P38766 (RRM3_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
ATP-dependent helicase RRM3
EC=3.6.4.-

Alternative name(s):
Regulation of Ty1 transposition protein 104
rDNA recombination mutation protein 3

Gene names

Name:	RRM3
Synonyms:	RTT104
Ordered Locus Names:	YHR031C

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

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

Protein attributes

Sequence length	723 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	5' to 3' DNA replicative helicase recruited to paused replisomes to promote fork progression throughout nonhistone protein-DNA complexes, naturally occurring impediments that are encountered in each S phase where replication forks pauses. Needed for normal fork progression through over 1000 discrete sites scattered throughout the genome, like rDNA, tRNA genes, centromeres, active replication origins, or transcriptional silencers. Required for timely replication of the telomere and subtelomeric DNA and for wild-type levels of telomeric silencing. Involved in regulation of Ty1 transposition and protects the genome from instability at nascent sites of retrotransposition. Involved in DNA repair during stalled replication fork, regulation of fragile sites expression and essential for genome stability. Plays also a role in mtDNA replication. Ref.3 Ref.4 Ref.5 Ref.6 Ref.8 Ref.9 Ref.11 Ref.12 Ref.13 Ref.14 Ref.15 Ref.16 Ref.17 Ref.18 Ref.21 Ref.22 Ref.23 Ref.24 Ref.25 Ref.27 Ref.28 Ref.29 Ref.30
Subunit structure	Interacts with DEF1 and POL30. Ref.7 Ref.20
Subcellular location	Chromosome. Chromosome › telomere.
Domain	The N-terminal part (residues 1 to 249) is essential for fonction and confers locus specificity. Ref.12
Miscellaneous	Present with 656 molecules/cell in log phase SD medium. Ref.10
Sequence similarities	Belongs to the helicase family.

Ontologies

Keywords
Biological process	DNA damage DNA repair
Cellular component	Chromosome Telomere
Ligand	ATP-binding DNA-binding Nucleotide-binding
Molecular function	Helicase Hydrolase
PTM	Phosphoprotein
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	DNA repair Inferred from electronic annotation. Source: UniProtKB-KW DNA replication Inferred from mutant phenotype Ref.4. Source: SGD mitochondrial genome maintenance Inferred from genetic interaction Ref.18. Source: SGD replication fork progression beyond termination site Inferred from mutant phenotype. Source: SGD
Cellular component	nuclear telomeric heterochromatin Inferred from physical interaction Ref.4. Source: SGD replication fork Inferred from direct assay Ref.25. Source: SGD
Molecular function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW ATP-dependent DNA helicase activity Inferred from direct assay Ref.6. Source: SGD DNA binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 723	723	ATP-dependent helicase RRM3		PRO_0000101986
Regions
	Nucleotide binding	254 – 261	8	ATP Potential
Amino acid modifications
	Modified residue	64	1	Phosphoserine Ref.26
	Modified residue	216	1	Phosphoserine Ref.26
Experimental info
	Mutagenesis	41	1	F → A or D: Reduces the interaction with POL30; when associated with A-42 or D-42. Ref.7
	Mutagenesis	42	1	F → A or D: Reduces the interaction with POL30; when associated with A-42 or D-42. Ref.7

