P40339 (RFC4_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Replication factor C subunit 4
Short name=Replication factor C4

Alternative name(s):
Activator 1 37 kDa subunit

Gene names

Name:	RFC4
Ordered Locus Names:	YOL094C
ORF Names:	O0923

Organism

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

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Fungi › Dikarya › Ascomycota › saccharomyceta › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces › Saccharomyces cerevisiae

Protein attributes

Sequence length	323 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	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. Ref.7 Ref.11 Ref.12
Subunit structure	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. RFC4 interacts with ECO1. Ref.2 Ref.6 Ref.7 Ref.8 Ref.9 Ref.11 Ref.12
Subcellular location	Nucleus Probable.
Miscellaneous	Present with 2760 molecules/cell in log phase SD medium.
Sequence similarities	Belongs to the activator 1 small subunits family.

Ontologies

Keywords
Biological process	Cell cycle DNA replication
Cellular component	Nucleus
Ligand	ATP-binding DNA-binding Nucleotide-binding
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	leading strand elongation Inferred from direct assay PubMed 1346062. Source: SGD mismatch repair Traceable author statement PubMed 10072354. Source: SGD sister chromatid cohesion Inferred from physical interaction Ref.6. Source: SGD
Cellular_component	Ctf18 RFC-like complex Inferred from physical interaction Ref.6. Source: SGD DNA replication factor C complex Inferred from direct assay Ref.1. Source: SGD Elg1 RFC-like complex Inferred from physical interaction PubMed 12909721Ref.8. Source: SGD Rad17 RFC-like complex Inferred from direct assay Ref.11. Source: SGD nucleus Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW DNA binding Inferred from electronic annotation. Source: UniProtKB-KW nucleoside-triphosphatase activity Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
CTF18	P49956	6	EBI-15009,EBI-4560
CTF8	P38877	2	EBI-15009,EBI-5216
ELG1	Q12050	5	EBI-15009,EBI-32195
RAD24	P32641	2	EBI-15009,EBI-14675
RFC3	P38629	3	EBI-15009,EBI-15000

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 323

323

Replication factor C subunit 4

PRO_0000121771

Regions

Nucleotide binding

49 – 57

9

ATP

Sites

Binding site

12

1

ATP; via carbonyl oxygen

Binding site

24

1

ATP; via amide nitrogen

Binding site

145

1

ATP

Binding site

203

1

ATP

Secondary structure

1

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323

Helix Strand Turn

Details...

Helix

11 – 14

4

Helix

20 – 22

3

Helix

28 – 38

11

Beta strand

45 – 48

4

Helix

55 – 67

13

Helix

68 – 70

3

Helix

71 – 74

4

Beta strand

75 – 78

4

Helix

86 – 90

5

Helix

92 – 98

7

Beta strand

109 – 115

7

Helix

116 – 118

3

Helix

121 – 125

5

Helix

128 – 133

6

Turn

134 – 137

4

Beta strand

138 – 145

8

Helix

147 – 149

3

Helix

152 – 155

4

Beta strand

158 – 162

5

Helix

168 – 182

15

Helix

188 – 198

11

Helix

202 – 216

15

Beta strand

217 – 219

3

Helix

221 – 228

8

Helix

233 – 240

8

Helix

245 – 254

10

Turn

255 – 260

6

Helix

263 – 275

13

Helix

282 – 300

19

Helix

306 – 319

14

Sequences

	Sequence		Length	Mass (Da)
	P40339 [UniParc]. Last modified February 1, 1995. Version 1. Checksum: 1F55F35F0713331F	FASTA	323	36,149
	10 20 30 40 50 60 MSKTLSLQLP WVEKYRPQVL SDIVGNKETI DRLQQIAKDG NMPHMIISGM PGIGKTTSVH 70 80 90 100 110 120 CLAHELLGRS YADGVLELNA SDDRGIDVVR NQIKHFAQKK LHLPPGKHKI VILDEADSMT 130 140 150 160 170 180 AGAQQALRRT MELYSNSTRF AFACNQSNKI IEPLQSRCAI LRYSKLSDED VLKRLLQIIK 190 200 210 220 230 240 LEDVKYTNDG LEAIIFTAEG DMRQAINNLQ STVAGHGLVN ADNVFKIVDS PHPLIVKKML 250 260 270 280 290 300 LASNLEDSIQ ILRTDLWKKG YSSIDIVTTS FRVTKNLAQV KESVRLEMIK EIGLTHMRIL 310 320 EGVGTYLQLA SMLAKIHKLN NKA

