RUVB2_YEAST
ID RUVB2_YEAST Reviewed; 471 AA.
AC Q12464; D6W3D5;
DT 30-AUG-2005, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 180.
DE RecName: Full=RuvB-like protein 2;
DE Short=RUVBL2;
DE EC=3.6.4.12;
DE AltName: Full=TIP49-homology protein 2;
DE AltName: Full=TIP49b homolog;
GN Name=RVB2; Synonyms=TIH2, TIP49B; OrderedLocusNames=YPL235W;
GN ORFNames=P1060;
OS Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX NCBI_TaxID=559292;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169875;
RA Bussey H., Storms R.K., Ahmed A., Albermann K., Allen E., Ansorge W.,
RA Araujo R., Aparicio A., Barrell B.G., Badcock K., Benes V., Botstein D.,
RA Bowman S., Brueckner M., Carpenter J., Cherry J.M., Chung E.,
RA Churcher C.M., Coster F., Davis K., Davis R.W., Dietrich F.S., Delius H.,
RA DiPaolo T., Dubois E., Duesterhoeft A., Duncan M., Floeth M., Fortin N.,
RA Friesen J.D., Fritz C., Goffeau A., Hall J., Hebling U., Heumann K.,
RA Hilbert H., Hillier L.W., Hunicke-Smith S., Hyman R.W., Johnston M.,
RA Kalman S., Kleine K., Komp C., Kurdi O., Lashkari D., Lew H., Lin A.,
RA Lin D., Louis E.J., Marathe R., Messenguy F., Mewes H.-W., Mirtipati S.,
RA Moestl D., Mueller-Auer S., Namath A., Nentwich U., Oefner P., Pearson D.,
RA Petel F.X., Pohl T.M., Purnelle B., Rajandream M.A., Rechmann S.,
RA Rieger M., Riles L., Roberts D., Schaefer M., Scharfe M., Scherens B.,
RA Schramm S., Schroeder M., Sdicu A.-M., Tettelin H., Urrestarazu L.A.,
RA Ushinsky S., Vierendeels F., Vissers S., Voss H., Walsh S.V., Wambutt R.,
RA Wang Y., Wedler E., Wedler H., Winnett E., Zhong W.-W., Zollner A.,
RA Vo D.H., Hani J.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome XVI.";
RL Nature 387:103-105(1997).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=24374639; DOI=10.1534/g3.113.008995;
RA Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
RT "The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
RL G3 (Bethesda) 4:389-398(2014).
RN [3]
RP FUNCTION, SUBCELLULAR LOCATION, MUTAGENESIS OF LYS-81, AND INTERACTION WITH
RP RVB1.
RX PubMed=10787406; DOI=10.1074/jbc.m001031200;
RA Lim C.R., Kimata Y., Ohdate H., Kokubo T., Kikuchi N., Horigome T.,
RA Kohno K.;
RT "The Saccharomyces cerevisiae RuvB-like protein, Tih2p, is required for
RT cell cycle progression and RNA polymerase II-directed transcription.";
RL J. Biol. Chem. 275:22409-22417(2000).
RN [4]
RP IDENTIFICATION IN THE INO80 COMPLEX, FUNCTION OF THE INO80 COMPLEX, AND
RP IDENTIFICATION BY MASS SPECTROMETRY.
RX PubMed=10952318; DOI=10.1038/35020123;
RA Shen X., Mizuguchi G., Hamiche A., Wu C.;
RT "A chromatin remodelling complex involved in transcription and DNA
RT processing.";
RL Nature 406:541-544(2000).
RN [5]
RP FUNCTION, INTERACTION WITH RVB1, IDENTIFICATION IN A COMPLEX WITH RBV1;
RP ACT1 AND ARP4, IDENTIFICATION BY MASS SPECTROMETRY, AND MUTAGENESIS OF
RP LYS-81 AND GLU-297.
RX PubMed=11278922; DOI=10.1074/jbc.m011523200;
RA Jonsson Z.O., Dhar S.K., Narlikar G.J., Auty R., Wagle N., Pellman D.,
RA Pratt R.E., Kingston R., Dutta A.;
RT "Rvb1p and Rvb2p are essential components of a chromatin remodeling complex
RT that regulates transcription of over 5% of yeast genes.";
RL J. Biol. Chem. 276:16279-16288(2001).
