NOP56_YEAST
ID NOP56_YEAST Reviewed; 504 AA.
AC Q12460; D6VYK0;
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 185.
DE RecName: Full=Nucleolar protein 56;
DE AltName: Full=Ribosome biosynthesis protein SIK1;
DE AltName: Full=Suppressor of I kappa b protein 1;
GN Name=NOP56; Synonyms=SIK1; OrderedLocusNames=YLR197W; ORFNames=L8167.9;
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 [GENOMIC DNA].
RC STRAIN=S288c / YPH1;
RX PubMed=7547500;
RA Morin P.J., Downs J.A., Snodgrass A.M., Gilmore T.D.;
RT "Genetic analysis of growth inhibition by GAL4-L kappa B-alpha in
RT Saccharomyces cerevisiae.";
RL Cell Growth Differ. 6:789-798(1995).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169871;
RA Johnston M., Hillier L.W., Riles L., Albermann K., Andre B., Ansorge W.,
RA Benes V., Brueckner M., Delius H., Dubois E., Duesterhoeft A.,
RA Entian K.-D., Floeth M., Goffeau A., Hebling U., Heumann K.,
RA Heuss-Neitzel D., Hilbert H., Hilger F., Kleine K., Koetter P., Louis E.J.,
RA Messenguy F., Mewes H.-W., Miosga T., Moestl D., Mueller-Auer S.,
RA Nentwich U., Obermaier B., Piravandi E., Pohl T.M., Portetelle D.,
RA Purnelle B., Rechmann S., Rieger M., Rinke M., Rose M., Scharfe M.,
RA Scherens B., Scholler P., Schwager C., Schwarz S., Underwood A.P.,
RA Urrestarazu L.A., Vandenbol M., Verhasselt P., Vierendeels F., Voet M.,
RA Volckaert G., Voss H., Wambutt R., Wedler E., Wedler H., Zimmermann F.K.,
RA Zollner A., Hani J., Hoheisel J.D.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome XII.";
RL Nature 387:87-90(1997).
RN [3]
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 [4]
RP FUNCTION, INTERACTION WITH NOP1 AND NOP58, SUBCELLULAR LOCATION, AND
RP MUTAGENESIS OF VAL-333; TYR-355 AND MET-385.
RX PubMed=9372940; DOI=10.1128/mcb.17.12.7088;
RA Gautier T., Berges T., Tollervey D., Hurt E.;
RT "Nucleolar KKE/D repeat proteins Nop56p and Nop58p interact with Nop1p and
RT are required for ribosome biogenesis.";
RL Mol. Cell. Biol. 17:7088-7098(1997).
RN [5]
RP IDENTIFICATION IN SSU PROCESSOME BY MASS SPECTROMETRY.
RX PubMed=12068309; DOI=10.1038/nature00769;
RA Dragon F., Gallagher J.E.G., Compagnone-Post P.A., Mitchell B.M.,
RA Porwancher K.A., Wehner K.A., Wormsley S., Settlage R.E., Shabanowitz J.,
RA Osheim Y., Beyer A.L., Hunt D.F., Baserga S.J.;
RT "A large nucleolar U3 ribonucleoprotein required for 18S ribosomal RNA
RT biogenesis.";
RL Nature 417:967-970(2002).
RN [6]
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 [7]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-321, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=18407956; DOI=10.1074/mcp.m700468-mcp200;
RA Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.;
RT "A multidimensional chromatography technology for in-depth phosphoproteome
RT analysis.";
RL Mol. Cell. Proteomics 7:1389-1396(2008).
CC -!- FUNCTION: Required for 60S ribosomal subunit synthesis.
CC {ECO:0000269|PubMed:9372940}.
CC -!- SUBUNIT: Interacts with NOP1 and NOP58. Component of the ribosomal
CC small subunit (SSU) processome composed of at least 40 protein subunits
CC and snoRNA U3. {ECO:0000269|PubMed:12068309,
CC ECO:0000269|PubMed:9372940}.
CC -!- INTERACTION:
CC Q12460; P15646: NOP1; NbExp=5; IntAct=EBI-17148, EBI-6838;
CC Q12460; P39990: SNU13; NbExp=4; IntAct=EBI-17148, EBI-12032;
CC -!- SUBCELLULAR LOCATION: Nucleus, nucleolus {ECO:0000269|PubMed:9372940}.
CC -!- MISCELLANEOUS: Present with 13500 molecules/cell in log phase SD
CC medium. {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the NOP5/NOP56 family. {ECO:0000305}.
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DR EMBL; U20237; AAC49066.1; -; Genomic_DNA.
DR EMBL; U14913; AAB67431.1; -; Genomic_DNA.
DR EMBL; BK006945; DAA09516.1; -; Genomic_DNA.
DR PIR; S48550; S48550.
DR RefSeq; NP_013298.1; NM_001182084.1.
DR PDB; 5WLC; EM; 3.80 A; SA=1-504.
DR PDB; 5WYJ; EM; 8.70 A; 3D=1-504.
