Q8U4J3 (RFCS_PYRFU) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Replication factor C small subunit
Short name=RFC small subunit

Alternative name(s):
Clamp loader small subunit
PfuRFC small subunit

Cleaved into the following chain:

1. Pfu RFC intein

Gene names

Name:	rfcS
Ordered Locus Names:	PF0093

Organism

Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)

Taxonomic identifier

186497 [NCBI]

Taxonomic lineage

Archaea › Euryarchaeota › Thermococci › Thermococcales › Thermococcaceae › Pyrococcus

Protein attributes

Sequence length	852 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Part of the RFC clamp loader complex which loads the PCNA sliding clamp onto DNA. The complex possesses DNA-dependent ATPase activity which is further stimulated by PCNA. Ref.2
Subunit structure	Heteromultimer composed of three to four small subunits (rfcS) and one to two large subunits (rfcL). Ref.2
Post-translational modification	This protein undergoes a protein self splicing that involves a post-translational excision of the intervening region (intein) followed by peptide ligation Potential. HAMAP MF_01509
Miscellaneous	The intein interrupts the potential ATP-binding site. HAMAP MF_01509
Sequence similarities	Belongs to the activator 1 small subunits family. RfcS subfamily. Contains 1 DOD-type homing endonuclease domain.

Ontologies

Keywords
Biological process	DNA replication
Ligand	ATP-binding Nucleotide-binding
PTM	Autocatalytic cleavage Protein splicing
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological process	DNA recombination Inferred from electronic annotation. Source: InterPro DNA repair Inferred from electronic annotation. Source: InterPro DNA replication Inferred from electronic annotation. Source: UniProtKB-KW intein-mediated protein splicing Inferred from electronic annotation. Source: InterPro
Cellular component	DNA replication factor C complex Inferred from electronic annotation. Source: InterPro
Molecular function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW DNA clamp loader activity Inferred from electronic annotation. Source: InterPro endonuclease activity Inferred from electronic annotation. Source: InterPro four-way junction helicase activity Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 59

59

Replication factor C small subunit, 1st part Potential

PRO_0000030376

Chain

60 – 584

525

Pfu RFC intein Potential

PRO_0000030377

Chain

585 – 852

268

Replication factor C small subunit, 2nd part Potential

PRO_0000030378

Regions

Domain

183 – 306

124

DOD-type homing endonuclease

Experimental info

Mutagenesis

785

1

E → A: Decreases the stability of the PCNA-RFC complex and reduces the clamp-loading activity; when associated with A-795; A-796; A-831 and A-835. Ref.4

Mutagenesis

795

1

E → A: Decreases the stability of the PCNA-RFC complex and reduces the clamp-loading activity; when associated with A-785; A-796; A-831 and A-835. Ref.4

Mutagenesis

796

1

D → A: Decreases the stability of the PCNA-RFC complex and reduces the clamp-loading activity; when associated with A-785; A-795; A-831 and A-835. Ref.4

Mutagenesis

831

1

E → A: Decreases the stability of the PCNA-RFC complex and reduces the clamp-loading activity; when associated with A-785; A-795; A-796 and A-835. Ref.4

Mutagenesis

835

1

E → A: Decreases the stability of the PCNA-RFC complex and reduces the clamp-loading activity; when associated with A-785; A-795; A-796 and A-831. Ref.4

Secondary structure

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852

Helix Strand Turn

Details...