RN [6]
RP FUNCTION IN SNORNA SYNTHESIS, SUBCELLULAR LOCATION, AND MUTAGENESIS OF
RP GLY-75; GLY-80; LYS-81 AND ASP-296.
RX PubMed=11604509; DOI=10.1128/mcb.21.22.7731-7746.2001;
RA King T.H., Decatur W.A., Bertrand E., Maxwell E.S., Fournier M.J.;
RT "A well-connected and conserved nucleoplasmic helicase is required for
RT production of box C/D and H/ACA snoRNAs and localization of snoRNP
RT proteins.";
RL Mol. Cell. Biol. 21:7731-7746(2001).
RN [7]
RP FUNCTION, AND INTERACTION WITH SPT15.
RX PubMed=12576485; DOI=10.1074/jbc.m213220200;
RA Ohdate H., Lim C.R., Kokubo T., Matsubara K., Kimata Y., Kohno K.;
RT "Impairment of the DNA binding activity of the TATA-binding protein renders
RT the transcriptional function of Rvb2p/Tih2p, the yeast RuvB-like protein,
RT essential for cell growth.";
RL J. Biol. Chem. 278:14647-14656(2003).
RN [8]
RP IDENTIFICATION BY MASS SPECTROMETRY.
RX PubMed=14690591; DOI=10.1016/s1097-2765(03)00476-3;
RA Hazbun T.R., Malmstroem L., Anderson S., Graczyk B.J., Fox B., Riffle M.,
RA Sundin B.A., Aranda J.D., McDonald W.H., Chiu C.-H., Snydsman B.E.,
RA Bradley P., Muller E.G.D., Fields S., Baker D., Yates J.R. III, Davis T.N.;
RT "Assigning function to yeast proteins by integration of technologies.";
RL Mol. Cell 12:1353-1365(2003).
RN [9]
RP IDENTIFICATION IN THE SWR1 COMPLEX, FUNCTION OF THE SWR1 COMPLEX, AND
RP IDENTIFICATION BY MASS SPECTROMETRY.
RX PubMed=14690608; DOI=10.1016/s1097-2765(03)00497-0;
RA Krogan N.J., Keogh M.-C., Datta N., Sawa C., Ryan O.W., Ding H., Haw R.A.,
RA Pootoolal J., Tong A., Canadien V., Richards D.P., Wu X., Emili A.,
RA Hughes T.R., Buratowski S., Greenblatt J.F.;
RT "A Snf2 family ATPase complex required for recruitment of the histone H2A
RT variant Htz1.";
RL Mol. Cell 12:1565-1576(2003).
RN [10]
RP LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
RX PubMed=14562106; DOI=10.1038/nature02046;
RA Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N.,
RA O'Shea E.K., Weissman J.S.;
RT "Global analysis of protein expression in yeast.";
RL Nature 425:737-741(2003).
RN [11]
RP FUNCTION, IDENTIFICATION IN THE INO80 COMPLEX, AND IDENTIFICATION BY MASS
RP SPECTROMETRY.
RX PubMed=15525518; DOI=10.1016/j.molcel.2004.09.033;
RA Jonsson Z.O., Jha S., Wohlschlegel J.A., Dutta A.;
RT "Rvb1p/Rvb2p recruit Arp5p and assemble a functional Ino80 chromatin
RT remodeling complex.";
RL Mol. Cell 16:465-477(2004).
RN [12]
RP IDENTIFICATION IN THE SWR1 COMPLEX, FUNCTION OF THE SWR1 COMPLEX, AND
RP IDENTIFICATION BY MASS SPECTROMETRY.
RX PubMed=15045029; DOI=10.1371/journal.pbio.0020131;
RA Kobor M.S., Venkatasubrahmanyam S., Meneghini M.D., Gin J.W.,
RA Jennings J.L., Link A.J., Madhani H.D., Rine J.;
RT "A protein complex containing the conserved Swi2/Snf2-related ATPase Swr1p
RT deposits histone variant H2A.Z into euchromatin.";
RL PLoS Biol. 2:587-599(2004).
RN [13]
RP IDENTIFICATION IN THE SWR1 COMPLEX, FUNCTION OF THE SWR1 COMPLEX, AND
RP IDENTIFICATION BY MASS SPECTROMETRY.