DR PDB; 5WYK; EM; 4.50 A; 3D=1-504.
DR PDB; 6KE6; EM; 3.40 A; 3D=1-504.
DR PDB; 6LQP; EM; 3.20 A; 3D=1-504.
DR PDB; 6LQQ; EM; 4.10 A; 3D=1-504.
DR PDB; 6LQR; EM; 8.60 A; 3D=1-504.
DR PDB; 6LQS; EM; 3.80 A; 3D=1-504.
DR PDB; 6LQT; EM; 4.90 A; 3D=1-504.
DR PDB; 6LQU; EM; 3.70 A; 3D=1-504.
DR PDB; 6LQV; EM; 4.80 A; 3D=1-504.
DR PDB; 6ND4; EM; 4.30 A; a=1-504.
DR PDB; 6ZDT; X-ray; 1.71 A; B=1-166.
DR PDB; 6ZQA; EM; 4.40 A; CD=1-504.
DR PDB; 6ZQB; EM; 3.90 A; CD=1-504.
DR PDB; 6ZQC; EM; 3.80 A; CD=1-504.
DR PDB; 6ZQD; EM; 3.80 A; CD=1-504.
DR PDB; 6ZQE; EM; 7.10 A; CD=1-504.
DR PDB; 7AJT; EM; 4.60 A; CD=1-504.
DR PDB; 7AJU; EM; 3.80 A; CD=1-504.
DR PDB; 7D4I; EM; 4.00 A; 3D=1-504.
DR PDB; 7D5S; EM; 4.60 A; 3D=1-504.
DR PDB; 7D5T; EM; 6.00 A; 3D=1-504.
DR PDB; 7D63; EM; 12.30 A; 3D=1-504.
DR PDBsum; 5WLC; -.
DR PDBsum; 5WYJ; -.
DR PDBsum; 5WYK; -.
DR PDBsum; 6KE6; -.
DR PDBsum; 6LQP; -.
DR PDBsum; 6LQQ; -.
DR PDBsum; 6LQR; -.
DR PDBsum; 6LQS; -.
DR PDBsum; 6LQT; -.
DR PDBsum; 6LQU; -.
DR PDBsum; 6LQV; -.
DR PDBsum; 6ND4; -.
DR PDBsum; 6ZDT; -.
DR PDBsum; 6ZQA; -.
DR PDBsum; 6ZQB; -.
DR PDBsum; 6ZQC; -.
DR PDBsum; 6ZQD; -.
DR PDBsum; 6ZQE; -.
DR PDBsum; 7AJT; -.
DR PDBsum; 7AJU; -.
DR PDBsum; 7D4I; -.
DR PDBsum; 7D5S; -.
DR PDBsum; 7D5T; -.
DR PDBsum; 7D63; -.
DR AlphaFoldDB; Q12460; -.
DR SMR; Q12460; -.
DR BioGRID; 31467; 490.
DR ComplexPortal; CPX-1604; Small ribosomal subunit processome, variant 1.
DR ComplexPortal; CPX-1607; Small ribosomal subunit processome, variant 2.
DR ComplexPortal; CPX-1608; Small ribosomal subunit processome, variant 3.
DR ComplexPortal; CPX-729; Box C/D snoRNP complex.
DR DIP; DIP-4405N; -.
DR IntAct; Q12460; 45.
DR MINT; Q12460; -.
DR STRING; 4932.YLR197W; -.
DR CarbonylDB; Q12460; -.
DR iPTMnet; Q12460; -.
DR MaxQB; Q12460; -.
DR PaxDb; Q12460; -.
DR PRIDE; Q12460; -.
DR EnsemblFungi; YLR197W_mRNA; YLR197W; YLR197W.
DR GeneID; 850894; -.
DR KEGG; sce:YLR197W; -.
DR SGD; S000004187; NOP56.
DR VEuPathDB; FungiDB:YLR197W; -.
DR eggNOG; KOG2573; Eukaryota.
DR GeneTree; ENSGT00940000153534; -.
DR HOGENOM; CLU_015495_4_0_1; -.
DR InParanoid; Q12460; -.
DR OMA; DNYMFAK; -.
DR BioCyc; YEAST:G3O-32318-MON; -.
DR Reactome; R-SCE-6791226; Major pathway of rRNA processing in the nucleolus and cytosol.
DR PRO; PR:Q12460; -.
DR Proteomes; UP000002311; Chromosome XII.
DR RNAct; Q12460; protein.
DR GO; GO:0030686; C:90S preribosome; HDA:SGD.
DR GO; GO:0031428; C:box C/D RNP complex; IDA:SGD.
DR GO; GO:0005730; C:nucleolus; IDA:SGD.
DR GO; GO:0005654; C:nucleoplasm; TAS:Reactome.
DR GO; GO:0005634; C:nucleus; HDA:SGD.
DR GO; GO:0032040; C:small-subunit processome; IDA:SGD.
DR GO; GO:0003729; F:mRNA binding; HDA:SGD.
