RAF1_SCHPO
ID RAF1_SCHPO Reviewed; 638 AA.
AC O74910;
DT 14-AUG-2001, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1998, sequence version 1.
DT 03-AUG-2022, entry version 153.
DE RecName: Full=Rik1-associated factor 1;
DE AltName: Full=Cryptic loci regulator 8;
DE AltName: Full=De-localization of swi6 protein 1;
GN Name=raf1; Synonyms=clr8, cmc1, dos1; ORFNames=SPCC613.12c;
OS Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina;
OC Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae;
OC Schizosaccharomyces.
OX NCBI_TaxID=284812;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=972 / ATCC 24843;
RX PubMed=11859360; DOI=10.1038/nature724;
RA Wood V., Gwilliam R., Rajandream M.A., Lyne M.H., Lyne R., Stewart A.,
RA Sgouros J.G., Peat N., Hayles J., Baker S.G., Basham D., Bowman S.,
RA Brooks K., Brown D., Brown S., Chillingworth T., Churcher C.M., Collins M.,
RA Connor R., Cronin A., Davis P., Feltwell T., Fraser A., Gentles S.,
RA Goble A., Hamlin N., Harris D.E., Hidalgo J., Hodgson G., Holroyd S.,
RA Hornsby T., Howarth S., Huckle E.J., Hunt S., Jagels K., James K.D.,
RA Jones L., Jones M., Leather S., McDonald S., McLean J., Mooney P.,
RA Moule S., Mungall K.L., Murphy L.D., Niblett D., Odell C., Oliver K.,
RA O'Neil S., Pearson D., Quail M.A., Rabbinowitsch E., Rutherford K.M.,
RA Rutter S., Saunders D., Seeger K., Sharp S., Skelton J., Simmonds M.N.,
RA Squares R., Squares S., Stevens K., Taylor K., Taylor R.G., Tivey A.,
RA Walsh S.V., Warren T., Whitehead S., Woodward J.R., Volckaert G., Aert R.,
RA Robben J., Grymonprez B., Weltjens I., Vanstreels E., Rieger M.,
RA Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Duesterhoeft A.,
RA Fritzc C., Holzer E., Moestl D., Hilbert H., Borzym K., Langer I., Beck A.,
RA Lehrach H., Reinhardt R., Pohl T.M., Eger P., Zimmermann W., Wedler H.,
RA Wambutt R., Purnelle B., Goffeau A., Cadieu E., Dreano S., Gloux S.,
RA Lelaure V., Mottier S., Galibert F., Aves S.J., Xiang Z., Hunt C.,
RA Moore K., Hurst S.M., Lucas M., Rochet M., Gaillardin C., Tallada V.A.,
RA Garzon A., Thode G., Daga R.R., Cruzado L., Jimenez J., Sanchez M.,
RA del Rey F., Benito J., Dominguez A., Revuelta J.L., Moreno S.,
RA Armstrong J., Forsburg S.L., Cerutti L., Lowe T., McCombie W.R.,
RA Paulsen I., Potashkin J., Shpakovski G.V., Ussery D., Barrell B.G.,
RA Nurse P.;
RT "The genome sequence of Schizosaccharomyces pombe.";
RL Nature 415:871-880(2002).
RN [2]
RP PARTIAL PROTEIN SEQUENCE, FUNCTION, IDENTIFICATION IN THE RIK1-ASSOCIATED
RP E3 UBIQUITIN LIGASE COMPLEX, AND SUBCELLULAR LOCATION.
RX PubMed=16024659; DOI=10.1101/gad.1328005;
RA Horn P.J., Bastie J.-N., Peterson C.L.;
RT "A Rik1-associated, cullin-dependent E3 ubiquitin ligase is essential for
RT heterochromatin formation.";
RL Genes Dev. 19:1705-1714(2005).
RN [3]
RP FUNCTION, INTERACTION WITH RIK1, AND SUBCELLULAR LOCATION.
RX PubMed=16040243; DOI=10.1016/j.cub.2005.07.021;
RA Li F., Goto D.B., Zaratiegui M., Tang X., Martienssen R., Cande W.Z.;
RT "Two novel proteins, dos1 and dos2, interact with rik1 to regulate
RT heterochromatic RNA interference and histone modification.";
RL Curr. Biol. 15:1448-1457(2005).
RN [4]
RP FUNCTION, AND INTERACTION WITH NUP189.
RX PubMed=16157682; DOI=10.1534/genetics.105.048298;
RA Thon G., Hansen K.R., Altes S.P., Sidhu D., Singh G., Verhein-Hansen J.,
RA Bonaduce M.J., Klar A.J.;
RT "The Clr7 and Clr8 directionality factors and the Pcu4 cullin mediate
RT heterochromatin formation in the fission yeast Schizosaccharomyces pombe.";
RL Genetics 171:1583-1595(2005).