RX PubMed=14645854; DOI=10.1126/science.1090701;
RA Mizuguchi G., Shen X., Landry J., Wu W.-H., Sen S., Wu C.;
RT "ATP-driven exchange of histone H2AZ variant catalyzed by SWR1 chromatin
RT remodeling complex.";
RL Science 303:343-348(2004).
RN [14]
RP IDENTIFICATION IN THE R2PT COMPLEX, AND IDENTIFICATION BY MASS
RP SPECTROMETRY.
RX PubMed=15766533; DOI=10.1016/j.cell.2004.12.024;
RA Zhao R., Davey M.G., Hsu Y.-C., Kaplanek P., Tong A., Parsons A.B.,
RA Krogan N.J., Cagney G., Mai D., Greenblatt J.F., Boone C., Emili A.,
RA Houry W.A.;
RT "Navigating the chaperone network: an integrative map of physical and
RT genetic interactions mediated by the hsp90 chaperone.";
RL Cell 120:715-727(2005).
CC -!- FUNCTION: DNA helicase which participates in several chromatin
CC remodeling complexes, including the SWR1 and the INO80 complexes. The
CC SWR1 complex mediates the ATP-dependent exchange of histone H2A for the
CC H2A variant HZT1 leading to transcriptional regulation of selected
CC genes by chromatin remodeling. The INO80 complex remodels chromatin by
CC shifting nucleosomes. Its ability to induce transcription of some
CC phosphate-responsive genes is modulated by inositol polyphosphates. The
CC INO80 complex is involved in DNA repair by associating to 'Ser-129'
CC phosphorylated H2A histones as a response to DNA damage. During
CC transcription may recruit SPT15/TBP to the TATA-boxes of involved
CC genes. Required for box C/D and box H/ACA snoRNA accumulation and
CC involved in pre-rRNA processing. {ECO:0000269|PubMed:10787406,
CC ECO:0000269|PubMed:10952318, ECO:0000269|PubMed:11278922,
CC ECO:0000269|PubMed:11604509, ECO:0000269|PubMed:12576485,
CC ECO:0000269|PubMed:14645854, ECO:0000269|PubMed:14690608,
CC ECO:0000269|PubMed:15045029, ECO:0000269|PubMed:15525518}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + H2O = ADP + H(+) + phosphate; Xref=Rhea:RHEA:13065,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:30616,
CC ChEBI:CHEBI:43474, ChEBI:CHEBI:456216; EC=3.6.4.12;
CC -!- SUBUNIT: Probably forms a homohexamer. Interacts with RVB1 and may form
CC heterododecamers with RVB1. Component of the SWR1 chromatin remodeling
CC complex composed of at least ACT1, ARP4, RVB1, RVB2, ARP6, YAF9, VPS71,
CC VPS72, SWC3, SWC4, SWC5, SWC7 and SWR1, and perhaps BDF1. Component of
CC the chromatin-remodeling INO80 complex, at least composed of ARP4,
CC ARP5, ARP8, RVB1, RVB2, TAF14, NHP10, IES1, IES3, IES4, IES6, ACT1,
CC IES2, IES5 and INO80. Belongs also to the R2TP complex composed of at
CC least RVB1, RVB2, TAH1 and PIH1. Interacts with SPT15/TBP.
CC {ECO:0000269|PubMed:10787406, ECO:0000269|PubMed:10952318,
CC ECO:0000269|PubMed:11278922, ECO:0000269|PubMed:12576485,
CC ECO:0000269|PubMed:14645854, ECO:0000269|PubMed:14690608,
CC ECO:0000269|PubMed:15045029, ECO:0000269|PubMed:15525518,
CC ECO:0000269|PubMed:15766533}.
CC -!- INTERACTION:
CC Q12464; P38768: PIH1; NbExp=7; IntAct=EBI-31814, EBI-24499;
CC Q12464; Q03940: RVB1; NbExp=21; IntAct=EBI-31814, EBI-30712;
CC Q12464; P13393: SPT15; NbExp=3; IntAct=EBI-31814, EBI-19129;
CC Q12464; P53201: SWC4; NbExp=4; IntAct=EBI-31814, EBI-23061;
CC -!- SUBCELLULAR LOCATION: Nucleus, nucleoplasm
CC {ECO:0000269|PubMed:10787406, ECO:0000269|PubMed:11604509}.
CC -!- MISCELLANEOUS: Present with 3030 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the RuvB family. {ECO:0000305}.