DR GO; GO:0030515; F:snoRNA binding; IBA:GO_Central.
DR GO; GO:0000494; P:box C/D RNA 3'-end processing; IDA:ComplexPortal.
DR GO; GO:0030490; P:maturation of SSU-rRNA; IC:ComplexPortal.
DR GO; GO:0000154; P:rRNA modification; TAS:SGD.
DR GO; GO:0006364; P:rRNA processing; IMP:SGD.
DR GO; GO:0000452; P:snoRNA guided rRNA 2'-O-methylation; IDA:ComplexPortal.
DR Gene3D; 1.10.246.90; -; 1.
DR InterPro; IPR045056; Nop56/Nop58.
DR InterPro; IPR012974; NOP5_N.
DR InterPro; IPR042239; Nop_C.
DR InterPro; IPR002687; Nop_dom.
DR InterPro; IPR036070; Nop_dom_sf.
DR InterPro; IPR012976; NOSIC.
DR PANTHER; PTHR10894; PTHR10894; 1.
DR Pfam; PF01798; Nop; 1.
DR Pfam; PF08156; NOP5NT; 1.
DR SMART; SM00931; NOSIC; 1.
DR SUPFAM; SSF89124; SSF89124; 1.
DR PROSITE; PS51358; NOP; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Nucleus; Phosphoprotein; Reference proteome;
KW Ribonucleoprotein; Ribosome biogenesis.
FT CHAIN 1..504
FT /note="Nucleolar protein 56"
FT /id="PRO_0000219030"
FT DOMAIN 299..417
FT /note="Nop"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00690"
FT REGION 439..504
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 439..470
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 321
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:18407956"
FT MUTAGEN 333
FT /note="V->A: Reduced growth rate at all temperatures; when
FT associated with R-385."
FT /evidence="ECO:0000269|PubMed:9372940"
FT MUTAGEN 355
FT /note="Y->C: At 37 degrees, growth slows after 6 to 8 hours
FT and cell division stops after 20 hours."
FT /evidence="ECO:0000269|PubMed:9372940"
FT MUTAGEN 385
FT /note="M->R: Reduced growth rate at all temperatures; when
FT associated with A-333."
FT /evidence="ECO:0000269|PubMed:9372940"
FT STRAND 6..11
FT /evidence="ECO:0007829|PDB:6ZDT"
FT STRAND 14..20
FT /evidence="ECO:0007829|PDB:6ZDT"
FT HELIX 27..30
FT /evidence="ECO:0007829|PDB:6ZDT"
FT HELIX 31..38
FT /evidence="ECO:0007829|PDB:6ZDT"
FT HELIX 41..44
FT /evidence="ECO:0007829|PDB:6ZDT"
FT TURN 45..47
FT /evidence="ECO:0007829|PDB:6ZDT"
FT STRAND 48..55
FT /evidence="ECO:0007829|PDB:6ZDT"
FT HELIX 59..70
FT /evidence="ECO:0007829|PDB:6ZDT"
FT HELIX 76..85
FT /evidence="ECO:0007829|PDB:6ZDT"
FT STRAND 96..99
FT /evidence="ECO:0007829|PDB:6ZDT"
FT HELIX 103..105
FT /evidence="ECO:0007829|PDB:6ZDT"
FT HELIX 106..112
FT /evidence="ECO:0007829|PDB:6ZDT"
FT STRAND 116..119
FT /evidence="ECO:0007829|PDB:6ZDT"
FT HELIX 122..134
FT /evidence="ECO:0007829|PDB:6ZDT"
FT HELIX 135..138
FT /evidence="ECO:0007829|PDB:6ZDT"
FT HELIX 146..163
FT /evidence="ECO:0007829|PDB:6ZDT"
SQ SEQUENCE 504 AA; 56864 MW; F8522A5870EF4842 CRC64;
MAPIEYLLFE EPTGYAVFKV KLQQDDIGSR LKEVQEQIND FGAFTKLIEL VSFAPFKGAA
EALENANDIS EGLVSESLKA ILDLNLPKAS SKKKNITLAI SDKNLGPSIK EEFPYVDCIS
NELAQDLIRG VRLHGEKLFK GLQSGDLERA QLGLGHAYSR AKVKFSVQKN DNHIIQAIAL
LDQLDKDINT FAMRVKEWYG WHFPELAKLV PDNYTFAKLV LFIKDKASLN DDSLHDLAAL
LNEDSGIAQR VIDNARISMG QDISETDMEN VCVFAQRVAS LADYRRQLYD YLCEKMHTVA
PNLSELIGEV IGARLISHAG SLTNLSKQAA STVQILGAEK ALFRALKTKG NTPKYGLIYH
SGFISKASAK NKGRISRYLA NKCSMASRID NYSEEPSNVF GSVLKKQVEQ RLEFYNTGKP
TLKNELAIQE AMELYNKDKP AAEVEETKEK ESSKKRKLED DDEEKKEKKE KKSKKEKKEK
KEKKDKKEKK DKKEKKDKKK KSKD