RN [5]
RP SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
RX PubMed=16823372; DOI=10.1038/nbt1222;
RA Matsuyama A., Arai R., Yashiroda Y., Shirai A., Kamata A., Sekido S.,
RA Kobayashi Y., Hashimoto A., Hamamoto M., Hiraoka Y., Horinouchi S.,
RA Yoshida M.;
RT "ORFeome cloning and global analysis of protein localization in the fission
RT yeast Schizosaccharomyces pombe.";
RL Nat. Biotechnol. 24:841-847(2006).
RN [6]
RP FUNCTION, AND SUBCELLULAR LOCATION.
RX PubMed=18345014; DOI=10.1038/nsmb.1406;
RA Zhang K., Mosch K., Fischle W., Grewal S.I.;
RT "Roles of the Clr4 methyltransferase complex in nucleation, spreading and
RT maintenance of heterochromatin.";
RL Nat. Struct. Mol. Biol. 15:381-388(2008).
RN [7]
RP FUNCTION.
RX PubMed=31468675; DOI=10.15252/embr.201948111;
RA Oya E., Nakagawa R., Yoshimura Y., Tanaka M., Nishibuchi G., Machida S.,
RA Shirai A., Ekwall K., Kurumizaka H., Tagami H., Nakayama J.I.;
RT "H3K14 ubiquitylation promotes H3K9 methylation for heterochromatin
RT assembly.";
RL EMBO Rep. 20:E48111-E48111(2019).
RN [8]
RP X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS) OF 213-638.
RX PubMed=24449894; DOI=10.1073/pnas.1313096111;
RA Kuscu C., Zaratiegui M., Kim H.S., Wah D.A., Martienssen R.A., Schalch T.,
RA Joshua-Tor L.;
RT "CRL4-like Clr4 complex in Schizosaccharomyces pombe depends on an exposed
RT surface of Dos1 for heterochromatin silencing.";
RL Proc. Natl. Acad. Sci. U.S.A. 111:1795-1800(2014).
CC -!- FUNCTION: Component of the Clr4 methyltransferase complex (ClrC) which
CC contributes to the establishment of heterochromatin by specifically
CC methylating histone H3 to form H3K9me (PubMed:16024659,
CC PubMed:16040243, PubMed:16157682). ClrC preferentially ubiquitylates
CC H3K14 and ClrC-mediated H3 ubiquitination promotes clr4
CC methyltransferase activity for the methylation of H3K9
CC (PubMed:31468675). H3K9me represents a specific tag for epigenetic
CC transcriptional repression by recruiting swi6/HP1 to methylated
CC histones which leads to transcriptional silencing within centromeric
CC heterochromatin, telomeric regions and at the silent mating-type loci
CC (PubMed:16024659, PubMed:16040243, PubMed:16157682, PubMed:18345014).
CC Has a role in both mitotic and meiotic chromosome segregation
CC (PubMed:16040243). {ECO:0000269|PubMed:16024659,
CC ECO:0000269|PubMed:16040243, ECO:0000269|PubMed:16157682,
CC ECO:0000269|PubMed:18345014, ECO:0000269|PubMed:31468675}.
CC -!- SUBUNIT: Component of the Clr4 methyltransferase complex (ClrC)
CC composed of at least clr4, rik1, pcu4, rbx1, raf1 and raf2. The cullin
CC pcu4, rik1, raf1, raf2 and the ring-box protein rbx1 are components of
CC an E3 ubiquitin ligase, whose activity is essential for heterochromatin
CC assembly (PubMed:16024659, PubMed:16040243, PubMed:16157682). Interacts
CC with nup189 (PubMed:16157682). {ECO:0000269|PubMed:16024659,
CC ECO:0000269|PubMed:16040243, ECO:0000269|PubMed:16157682}.
CC -!- INTERACTION:
CC O74910; Q9HDV4: lid2; NbExp=2; IntAct=EBI-904913, EBI-2105919;
CC O74910; Q10426: rik1; NbExp=3; IntAct=EBI-904913, EBI-1111936;
CC O74910; O94276: SPBP8B7.28c; NbExp=2; IntAct=EBI-904913, EBI-2651917;
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:16823372}. Nucleus
CC {ECO:0000269|PubMed:16823372, ECO:0000269|PubMed:18345014}. Chromosome
CC {ECO:0000269|PubMed:18345014}.
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DR EMBL; CU329672; CAA21064.1; -; Genomic_DNA.
DR PIR; T41478; T41478.
DR RefSeq; NP_587700.1; NM_001022695.2.
DR PDB; 4O9D; X-ray; 2.00 A; A/B=213-638.