Helix

556 – 568

13

Beta strand

573 – 578

6

Helix

584 – 596

13

Helix

597 – 599

3

Helix

600 – 603

4

Beta strand

604 – 608

5

Helix

612 – 616

5

Helix

619 – 627

9

Helix

631 – 633

3

Beta strand

637 – 642

6

Helix

644 – 646

3

Helix

649 – 661

13

Turn

662 – 665

4

Beta strand

666 – 673

8

Helix

675 – 677

3

Helix

680 – 684

5

Beta strand

686 – 690

5

Helix

696 – 708

13

Turn

709 – 711

3

Helix

716 – 726

11

Helix

730 – 741

12

Beta strand

745 – 747

3

Helix

749 – 755

7

Helix

761 – 773

13

Helix

776 – 790

15

Helix

794 – 804

11

Helix

805 – 807

3

Beta strand

808 – 810

3

Helix

812 – 830

19

Helix

835 – 850

16

Sequences

	Sequence		Length	Mass (Da)
	Q8U4J3 [UniParc]. Last modified June 1, 2002. Version 1. Checksum: D4C8B4B945F9946A	FASTA	852	97,793
	10 20 30 40 50 60 MSEEIREVKV LEKPWVEKYR PQRLDDIVGQ EHIVKRLKHY VKTGSMPHLL FAGPPGVGKC 70 80 90 100 110 120 LTGDTKVIAN GQLFELGELV EKLSGGRFGP TPVKGLKVLG IDEDGKLREF EVQYVYKDRT 130 140 150 160 170 180 DRLIKIKTQL GRELKVTPYH PLLVNRENGE IKWIKAEELK PGDKLAIPSF LPLITGENPL 190 200 210 220 230 240 AEWLGYFMGS GYAYPSNSVI TFTNEDPLIR QRFMELTEKL FPDAKIRERI HADGTPEVYV 250 260 270 280 290 300 VSRKAWSLVN SISLTLIPRE GWKGIRSFLR AYSDCNGRIE SDAIVLSTDN NDMAQQIAYA 310 320 330 340 350 360 LASFGIIAKM DGEDVIISGS DNIERFLNEI GFSTQSKLKE AQKLIRKTNV RSDGLKINYE 370 380 390 400 410 420 LISYVKDRLR LNVNDKRNLS YRNAKELSWE LMKEIYYRLE ELERLKKVLS EPILIDWNEV 430 440 450 460 470 480 AKKSDEVIEK AKIRAEKLLE YIKGERKPSF KEYIEIAKVL GINVERTIEA MKIFAKRYSS 490 500 510 520 530 540 YAEIGRKLGT WNFNVKTILE SDTVDNVEIL EKIRKIELEL IEEILSDGKL KEGIAYLIFL 550 560 570 580 590 600 FQNELYWDEI TEVKELRGDF IIYDLHVPGY HNFIAGNMPT VVHNTTAALA LARELFGENW 610 620 630 640 650 660 RHNFLELNAS DERGINVIRE KVKEFARTKP IGGASFKIIF LDEADALTQD AQQALRRTME 670 680 690 700 710 720 MFSSNVRFIL SCNYSSKIIE PIQSRCAIFR FRPLRDEDIA KRLRYIAENE GLELTEEGLQ 730 740 750 760 770 780 AILYIAEGDM RRAINILQAA AALDKKITDE NVFMVASRAR PEDIREMMLL ALKGNFLKAR 790 800 810 820 830 840 EKLREILLKQ GLSGEDVLVQ MHKEVFNLPI EEPKKVLLAD KIGEYNFRLV EGANEIIQLE 850 ALLAQFTLIG KK

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Divergence of the hyperthermophilic archaea Pyrococcus furiosus and P. horikoshii inferred from complete genomic sequences." Maeder D.L., Weiss R.B., Dunn D.M., Cherry J.L., Gonzalez J.M., DiRuggiero J., Robb F.T. Genetics 152:1299-1305(1999) [PubMed: 10430560] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1.
[2]	"Biochemical analysis of replication factor C from the hyperthermophilic archaeon Pyrococcus furiosus." Cann I.K.O., Ishino S., Yuasa M., Daiyasu H., Toh H., Ishino Y. J. Bacteriol. 183:2614-2623(2001) [PubMed: 11274122] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-59 AND 585-852, PROTEIN SEQUENCE OF 2-9, FUNCTION, SUBUNIT. Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1.
[3]	"Three-dimensional electron microscopy of the clamp loader small subunit from Pyrococcus furiosus." Mayanagi K., Miyata T., Oyama T., Ishino Y., Morikawa K. J. Struct. Biol. 134:35-45(2001) [PubMed: 11469875] [Abstract] Cited for: ELECTRON MICROSCOPY.
[4]	"Mutational analysis of Pyrococcus furiosus replication factor C based on the three-dimensional structure." Ishino S., Oyama T., Yuasa M., Morikawa K., Ishino Y. Extremophiles 7:169-175(2003) [PubMed: 12768447] [Abstract] Cited for: MUTAGENESIS OF GLU-785; GLU-795; ASP-796; GLU-831 AND GLU-835.
[5]	"Atomic structure of the clamp loader small subunit from Pyrococcus furiosus." Oyama T., Ishino Y., Cann I.K.O., Ishino S., Morikawa K. Mol. Cell 8:455-463(2001) [PubMed: 11545747] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS).

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AE009950 Genomic DNA. Translation: AAL80217.1.
AB037375 Genomic DNA. Translation: BAB03291.1.
AB037375 Genomic DNA. Translation: BAB03292.1.

RefSeq

NP_577822.1. NC_003413.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1IQP	X-ray	2.80	A/B/C/D/E/F	1-852	[»]

ProteinModelPortal

Q8U4J3.

SMR

Q8U4J3. Positions 2-59, 571-852.

ModBase

Search...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

EBPYRT00000005164; EBPYRP00000005025; EBPYRG00000005163.

GeneID

1467922.

GenomeReviews

Gene locus PF0093 in contig AE009950_GR.

KEGG

pfu:PF0093.

NMPDR

fig|186497.1.peg.93.

Phylogenomic databases

GeneTree

EBGT00050000022153.

HOGENOM

HBG645568.

OMA

ILIDWNE.

PhylomeDB

Q8U4J3.

ProtClustDB

PRK04132.

Family and domain databases

HAMAP

MF_01509. RfcS. Divergent sequence.
[Tree]

InterPro

IPR003959. ATPase_AAA_core.
IPR008824. DNA_helicase_Holl-junc_RuvB_N.
IPR008921. DNA_pol3_clamp-load_cplx_C.
IPR003586. Hedgehog_hint_C.
IPR003587. Hedgehog_hint_N.
IPR006142. INTEIN.
IPR004042. Intein_endonuc.
IPR006141. Intein_splice_site.
IPR013748. Rep_factor-C.
[Graphical view]

KO

K04801.

Pfam

PF00004. AAA. 1 hit.
PF08542. Rep_fac_C. 1 hit.
PF05496. RuvB_N. 1 hit.
[Graphical view]

PRINTS

PR00379. INTEIN.

SMART

SM00305. HintC. 1 hit.
SM00306. HintN. 1 hit.
[Graphical view]

SUPFAM

SSF48019. Pol_clamp_load_C. 1 hit.

TIGRFAMs

TIGR01443. Intein_Cterm. 1 hit.
TIGR01445. Intein_Nterm. 1 hit.

PROSITE

PS50818. INTEIN_C_TER. 1 hit.
PS50819. INTEIN_ENDONUCLEASE. 1 hit.
PS50817. INTEIN_N_TER. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

RFCS_PYRFU

Accession

Primary (citable) accession number: Q8U4J3
Secondary accession number(s): Q9P9H2, Q9P9H3

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 16, 2004
Last sequence update:	June 1, 2002
Last modified:	December 14, 2011
This is version 71 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program