKSL SMGFSSTLIP
410 420 430 440 450
NPEIPEAYAL KGWYDSKGRN ANFITLKQEP GMGGQSAASL TKFIAQRITI
460 470 480 490 500
ARAQAENLGR SEKGDFFSVK AAISFLKVDN FAYPACSNEN CNKKVLEQPD
510 520 530 540 550
GTWRCEKCDT NNARPNWRYI LTISIIDETN QLWLTLFDDQ AKQLLGVDAN
560 570 580 590 600
TLMSLKEEDP NEFTKITQSI QMNEYDFRIR AREDTYNDQS RIRYTVANLH
610 620
SLNYRAEADY LADELSKALL A
Length:621
Mass (Da):70,348
Last modified:August 1, 1991 - v1
Checksum:i7EB8DFA6910EF8A8
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X59748 Genomic DNA. Translation: CAA42420.1.
M60262 Genomic DNA. Translation: AAA34994.1.
S64901 Genomic DNA. Translation: AAB27889.1.
L22015 Genomic DNA. Translation: AAC04960.1.
BK006935 Genomic DNA. Translation: DAA06989.1.
PIRiS20145.
RefSeqiNP_009404.1. NM_001178211.1.

Genome annotation databases

EnsemblFungiiYAR007C; YAR007C; YAR007C.
GeneIDi851266.
KEGGisce:YAR007C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X59748 Genomic DNA. Translation: CAA42420.1.
M60262 Genomic DNA. Translation: AAA34994.1.
S64901 Genomic DNA. Translation: AAB27889.1.
L22015 Genomic DNA. Translation: AAC04960.1.
BK006935 Genomic DNA. Translation: DAA06989.1.
PIRiS20145.
RefSeqiNP_009404.1. NM_001178211.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1YNXNMR-A181-294[»]
ProteinModelPortaliP22336.
SMRiP22336. Positions 181-615.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi31793. 196 interactions.
DIPiDIP-2512N.
IntActiP22336. 33 interactions.
MINTiMINT-476157.

PTM databases

iPTMnetiP22336.

Proteomic databases

MaxQBiP22336.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYAR007C; YAR007C; YAR007C.
GeneIDi851266.
KEGGisce:YAR007C.

Organism-specific databases

EuPathDBiFungiDB:YAR007C.
SGDiS000000065. RFA1.

Phylogenomic databases

GeneTreeiENSGT00390000012403.
HOGENOMiHOG000162322.
InParanoidiP22336.
KOiK07466.
OMAiNDVGPRR.
OrthoDBiEOG71P2KR.

Enzyme and pathway databases

BioCyciYEAST:G3O-28869-MONOMER.
ReactomeiR-SCE-110312. Translesion synthesis by REV1.
R-SCE-110314. Recognition of DNA damage by PCNA-containing replication complex.
R-SCE-110320. Translesion Synthesis by POLH.
R-SCE-3108214. SUMOylation of DNA damage response and repair proteins.
R-SCE-5651801. PCNA-Dependent Long Patch Base Excision Repair.
R-SCE-5655862. Translesion synthesis by POLK.
R-SCE-5656121. Translesion synthesis by POLI.
R-SCE-5656169. Termination of translesion DNA synthesis.
R-SCE-5696395. Formation of Incision Complex in GG-NER.
R-SCE-5696397. Gap-filling DNA repair synthesis and ligation in GG-NER.
R-SCE-5696400. Dual Incision in GG-NER.
R-SCE-6782135. Dual incision in TC-NER.
R-SCE-6782210. Gap-filling DNA repair synthesis and ligation in TC-NER.
R-SCE-68962. Activation of the pre-replicative complex.
R-SCE-69166. Removal of the Flap Intermediate.

Miscellaneous databases

EvolutionaryTraceiP22336.
PROiP22336.

Family and domain databases

Gene3Di2.40.50.140. 4 hits.
InterProiIPR012340. NA-bd_OB-fold.
IPR004365. NA-bd_OB_tRNA.
IPR013955. Rep_factor-A_C.
IPR007199. Rep_factor-A_N.
IPR031657. REPA_OB_2.
IPR004591. Rfa1.
[Graphical view]
PfamiPF04057. Rep-A_N. 1 hit.
PF08646. Rep_fac-A_C. 1 hit.
PF16900. REPA_OB_2. 1 hit.
PF01336. tRNA_anti-codon. 1 hit.
[Graphical view]
SUPFAMiSSF50249. SSF50249. 4 hits.
TIGRFAMsiTIGR00617. rpa1. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Replication factor-A from Saccharomyces cerevisiae is encoded by three essential genes coordinately expressed at S phase."
    Brill S.J., Stillman B.
    Genes Dev. 5:1589-1600(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 111-129 AND 495-503.
    Strain: ATCC 208353 / W303-1A.
  2. "An essential Saccharomyces cerevisiae single-stranded DNA binding protein is homologous to the large subunit of human RP-A."
    Heyer W.-D., Rao M.R., Erdile L.F., Kelley T.J., Kolodner R.D.
    EMBO J. 9:2321-2329(1990) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PARTIAL PROTEIN SEQUENCE.
  3. "Saccharomyces cerevisiae BUF protein binds to sequences participating in DNA replication in addition to those mediating transcriptional repression (URS1) and activation."
    Luche R.M., Smart W.C., Marion T., Tillman M., Sumrada R.A., Cooper T.G.
    Mol. Cell. Biol. 13:5749-5761(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  4. "Sequencing of chromosome I of Saccharomyces cerevisiae: analysis of the 42 kbp SPO7-CENI-CDC15 region."
    Clark M.W., Keng T., Storms R.K., Zhong W.-W., Fortin N., Zeng B., Delaney S., Ouellette B.F.F., Barton A.B., Kaback D.B., Bussey H.
    Yeast 10:535-541(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 204511 / S288c / AB972.
  5. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  6. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  7. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  8. "The structure of the yFACT Pob3-M domain, its interaction with the DNA replication factor RPA, and a potential role in nucleosome deposition."
    Vandemark A.P., Blanksma M., Ferris E., Heroux A., Hill C.P., Formosa T.
    Mol. Cell 22:363-374(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH POB3.
  9. "A multidimensional chromatography technology for in-depth phosphoproteome analysis."
    Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.
    Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-178, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  10. Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT SER-2, CLEAVAGE OF INITIATOR METHIONINE [LARGE SCALE ANALYSIS], IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

Entry informationi

Entry nameiRFA1_YEAST
AccessioniPrimary (citable) accession number: P22336
Secondary accession number(s): D6VPL9, P38906
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 1, 1991
Last sequence update: August 1, 1991
Last modified: July 6, 2016
This is version 162 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 4100 molecules/cell in log phase SD medium.1 Publication

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families
  3. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  4. Yeast chromosome I
    Yeast (Saccharomyces cerevisiae) chromosome I: entries and gene names

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.