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Cloning and characterization of the essential Saccharomyces cerevisiae RFC4 gene encoding the 37-kDa subunit of replication factor C." Li X., Burgers P.M.J. J. Biol. Chem. 269:21880-21884(1994) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 200060 / W303.
[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]	"A 29.425 kb segment on the left arm of yeast chromosome XV contains more than twice as many unknown as known open reading frames." Zumstein E., Pearson B.M., Kalogeropoulos A., Schweizer M. Yeast 11:975-986(1995) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 96604 / S288c / FY1679.
[4]	"The nucleotide sequence of Saccharomyces cerevisiae chromosome XV." Dujon B., Albermann K., Aldea M., Alexandraki D., Ansorge W., Arino J., Benes V., Bohn C., Bolotin-Fukuhara M., Bordonne R., Boyer J., Camasses A., Casamayor A., Casas C., Cheret G., Cziepluch C., Daignan-Fornier B., Dang V.-D. , de Haan M., Delius H., Durand P., Fairhead C., Feldmann H., Gaillon L., Galisson F., Gamo F.-J., Gancedo C., Goffeau A., Goulding S.E., Grivell L.A., Habbig B., Hand N.J., Hani J., Hattenhorst U., Hebling U., Hernando Y., Herrero E., Heumann K., Hiesel R., Hilger F., Hofmann B., Hollenberg C.P., Hughes B., Jauniaux J.-C., Kalogeropoulos A., Katsoulou C., Kordes E., Lafuente M.J., Landt O., Louis E.J., Maarse A.C., Madania A., Mannhaupt G., Marck C., Martin R.P., Mewes H.-W., Michaux G., Paces V., Parle-McDermott A.G., Pearson B.M., Perrin A., Pettersson B., Poch O., Pohl T.M., Poirey R., Portetelle D., Pujol A., Purnelle B., Ramezani Rad M., Rechmann S., Schwager C., Schweizer M., Sor F., Sterky F., Tarassov I.A., Teodoru C., Tettelin H., Thierry A., Tobiasch E., Tzermia M., Uhlen M., Unseld M., Valens M., Vandenbol M., Vetter I., Vlcek C., Voet M., Volckaert G., Voss H., Wambutt R., Wedler H., Wiemann S., Winsor B., Wolfe K.H., Zollner A., Zumstein E., Kleine K. Nature 387:98-102(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 96604 / S288c / FY1679.
[5]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[6]	"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.
[7]	"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.
[8]	"Elg1 forms an alternative RFC complex important for DNA replication and genome integrity." Bellaoui M., Chang M., Ou J., Xu H., Boone C., Brown G.W. EMBO J. 22:4304-4313(2003) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH ELG1.
[9]	"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.
[10]	"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].
[11]	"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.
[12]	"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.
[13]	"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; RCF3; RCF5 AND PCNA.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

L20502 Genomic DNA. Translation: AAA34970.1.
U26030 Genomic DNA. Translation: AAC49063.1.
X83121 Genomic DNA. Translation: CAA58185.1.
Z74836 Genomic DNA. Translation: CAA99106.1.
BK006948 Genomic DNA. Translation: DAA10690.1.

PIR

A53845.

RefSeq

NP_014547.1. NM_001183348.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1SXJ	X-ray	2.85	B	1-323	[»]

ProteinModelPortal

P40339.

SMR

P40339. Positions 7-322.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-2530N.

IntAct

P40339. 30 interactions.

MINT

MINT-540691.

STRING

4932.YOL094C.

Proteomic databases

PaxDb

P40339.

PeptideAtlas

P40339.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YOL094C; YOL094C; YOL094C.

GeneID

854059.

KEGG

sce:YOL094C.

Organism-specific databases

CYGD

YOL094c.

SGD

S000005454. RFC4.

Phylogenomic databases

eggNOG

COG0470.

GeneTree

ENSGT00550000075050.

HOGENOM

HOG000224155.

KO

K10755.

OMA

TMELYSN.

OrthoDB

EOG4PP1RM.

Gene expression databases

Genevestigator

P40339.

GermOnline

YOL094C. Saccharomyces cerevisiae.

Family and domain databases

InterPro

IPR003593. AAA+_ATPase.
IPR003959. ATPase_AAA_core.
IPR008921. DNA_pol3_clamp-load_cplx_C.
IPR013748. Rep_factorC_C_dom.
[Graphical view]

Pfam

PF00004. AAA. 1 hit.
PF08542. Rep_fac_C. 1 hit.
[Graphical view]

SMART

SM00382. AAA. 1 hit.
[Graphical view]

SUPFAM

SSF48019. Pol_clamp_load_C. 1 hit.

ProtoNet

Search...

Other

EvolutionaryTrace

P40339.

NextBio

975656.

Entry information

Entry name

RFC4_YEAST

Accession

Primary (citable) accession number: P40339
Secondary accession number(s): D6W1X4

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 1, 1995
Last sequence update:	February 1, 1995
Last modified:	April 3, 2013
This is version 112 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program