DR PDBsum; 4O9D; -.
DR AlphaFoldDB; O74910; -.
DR SMR; O74910; -.
DR BioGRID; 275429; 258.
DR DIP; DIP-37644N; -.
DR IntAct; O74910; 7.
DR STRING; 4896.SPCC613.12c.1; -.
DR iPTMnet; O74910; -.
DR MaxQB; O74910; -.
DR PaxDb; O74910; -.
DR EnsemblFungi; SPCC613.12c.1; SPCC613.12c.1:pep; SPCC613.12c.
DR GeneID; 2538848; -.
DR KEGG; spo:SPCC613.12c; -.
DR PomBase; SPCC613.12c; raf1.
DR VEuPathDB; FungiDB:SPCC613.12c; -.
DR eggNOG; ENOG502RZG9; Eukaryota.
DR HOGENOM; CLU_429036_0_0_1; -.
DR InParanoid; O74910; -.
DR OMA; TKMIHFD; -.
DR PhylomeDB; O74910; -.
DR PRO; PR:O74910; -.
DR Proteomes; UP000002485; Chromosome III.
DR GO; GO:0000785; C:chromatin; IDA:PomBase.
DR GO; GO:0000781; C:chromosome, telomeric region; IEA:GOC.
DR GO; GO:0043494; C:CLRC complex; IDA:PomBase.
DR GO; GO:0005829; C:cytosol; HDA:PomBase.
DR GO; GO:0031934; C:mating-type region heterochromatin; TAS:PomBase.
DR GO; GO:0005634; C:nucleus; IDA:PomBase.
DR GO; GO:0005721; C:pericentric heterochromatin; IDA:PomBase.
DR GO; GO:0017053; C:transcription repressor complex; IBA:GO_Central.
DR GO; GO:0034080; P:CENP-A containing chromatin assembly; IMP:PomBase.
DR GO; GO:0031048; P:heterochromatin assembly by small RNA; IMP:PomBase.
DR GO; GO:0045141; P:meiotic telomere clustering; IMP:PomBase.
DR GO; GO:0000122; P:negative regulation of transcription by RNA polymerase II; IBA:GO_Central.
DR GO; GO:0031508; P:pericentric heterochromatin assembly; IMP:PomBase.
DR GO; GO:0030466; P:silent mating-type cassette heterochromatin assembly; IMP:PomBase.
DR GO; GO:0031509; P:subtelomeric heterochromatin assembly; IMP:PomBase.
DR Gene3D; 2.130.10.10; -; 1.
DR InterPro; IPR020472; G-protein_beta_WD-40_rep.
DR InterPro; IPR015943; WD40/YVTN_repeat-like_dom_sf.
DR InterPro; IPR001680; WD40_repeat.
DR InterPro; IPR019775; WD40_repeat_CS.
DR InterPro; IPR036322; WD40_repeat_dom_sf.
DR Pfam; PF00400; WD40; 2.
DR PRINTS; PR00320; GPROTEINBRPT.
DR SMART; SM00320; WD40; 5.
DR SUPFAM; SSF50978; SSF50978; 1.
DR PROSITE; PS00678; WD_REPEATS_1; 2.
DR PROSITE; PS50082; WD_REPEATS_2; 2.
DR PROSITE; PS50294; WD_REPEATS_REGION; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Chromatin regulator; Chromosome; Cytoplasm;
KW Direct protein sequencing; Nucleus; Reference proteome; Repeat;
KW Transcription; Transcription regulation; WD repeat.