Sequences

	Sequence		Length	Mass (Da)
	P38766 [UniParc]. Last modified February 1, 1995. Version 1. Checksum: 8E0010ABB870CAB6	FASTA	723	81,581
	10 20 30 40 50 60 MFRSHASGNK KQWSKRSSNG STPAASASGS HAYRQQTLSS FFMGCGKKSA AASKNSTTII 70 80 90 100 110 120 DLESGDEGNR NITAPPRPRL IRNNSSSLFS QSQGSFGDDD PDAEFKKLVD VPRLNSYKKS 130 140 150 160 170 180 SRSLSMTSSL HKTASASTTQ KTYHFDEDET LREVTSVKSN SRQLSFTSTI NIEDSSMKLS 190 200 210 220 230 240 TDSERPAKRS KPSMEFQGLK LTVPKKIKPL LRKTVSNMDS MNHRSASSPV VLTMEQERVV 250 260 270 280 290 300 NLIVKKRTNV FYTGSAGTGK SVILQTIIRQ LSSLYGKESI AITASTGLAA VTIGGSTLHK 310 320 330 340 350 360 WSGIGIGNKT IDQLVKKIQS QKDLLAAWRY TKVLIIDEIS MVDGNLLDKL EQIARRIRKN 370 380 390 400 410 420 DDPFGGIQLV LTGDFFQLPP VAKKDEHNVV KFCFESEMWK RCIQKTILLT KVFRQQDNKL 430 440 450 460 470 480 IDILNAIRYG ELTVDIAKTI RNLNRDIDYA DGIAPTELYA TRREVELSNV KKLQSLPGDL 490 500 510 520 530 540 YEFKAVDNAP ERYQAILDSS LMVEKVVALK EDAQVMMLKN KPDVELVNGS LGKVLFFVTE 550 560 570 580 590 600 SLVVKMKEIY KIVDDEVVMD MRLVSRVIGN PLLKESKEFR QDLNARPLAR LERLKILINY 610 620 630 640 650 660 AVKISPHKEK FPYVRWTVGK NKYIHELMVP ERFPIDIPRE NVGLERTQIP LMLCWALSIH 670 680 690 700 710 720 KAQGQTIQRL KVDLRRIFEA GQVYVALSRA VTMDTLQVLN FDPGKIRTNE RVKDFYKRLE TLK

