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Protein

Replication factor C subunit 3

Gene

RFC3

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

Component of ATP-dependent clamp loader (RFC and RFC-like) complexes for DNA clamps, such as the POL30/PCNA homotrimer and the checkpoint clamp DDC1:MEC3:RAD17 complex. During a clamp loading circle, the RFC:clamp complex binds to DNA and the recognition of the double-stranded/single-stranded junction stimulates ATP hydrolysis by RFC. The complex presumably provides bipartite ATP sites in which one subunit supplies a catalytic site for hydrolysis of ATP bound to the neighboring subunit. Dissociation of RFC from the clamp leaves the clamp encircling DNA. Component of the replication factor C (RFC or activator 1) complex which loads POL30/PCNA and acts during elongation of primed DNA templates by DNA polymerase delta and epsilon. RFC has an essential but redundant activity in sister chromatid cohesion establishment. Component of the RFC-like complex CTF18-RFC which is required for efficient establishment of chromosome cohesion during S-phase and may load or unload POL30/PCNA. Component of the RFC-like RAD24-RFC complex which loads the checkpoint clamp DDC1:MEC3:RAD17 complex and is involved in DNA repair pathways. Component of the RFC-like ELG1-RFC complex which appears to have a role in DNA replication, replication fork re-start, recombination and repair. RFC3 supplies a catalytic site to the ATP site of RFC4.4 Publications

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei20 – 201ATP
Binding sitei28 – 281ATP; via amide nitrogen and carbonyl oxygen
Binding sitei148 – 1481ATP
Binding sitei206 – 2061ATP

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi16 – 194ATP
Nucleotide bindingi53 – 619ATP

GO - Molecular functioni

  • ATPase activity Source: SGD
  • ATP binding Source: UniProtKB-KW
  • DNA binding Source: UniProtKB-KW

GO - Biological processi

  • leading strand elongation Source: SGD
  • mismatch repair Source: SGD
  • sister chromatid cohesion Source: SGD
Complete GO annotation...

Keywords - Biological processi

Cell cycle, DNA replication

Keywords - Ligandi

ATP-binding, DNA-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciYEAST:G3O-33280-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-174411. Polymerase switching on the C-strand of the telomere.
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-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-69091. Polymerase switching.

Names & Taxonomyi

Protein namesi
Recommended name:
Replication factor C subunit 3
Short name:
Replication factor C3
Alternative name(s):
Activator 1 40 kDa subunit
Gene namesi
Name:RFC3
Ordered Locus Names:YNL290W
ORF Names:N0533
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome XIV

Organism-specific databases

EuPathDBiFungiDB:YNL290W.
SGDiS000005234. RFC3.

Subcellular locationi

GO - Cellular componenti

  • Ctf18 RFC-like complex Source: SGD
  • cytosol Source: SGD
  • DNA replication factor C complex Source: SGD
  • Elg1 RFC-like complex Source: SGD
  • nucleus Source: SGD
  • Rad17 RFC-like complex Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemovedCombined sources
Chaini2 – 340339Replication factor C subunit 3PRO_0000121756Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei2 – 21N-acetylserineCombined sources

Keywords - PTMi

Acetylation

Proteomic databases

MaxQBiP38629.

Interactioni

Subunit structurei

Replication factor C (RFC) is a heteropentamer of subunits RFC1, RFC2, RFC3, RFC4 and RFC5 and forms a complex with POL30/PCNA in the presence of ATP. Component of the RAD24-RFC complex which consists of RAD14, RFC2, RFC3, RFC4 and RFC5 and associates with the checkpoint clamp DDC1:MEC3:RAD17 complex. Component of the ELG1-RFC complex which consists of ELG1, RFC2, RFC3, RFC4 and RFC5. Component of the CTF18-RFC complex, which consists of CTF18, CTF8, DCC1, RFC2, RFC3, RFC4 and RFC5. RFC3 interacts with ECO1 and POL30/PCNA.9 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
CTF18P499564EBI-15000,EBI-4560
CTF8P388772EBI-15000,EBI-5216
RAD24P326413EBI-15000,EBI-14675
RFC2P403484EBI-15000,EBI-14992

Protein-protein interaction databases

BioGridi35547. 90 interactions.
DIPiDIP-2529N.
IntActiP38629. 14 interactions.
MINTiMINT-540713.