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DR EMBL; Z67751; CAA91609.1; -; Genomic_DNA.
DR EMBL; X94561; CAA64252.1; -; Genomic_DNA.
DR EMBL; Z73591; CAA97952.1; -; Genomic_DNA.
DR EMBL; BK006949; DAA11201.1; -; Genomic_DNA.
DR PIR; S61029; S61029.
DR RefSeq; NP_015089.1; NM_001184049.1.
DR PDB; 5OUN; NMR; -; A=132-234.
DR PDB; 6GEJ; EM; 3.60 A; U/W/Y=1-471.
DR PDB; 6GEN; EM; 3.60 A; U/W/Y=1-471.
DR PDBsum; 5OUN; -.
DR PDBsum; 6GEJ; -.
DR PDBsum; 6GEN; -.
DR AlphaFoldDB; Q12464; -.
DR SMR; Q12464; -.
DR BioGRID; 35927; 523.
DR ComplexPortal; CPX-1814; R2TP co-chaperone complex.
DR ComplexPortal; CPX-2122; Swr1 chromatin remodelling complex.
DR ComplexPortal; CPX-863; INO80 chromatin remodeling complex.
DR DIP; DIP-5207N; -.
DR IntAct; Q12464; 207.
DR MINT; Q12464; -.
DR STRING; 4932.YPL235W; -.
DR iPTMnet; Q12464; -.
DR MaxQB; Q12464; -.
DR PaxDb; Q12464; -.
DR PRIDE; Q12464; -.
DR EnsemblFungi; YPL235W_mRNA; YPL235W; YPL235W.
DR GeneID; 855841; -.
DR KEGG; sce:YPL235W; -.
DR SGD; S000006156; RVB2.
DR VEuPathDB; FungiDB:YPL235W; -.
DR eggNOG; KOG2680; Eukaryota.
DR GeneTree; ENSGT00940000153556; -.
DR HOGENOM; CLU_028311_4_0_1; -.
DR InParanoid; Q12464; -.
DR OMA; YDMGAKM; -.
DR BioCyc; YEAST:G3O-34122-MON; -.
DR PRO; PR:Q12464; -.
DR Proteomes; UP000002311; Chromosome XVI.
DR RNAct; Q12464; protein.
DR GO; GO:0070209; C:ASTRA complex; HDA:SGD.
DR GO; GO:0000785; C:chromatin; IDA:ComplexPortal.
DR GO; GO:0031011; C:Ino80 complex; IPI:SGD.
DR GO; GO:0035267; C:NuA4 histone acetyltransferase complex; IBA:GO_Central.
DR GO; GO:0005634; C:nucleus; IDA:SGD.
DR GO; GO:0097255; C:R2TP complex; IDA:SGD.
DR GO; GO:0000812; C:Swr1 complex; IDA:SGD.
DR GO; GO:0043138; F:3'-5' DNA helicase activity; IDA:SGD.
DR GO; GO:0043139; F:5'-3' DNA helicase activity; IDA:SGD.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0016887; F:ATP hydrolysis activity; IEA:RHEA.
DR GO; GO:0003678; F:DNA helicase activity; IBA:GO_Central.
DR GO; GO:0000492; P:box C/D snoRNP assembly; IMP:SGD.
DR GO; GO:0006338; P:chromatin remodeling; IDA:ComplexPortal.
DR GO; GO:0006281; P:DNA repair; IC:ComplexPortal.
DR GO; GO:0016573; P:histone acetylation; IBA:GO_Central.
DR GO; GO:0043486; P:histone exchange; IPI:SGD.
DR GO; GO:0050821; P:protein stabilization; IC:ComplexPortal.
DR GO; GO:0006357; P:regulation of transcription by RNA polymerase II; IMP:SGD.
DR GO; GO:0006355; P:regulation of transcription, DNA-templated; IC:ComplexPortal.
DR GO; GO:0006364; P:rRNA processing; IMP:SGD.
DR Gene3D; 2.40.50.360; -; 1.
DR Gene3D; 3.40.50.300; -; 1.
DR InterPro; IPR003593; AAA+_ATPase.
DR InterPro; IPR027417; P-loop_NTPase.
DR InterPro; IPR027238; RuvB-like.
DR InterPro; IPR041048; RuvB-like_C.