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Complete nucleotide sequence of Saccharomyces cerevisiae chromosome VIII." Johnston M., Andrews S., Brinkman R., Cooper J., Ding H., Dover J., Du Z., Favello A., Fulton L., Gattung S., Geisel C., Kirsten J., Kucaba T., Hillier L.W., Jier M., Johnston L., Langston Y., Latreille P. , Louis E.J., Macri C., Mardis E., Menezes S., Mouser L., Nhan M., Rifkin L., Riles L., St Peter H., Trevaskis E., Vaughan K., Vignati D., Wilcox L., Wohldman P., Waterston R., Wilson R., Vaudin M. Science 265:2077-2082(1994) [PubMed: 8091229] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204511 / S288c / AB972.
[2]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[3]	"A gene with specific and global effects on recombination of sequences from tandemly repeated genes in Saccharomyces cerevisiae." Keil R.L., McWilliams A.D. Genetics 135:711-718(1993) [PubMed: 8293975] [Abstract] Cited for: FUNCTION.
[4]	"The Saccharomyces Pif1p DNA helicase and the highly related Rrm3p have opposite effects on replication fork progression in ribosomal DNA." Ivessa A.S., Zhou J.-Q., Zakian V.A. Cell 100:479-489(2000) [PubMed: 10693764] [Abstract] Cited for: FUNCTION.
[5]	"Multiple regulators of Ty1 transposition in Saccharomyces cerevisiae have conserved roles in genome maintenance." Scholes D.T., Banerjee M., Bowen B., Curcio M.J. Genetics 159:1449-1465(2001) [PubMed: 11779788] [Abstract] Cited for: FUNCTION.
[6]	"Saccharomyces Rrm3p, a 5' to 3' DNA helicase that promotes replication fork progression through telomeric and subtelomeric DNA." Ivessa A.S., Zhou J.Q., Schulz V.P., Monson E.K., Zakian V.A. Genes Dev. 16:1383-1396(2002) [PubMed: 12050116] [Abstract] Cited for: FUNCTION, DNA-BINDING.
[7]	"Saccharomyces cerevisiae RRM3, a 5' to 3' DNA helicase, physically interacts with proliferating cell nuclear antigen." Schmidt K.H., Derry K.L., Kolodner R.D. J. Biol. Chem. 277:45331-45337(2002) [PubMed: 12239216] [Abstract] Cited for: INTERACTION WITH POL30, MUTAGENESIS OF PHE-41 AND PHE-42.
[8]	"Dna2 helicase/nuclease causes replicative fork stalling and double-strand breaks in the ribosomal DNA of Saccharomyces cerevisiae." Weitao T., Budd M., Hoopes L.L., Campbell J.L. J. Biol. Chem. 278:22513-22522(2003) [PubMed: 12686542] [Abstract] Cited for: FUNCTION.
[9]	"The Saccharomyces cerevisiae helicase Rrm3p facilitates replication past nonhistone protein-DNA complexes." Ivessa A.S., Lenzmeier B.A., Bessler J.B., Goudsouzian L.K., Schnakenberg S.L., Zakian V.A. Mol. Cell 12:1525-1536(2003) [PubMed: 14690605] [Abstract] Cited for: FUNCTION.
[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: 14562106] [Abstract] Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[11]	"Local chromatin structure at the ribosomal DNA causes replication fork pausing and genome instability in the absence of the S. cerevisiae DNA helicase Rrm3p." Torres J.Z., Bessler J.B., Zakian V.A. Genes Dev. 18:498-503(2004) [PubMed: 15037547] [Abstract] Cited for: FUNCTION.
[12]	"The amino terminus of the Saccharomyces cerevisiae DNA helicase Rrm3p modulates protein function altering replication and checkpoint activity." Bessler J.B., Zakian V.A. Genetics 168:1205-1218(2004) [PubMed: 15579680] [Abstract] Cited for: FUNCTION, DOMAIN.
[13]	"Saccharomyces cerevisiae Rrm3p DNA helicase promotes genome integrity by preventing replication fork stalling: viability of rrm3 cells requires the intra-S-phase checkpoint and fork restart activities." Torres J.Z., Schnakenberg S.L., Zakian V.A. Mol. Cell. Biol. 24:3198-3212(2004) [PubMed: 15060144] [Abstract] Cited for: FUNCTION.
[14]	"Requirement of Rrm3 helicase for repair of spontaneous DNA lesions in cells lacking Srs2 or Sgs1 helicase." Schmidt K.H., Kolodner R.D. Mol. Cell. Biol. 24:3213-3226(2004) [PubMed: 15060145] [Abstract] Cited for: FUNCTION.
[15]	"Anatomy and dynamics of DNA replication fork movement in yeast telomeric regions." Makovets S., Herskowitz I., Blackburn E.H. Mol. Cell. Biol. 24:4019-4031(2004) [PubMed: 15082794] [Abstract] Cited for: FUNCTION.
[16]	"Diminished S-phase cyclin-dependent kinase function elicits vital Rad53-dependent checkpoint responses in Saccharomyces cerevisiae." Gibson D.G., Aparicio J.G., Hu F., Aparicio O.M. Mol. Cell. Biol. 24:10208-10222(2004) [PubMed: 15542831] [Abstract] Cited for: FUNCTION.
[17]	"Impairment of replication fork progression mediates RNA polII transcription-associated recombination." Prado F., Aguilera A. EMBO J. 24:1267-1276(2005) [PubMed: 15775982] [Abstract] Cited for: FUNCTION.