Structurei

Secondary structure

1
340
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi15 – 184Combined sources
Helixi24 – 263Combined sources
Helixi31 – 4212Combined sources
Beta strandi49 – 524Combined sources
Beta strandi54 – 585Combined sources
Helixi59 – 7113Combined sources
Helixi75 – 784Combined sources
Beta strandi79 – 824Combined sources
Helixi90 – 945Combined sources
Helixi96 – 1027Combined sources
Beta strandi106 – 1083Combined sources
Beta strandi112 – 1165Combined sources
Helixi119 – 1213Combined sources
Helixi124 – 13613Combined sources
Turni137 – 1404Combined sources
Beta strandi141 – 1488Combined sources
Helixi150 – 1523Combined sources
Helixi155 – 1584Combined sources
Beta strandi161 – 1655Combined sources
Helixi171 – 18313Combined sources
Turni184 – 1863Combined sources
Helixi191 – 20111Combined sources
Helixi205 – 2117Combined sources
Turni212 – 2187Combined sources
Beta strandi221 – 2233Combined sources
Helixi229 – 2357Combined sources
Helixi241 – 25212Combined sources
Helixi256 – 26813Combined sources
Turni269 – 2713Combined sources
Helixi274 – 28512Combined sources
Helixi293 – 31018Combined sources
Helixi316 – 33015Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1SXJX-ray2.85C1-340[»]
ProteinModelPortaliP38629.
SMRiP38629. Positions 12-333.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP38629.

Family & Domainsi

Sequence similaritiesi

Belongs to the activator 1 small subunits family.Curated

Phylogenomic databases

GeneTreeiENSGT00550000075072.
HOGENOMiHOG000224152.
InParanoidiP38629.
KOiK10756.
OMAiTIKACAY.
OrthoDBiEOG7DZ8VQ.

Family and domain databases

Gene3Di3.40.50.300. 1 hit.
InterProiIPR003593. AAA+_ATPase.
IPR003959. ATPase_AAA_core.
IPR008921. DNA_pol3_clamp-load_cplx_C.
IPR027417. P-loop_NTPase.
IPR013748. Rep_factorC_C.
[Graphical view]
PfamiPF00004. AAA. 1 hit.
PF08542. Rep_fac_C. 1 hit.
[Graphical view]
SMARTiSM00382. AAA. 1 hit.
[Graphical view]
SUPFAMiSSF48019. SSF48019. 1 hit.
SSF52540. SSF52540. 1 hit.

Sequencei

Sequence statusi: Complete.

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

P38629-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSTSTEKRSK ENLPWVEKYR PETLDEVYGQ NEVITTVRKF VDEGKLPHLL
60 70 80 90 100
FYGPPGTGKT STIVALAREI YGKNYSNMVL ELNASDDRGI DVVRNQIKDF
110 120 130 140 150
ASTRQIFSKG FKLIILDEAD AMTNAAQNAL RRVIERYTKN TRFCVLANYA
160 170 180 190 200
HKLTPALLSR CTRFRFQPLP QEAIERRIAN VLVHEKLKLS PNAEKALIEL
210 220 230 240 250
SNGDMRRVLN VLQSCKATLD NPDEDEISDD VIYECCGAPR PSDLKAVLKS
260 270 280 290 300
ILEDDWGTAH YTLNKVRSAK GLALIDLIEG IVKILEDYEL QNEETRVHLL
310 320 330 340
TKLADIEYSI SKGGNDQIQG SAVIGAIKAS FENETVKANV
Length:340
Mass (Da):38,204
Last modified:October 1, 1994 - v1
Checksum:i0170EDABAB5CEA52
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L18755 Genomic DNA. Translation: AAA34969.1.
U26029 Genomic DNA. Translation: AAC49062.1.
U23084 Genomic DNA. Translation: AAC49110.1.
Z71566 Genomic DNA. Translation: CAA96207.1.
BK006947 Genomic DNA. Translation: DAA10269.1.
PIRiA36988.
RefSeqiNP_014109.1. NM_001183128.1.