DR InterPro; IPR042487; RuvBL1/2_DNA/RNA_bd_dom.
DR InterPro; IPR037942; RUVBL2.
DR InterPro; IPR010339; TIP49_P-loop.
DR PANTHER; PTHR11093; PTHR11093; 1.
DR PANTHER; PTHR11093:SF2; PTHR11093:SF2; 1.
DR Pfam; PF06068; TIP49; 1.
DR Pfam; PF17856; TIP49_C; 1.
DR SMART; SM00382; AAA; 1.
DR SUPFAM; SSF52540; SSF52540; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Activator; ATP-binding; Chromatin regulator; DNA damage;
KW DNA repair; Helicase; Hydrolase; Nucleotide-binding; Nucleus;
KW Reference proteome; rRNA processing; Transcription;
KW Transcription regulation.
FT CHAIN 1..471
FT /note="RuvB-like protein 2"
FT /id="PRO_0000165675"
FT BINDING 75..82
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT MUTAGEN 75
FT /note="G->A: Lethal."
FT /evidence="ECO:0000269|PubMed:11604509"
FT MUTAGEN 80
FT /note="G->A: Growth defect at 37 degrees Celsius."
FT /evidence="ECO:0000269|PubMed:11604509"
FT MUTAGEN 81
FT /note="K->A: Defect in snoRNA accumulation. Growth defect
FT at 37 degrees Celsius."
FT /evidence="ECO:0000269|PubMed:10787406,
FT ECO:0000269|PubMed:11278922, ECO:0000269|PubMed:11604509"
FT MUTAGEN 81
FT /note="K->E: Lethal."
FT /evidence="ECO:0000269|PubMed:10787406,
FT ECO:0000269|PubMed:11278922, ECO:0000269|PubMed:11604509"
FT MUTAGEN 81
FT /note="K->R: Growth defect at 37 degrees Celsius."
FT /evidence="ECO:0000269|PubMed:10787406,
FT ECO:0000269|PubMed:11278922, ECO:0000269|PubMed:11604509"
FT MUTAGEN 296
FT /note="D->N: Lethal."
FT /evidence="ECO:0000269|PubMed:11604509"
FT MUTAGEN 297
FT /note="E->G: Lethal."
FT /evidence="ECO:0000269|PubMed:11278922"
FT STRAND 135..145
FT /evidence="ECO:0007829|PDB:5OUN"
FT STRAND 147..149
FT /evidence="ECO:0007829|PDB:5OUN"
FT STRAND 156..161
FT /evidence="ECO:0007829|PDB:5OUN"
FT STRAND 166..171
FT /evidence="ECO:0007829|PDB:5OUN"
FT HELIX 173..182
FT /evidence="ECO:0007829|PDB:5OUN"
FT STRAND 189..193
FT /evidence="ECO:0007829|PDB:5OUN"
FT TURN 194..196
FT /evidence="ECO:0007829|PDB:5OUN"
FT STRAND 199..201
FT /evidence="ECO:0007829|PDB:5OUN"
FT STRAND 203..205
FT /evidence="ECO:0007829|PDB:5OUN"
SQ SEQUENCE 471 AA; 51612 MW; 0D8EFBA7EC711AB8 CRC64;
MSIQTSDPNE TSDLKSLSLI AAHSHITGLG LDENLQPRPT SEGMVGQLQA RRAAGVILKM
VQNGTIAGRA VLVAGPPSTG KTALAMGVSQ SLGKDVPFTA IAGSEIFSLE LSKTEALTQA
FRKSIGIKIK EETELIEGEV VEIQIDRSIT GGHKQGKLTI KTTDMETIYE LGNKMIDGLT
KEKVLAGDVI SIDKASGKIT KLGRSFARSR DYDAMGADTR FVQCPEGELQ KRKTVVHTVS
LHEIDVINSR TQGFLALFTG DTGEIRSEVR DQINTKVAEW KEEGKAEIVP GVLFIDEVHM
LDIECFSFIN RALEDEFAPI VMMATNRGVS KTRGTNYKSP HGLPLDLLDR SIIITTKSYN
EQEIKTILSI RAQEEEVELS SDALDLLTKT GVETSLRYSS NLISVAQQIA MKRKNNTVEV
EDVKRAYLLF LDSARSVKYV QENESQYIDD QGNVQISIAK SADPDAMDTT E