[18]	"Differential involvement of the related DNA helicases Pif1p and Rrm3p in mtDNA point mutagenesis and stability." O'Rourke T.W., Doudican N.A., Zhang H., Eaton J.S., Doetsch P.W., Shadel G.S. Gene 354:86-92(2005) [PubMed: 15907372] [Abstract] Cited for: FUNCTION.
[19]	"Molecular anatomy and regulation of a stable replisome at a paused eukaryotic DNA replication fork." Calzada A., Hodgson B., Kanemaki M., Bueno A., Labib K. Genes Dev. 19:1905-1919(2005) [PubMed: 16103218] [Abstract] Cited for: RECRUITMENT TO PAUSED REPLISOME.
[20]	"Def1p is involved in telomere maintenance in budding yeast." Chen Y.B., Yang C.P., Li R.X., Zeng R., Zhou J.Q. J. Biol. Chem. 280:24784-24791(2005) [PubMed: 15863512] [Abstract] Cited for: INTERACTION WITH DEF1.
[21]	"The conserved Mec1/Rad53 nuclear checkpoint pathway regulates mitochondrial DNA copy number in Saccharomyces cerevisiae." Taylor S.D., Zhang H., Eaton J.S., Rodeheffer M.S., Lebedeva M.A., O'rourke T.W., Siede W., Shadel G.S. Mol. Biol. Cell 16:3010-3018(2005) [PubMed: 15829566] [Abstract] Cited for: FUNCTION.
[22]	"Mrc1 is required for normal progression of replication forks throughout chromatin in S. cerevisiae." Szyjka S.J., Viggiani C.J., Aparicio O.M. Mol. Cell 19:691-697(2005) [PubMed: 16137624] [Abstract] Cited for: FUNCTION.
[23]	"A network of multi-tasking proteins at the DNA replication fork preserves genome stability." Budd M.E., Tong A.H., Polaczek P., Peng X., Boone C., Campbell J.L. PLoS Genet. 1:E61-E61(2005) [PubMed: 16327883] [Abstract] Cited for: FUNCTION.
[24]	"The cullin Rtt101p promotes replication fork progression through damaged DNA and natural pause sites." Luke B., Versini G., Jaquenoud M., Zaidi I.W., Kurz T., Pintard L., Pasero P., Peter M. Curr. Biol. 16:786-792(2006) [PubMed: 16631586] [Abstract] Cited for: FUNCTION.
[25]	"The S. cerevisiae Rrm3p DNA helicase moves with the replication fork and affects replication of all yeast chromosomes." Azvolinsky A., Dunaway S., Torres J.Z., Bessler J.B., Zakian V.A. Genes Dev. 20:3104-3116(2006) [PubMed: 17114583] [Abstract] Cited for: FUNCTION, DNA-BINDING.
[26]	"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: 18407956] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-64 AND SER-216, MASS SPECTROMETRY.
[27]	"Stimulation of direct-repeat recombination by RNA polymerase III transcription." de la Loza M.C., Wellinger R.E., Aguilera A. DNA Repair 8:620-626(2009) [PubMed: 19168400] [Abstract] Cited for: FUNCTION.
[28]	"Rrm3 protects the Saccharomyces cerevisiae genome from instability at nascent sites of retrotransposition." Stamenova R., Maxwell P.H., Kenny A.E., Curcio M.J. Genetics 182:711-723(2009) [PubMed: 19414561] [Abstract] Cited for: FUNCTION.
[29]	"The intra-S phase checkpoint protein Tof1 collaborates with the helicase Rrm3 and the F-box protein Dia2 to maintain genome stability in Saccharomyces cerevisiae." Bairwa N.K., Mohanty B.K., Stamenova R., Curcio M.J., Bastia D. J. Biol. Chem. 286:2445-2454(2011) [PubMed: 21087929] [Abstract] Cited for: FUNCTION.
[30]	"Regulation of fragile sites expression in budding yeast by MEC1, RRM3 and hydroxyurea." Hashash N., Johnson A.L., Cha R.S. J. Cell Sci. 124:181-185(2011) [PubMed: 21172804] [Abstract] Cited for: FUNCTION.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	U00062 Genomic DNA. Translation: AAB68913.1. BK006934 Genomic DNA. Translation: DAA06722.1.
PIR	S46744.
RefSeq	NP_011896.1. NM_001179161.1.
3D structure databases
ProteinModelPortal	P38766.
SMR	P38766. Positions 239-356.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-2858N.
IntAct	P38766. 3 interactions.
STRING	P38766.
Proteomic databases
PRIDE	P38766.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblFungi	YHR031C; YHR031C; YHR031C.
GeneID	856426.
KEGG	sce:YHR031C.
NMPDR	fig|4932.3.peg.3043.
Organism-specific databases
CYGD	YHR031c.
SGD	S000001073. RRM3.
Phylogenomic databases
eggNOG	fuNOG04681.
GeneTree	EFGT00050000006493.
HOGENOM	HBG398055.
OMA	KEDAQVM.
OrthoDB	EOG486CNB.
Gene expression databases
ArrayExpress	P38766.
Genevestigator	P38766.
GermOnline	YHR031C. Saccharomyces cerevisiae.
Family and domain databases
InterPro	IPR003593. ATPase_AAA+_core. IPR010285. DNA_helicase_PIF1. [Graphical view]
KO	K15255.
Pfam	PF05970. PIF1. 1 hit. [Graphical view]
SMART	SM00382. AAA. 1 hit. [Graphical view]
ProtoNet	Search...
Other
NextBio	982006.

Entry information

Entry name

RRM3_YEAST

Accession

Primary (citable) accession number: P38766
Secondary accession number(s): D3DKX8

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 1, 1995
Last sequence update:	February 1, 1995
Last modified:	January 25, 2012
This is version 93 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program