Genome annotation databases

EnsemblFungiiYNL290W; YNL290W; YNL290W.
GeneIDi855426.
KEGGisce:YNL290W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L18755 Genomic DNA. Translation: AAA34969.1.
U26029 Genomic DNA. Translation: AAC49062.1.
U23084 Genomic DNA. Translation: AAC49110.1.
Z71566 Genomic DNA. Translation: CAA96207.1.
BK006947 Genomic DNA. Translation: DAA10269.1.
PIRiA36988.
RefSeqiNP_014109.1. NM_001183128.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1SXJX-ray2.85C1-340[»]
ProteinModelPortaliP38629.
SMRiP38629. Positions 12-333.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi35547. 90 interactions.
DIPiDIP-2529N.
IntActiP38629. 14 interactions.
MINTiMINT-540713.

Proteomic databases

MaxQBiP38629.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYNL290W; YNL290W; YNL290W.
GeneIDi855426.
KEGGisce:YNL290W.

Organism-specific databases

EuPathDBiFungiDB:YNL290W.
SGDiS000005234. RFC3.

Phylogenomic databases

GeneTreeiENSGT00550000075072.
HOGENOMiHOG000224152.
InParanoidiP38629.
KOiK10756.
OMAiTIKACAY.
OrthoDBiEOG7DZ8VQ.

Enzyme and pathway databases

BioCyciYEAST:G3O-33280-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-174411. Polymerase switching on the C-strand of the telomere.
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-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-69091. Polymerase switching.

Miscellaneous databases

EvolutionaryTraceiP38629.
PROiP38629.