FT CHAIN 1..638
FT /note="Rik1-associated factor 1"
FT /id="PRO_0000051497"
FT REPEAT 297..336
FT /note="WD 1"
FT REPEAT 486..525
FT /note="WD 2"
FT REPEAT 544..583
FT /note="WD 3"
FT REPEAT 587..626
FT /note="WD 4"
FT HELIX 226..228
FT /evidence="ECO:0007829|PDB:4O9D"
FT STRAND 231..236
FT /evidence="ECO:0007829|PDB:4O9D"
FT STRAND 243..248
FT /evidence="ECO:0007829|PDB:4O9D"
FT STRAND 252..259
FT /evidence="ECO:0007829|PDB:4O9D"
FT STRAND 271..276
FT /evidence="ECO:0007829|PDB:4O9D"
FT TURN 277..280
FT /evidence="ECO:0007829|PDB:4O9D"
FT STRAND 281..284
FT /evidence="ECO:0007829|PDB:4O9D"
FT STRAND 289..291
FT /evidence="ECO:0007829|PDB:4O9D"
FT STRAND 297..299
FT /evidence="ECO:0007829|PDB:4O9D"
FT STRAND 302..307
FT /evidence="ECO:0007829|PDB:4O9D"
FT STRAND 311..318
FT /evidence="ECO:0007829|PDB:4O9D"
FT STRAND 323..327
FT /evidence="ECO:0007829|PDB:4O9D"
FT STRAND 332..336
FT /evidence="ECO:0007829|PDB:4O9D"
FT STRAND 343..348
FT /evidence="ECO:0007829|PDB:4O9D"
FT STRAND 354..358
FT /evidence="ECO:0007829|PDB:4O9D"
FT STRAND 363..368
FT /evidence="ECO:0007829|PDB:4O9D"
FT TURN 370..372
FT /evidence="ECO:0007829|PDB:4O9D"
FT STRAND 375..381
FT /evidence="ECO:0007829|PDB:4O9D"
FT HELIX 384..388
FT /evidence="ECO:0007829|PDB:4O9D"
FT STRAND 392..399
FT /evidence="ECO:0007829|PDB:4O9D"
FT TURN 401..404
FT /evidence="ECO:0007829|PDB:4O9D"
FT STRAND 408..414
FT /evidence="ECO:0007829|PDB:4O9D"
FT STRAND 424..429
FT /evidence="ECO:0007829|PDB:4O9D"
FT TURN 430..433
FT /evidence="ECO:0007829|PDB:4O9D"
FT STRAND 434..438
FT /evidence="ECO:0007829|PDB:4O9D"
FT STRAND 445..451
FT /evidence="ECO:0007829|PDB:4O9D"
FT STRAND 456..463
FT /evidence="ECO:0007829|PDB:4O9D"
FT STRAND 465..474
FT /evidence="ECO:0007829|PDB:4O9D"
FT TURN 475..478
FT /evidence="ECO:0007829|PDB:4O9D"
FT STRAND 479..487
FT /evidence="ECO:0007829|PDB:4O9D"
FT STRAND 489..496
FT /evidence="ECO:0007829|PDB:4O9D"
FT STRAND 502..507
FT /evidence="ECO:0007829|PDB:4O9D"
FT STRAND 510..516
FT /evidence="ECO:0007829|PDB:4O9D"
FT STRAND 524..528
FT /evidence="ECO:0007829|PDB:4O9D"
FT STRAND 551..554
FT /evidence="ECO:0007829|PDB:4O9D"
FT STRAND 561..564
FT /evidence="ECO:0007829|PDB:4O9D"
FT STRAND 568..573
FT /evidence="ECO:0007829|PDB:4O9D"
FT STRAND 577..579
FT /evidence="ECO:0007829|PDB:4O9D"
FT STRAND 581..587
FT /evidence="ECO:0007829|PDB:4O9D"
FT STRAND 592..597
FT /evidence="ECO:0007829|PDB:4O9D"
FT STRAND 601..608
FT /evidence="ECO:0007829|PDB:4O9D"
FT STRAND 613..617
FT /evidence="ECO:0007829|PDB:4O9D"
FT STRAND 630..632
FT /evidence="ECO:0007829|PDB:4O9D"
SQ SEQUENCE 638 AA; 71536 MW; 6CD360D8748AAF98 CRC64;
MTNSSPRVKR RTDTQYLHSV SSKLPKVDFD TNNEEFFEEE FEIYDPFYRA ELPCPKPSLS
ISKHSIAKVP SNVNKRLELQ LLLTSGTFLP NSRPYLSERV RKHTHLLSNS ITGDDKPSLI
HVDFTPEECF ILQEAKLKFG PVNSVQFNDA YSTHISPKLP GRAYEDCQKF EIDNPSLSPV
DKHGAIILRT YKKNKKLLPD YLKSFYNAGS SYFQREQVHQ LMDGESVFFL KPWKHFNETS
GDTVCVAYNP LCEKFALGST AQDGAYNRLG NLWIGDFHSE TIQSLESHYK LNQVGEKEYS
TISDLCFSKG NLFLYTGAFD NAVKVWDMEG NLCGIFNAPT DYIHKLALSD DDLLAVACKN
GYGYLLSTDN STGEILTSAN LIYPEALEKG YSASLIEFSN FLGRSSDKVI IGYDSFHTSN
NRGCLALFDA STASFVQKFN TADEAFTSLY MHPSQVGFVA SSNTLSNGRV YYLDTRMYKV
CLNFTTTQKD INHATISNSG ILVTSSGTDN QTFVWDSRKP DKPLSLLKHG KTKMIHFDGA
NEEEVDAGIN MAQWQPKGNL FVTGGSDGIV KVWDLRLNNP FIQNFTEMNS AITYGGFSED
ASKLTVCCVG GDVNMYSLGN DNGNKFGEFR IIENRLLT