Family and domain databases

Gene3Di3.40.50.300. 1 hit.
InterProiIPR003593. AAA+_ATPase.
IPR003959. ATPase_AAA_core.
IPR008921. DNA_pol3_clamp-load_cplx_C.
IPR027417. P-loop_NTPase.
IPR013748. Rep_factorC_C.
[Graphical view]
PfamiPF00004. AAA. 1 hit.
PF08542. Rep_fac_C. 1 hit.
[Graphical view]
SMARTiSM00382. AAA. 1 hit.
[Graphical view]
SUPFAMiSSF48019. SSF48019. 1 hit.
SSF52540. SSF52540. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Molecular cloning and expression of the Saccharomyces cerevisiae RFC3 gene, an essential component of replication factor C."
    Li X., Burgers P.M.J.
    Proc. Natl. Acad. Sci. U.S.A. 91:868-872(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "Characterization of the five replication factor C genes of Saccharomyces cerevisiae."
    Cullmann G., Fien K., Kobayashi R., Stillman B.
    Mol. Cell. Biol. 15:4661-4671(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], IDENTIFICATION IN THE RFC COMPLEX.
    Strain: ATCC 204508 / S288c.
  3. "Sequence analysis of a 30 kb DNA segment from yeast chromosome XIV carrying a ribosomal protein gene cluster, the genes encoding a plasma membrane protein and a subunit of replication factor C, and a novel putative serine/threonine protein kinase gene."
    Maurer K.C.T., Urbanus J.H.M., Planta R.J.
    Yeast 11:1303-1310(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 96604 / S288c / FY1679.
  4. "The nucleotide sequence of Saccharomyces cerevisiae chromosome XIV and its evolutionary implications."
    Philippsen P., Kleine K., Poehlmann R., Duesterhoeft A., Hamberg K., Hegemann J.H., Obermaier B., Urrestarazu L.A., Aert R., Albermann K., Altmann R., Andre B., Baladron V., Ballesta J.P.G., Becam A.-M., Beinhauer J.D., Boskovic J., Buitrago M.J.
    , Bussereau F., Coster F., Crouzet M., D'Angelo M., Dal Pero F., De Antoni A., del Rey F., Doignon F., Domdey H., Dubois E., Fiedler T.A., Fleig U., Floeth M., Fritz C., Gaillardin C., Garcia-Cantalejo J.M., Glansdorff N., Goffeau A., Gueldener U., Herbert C.J., Heumann K., Heuss-Neitzel D., Hilbert H., Hinni K., Iraqui Houssaini I., Jacquet M., Jimenez A., Jonniaux J.-L., Karpfinger-Hartl L., Lanfranchi G., Lepingle A., Levesque H., Lyck R., Maftahi M., Mallet L., Maurer C.T.C., Messenguy F., Mewes H.-W., Moestl D., Nasr F., Nicaud J.-M., Niedenthal R.K., Pandolfo D., Pierard A., Piravandi E., Planta R.J., Pohl T.M., Purnelle B., Rebischung C., Remacha M.A., Revuelta J.L., Rinke M., Saiz J.E., Sartorello F., Scherens B., Sen-Gupta M., Soler-Mira A., Urbanus J.H.M., Valle G., Van Dyck L., Verhasselt P., Vierendeels F., Vissers S., Voet M., Volckaert G., Wach A., Wambutt R., Wedler H., Zollner A., Hani J.
    Nature 387:93-98(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  5. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  6. "A novel Rad24 checkpoint protein complex closely related to replication factor C."
    Green C.M., Erdjument-Bromage H., Tempst P., Lowndes N.F.
    Curr. Biol. 10:39-42(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH RAD24, IDENTIFICATION IN THE RAD24-RFC COMPLEX.
  7. "Identification of RFC(Ctf18p, Ctf8p, Dcc1p): an alternative RFC complex required for sister chromatid cohesion in S. cerevisiae."
    Mayer M.L., Gygi S.P., Aebersold R., Hieter P.
    Mol. Cell 7:959-970(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION IN THE CTF18-RFC COMPLEX.
  8. "Chl12 (Ctf18) forms a novel replication factor C-related complex and functions redundantly with Rad24 in the DNA replication checkpoint pathway."
    Naiki T., Kondo T., Nakada D., Matsumoto K., Sugimoto K.
    Mol. Cell. Biol. 21:5838-5845(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INTERACTION WITH CTF18.
  9. "Replication factor C clamp loader subunit arrangement within the circular pentamer and its attachment points to proliferating cell nuclear antigen."
    Yao N., Coryell L., Zhang D., Georgescu R.E., Finkelstein J., Coman M.M., Hingorani M.M., O'Donnell M.
    J. Biol. Chem. 278:50744-50753(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INTERACTION WITH POL30.
  10. "Mechanical link between cohesion establishment and DNA replication: Ctf7p/Eco1p, a cohesion establishment factor, associates with three different replication factor C complexes."
    Kenna M.A., Skibbens R.V.
    Mol. Cell. Biol. 23:2999-3007(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH ECO1.
  11. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  12. "Yeast Rad17/Mec3/Ddc1: a sliding clamp for the DNA damage checkpoint."
    Majka J., Burgers P.M.J.
    Proc. Natl. Acad. Sci. U.S.A. 100:2249-2254(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION IN THE RAD24-RFC COMPLEX, FUNCTION OF THE RAD24-RFC COMPLEX.
  13. "Replication protein A-directed unloading of PCNA by the Ctf18 cohesion establishment complex."
    Bylund G.O., Burgers P.M.
    Mol. Cell. Biol. 25:5445-5455(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION IN THE RFC COMPLEX, IDENTIFICATION IN THE RAD24-RFC COMPLEX, IDENTIFICATION IN THE ELG1-RFC COMPLEX, IDENTIFICATION IN THE CTF18-RFC COMPLEX, FUNCTION OF THE CTF18-RFC COMPLEX.
  14. Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT SER-2, CLEAVAGE OF INITIATOR METHIONINE [LARGE SCALE ANALYSIS], IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  15. "Structural analysis of a eukaryotic sliding DNA clamp-clamp loader complex."
    Bowman G.D., O'Donnell M., Kuriyan J.
    Nature 429:724-730(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.85 ANGSTROMS) IN COMPLEX WITH AN ATP ANALOG; RCF1; RCF2; RCF4; RCF5 AND PCNA.

Entry informationi

Entry nameiRFC3_YEAST
AccessioniPrimary (citable) accession number: P38629
Secondary accession number(s): D6W0Q3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1994
Last sequence update: October 1, 1994
Last modified: July 6, 2016
This is version 136 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 3140 molecules/cell in log phase SD medium.1 Publication

Keywords - Technical termi

3D-structure, Complete proteome, 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 XIV
    Yeast (Saccharomyces cerevisiae) chromosome XIV: 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.