NAF1_YEAST
ID NAF1_YEAST Reviewed; 492 AA.
AC P53919; B0KZR2; B0KZS1; B0KZT9; B0KZZ3; B0L002; D6W159;
DT 01-OCT-1996, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-1996, sequence version 1.
DT 03-AUG-2022, entry version 166.
DE RecName: Full=H/ACA ribonucleoprotein complex non-core subunit NAF1;
DE AltName: Full=Nuclear assembly factor 1;
GN Name=NAF1; OrderedLocusNames=YNL124W; ORFNames=N1888;
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].
RX PubMed=9090055;
RX DOI=10.1002/(sici)1097-0061(19970315)13:3<261::aid-yea64>3.0.co;2-l;
RA de Antoni A., D'Angelo M., Dal Pero F., Sartorello F., Pandolfo D.,
RA Pallavicini A., Lanfranchi G., Valle G.;
RT "The DNA sequence of cosmid 14-13b from chromosome XIV of Saccharomyces
RT cerevisiae reveals an unusually high number of overlapping open reading
RT frames.";
RL Yeast 13:261-266(1997).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169873;
RA Philippsen P., Kleine K., Poehlmann R., Duesterhoeft A., Hamberg K.,
RA Hegemann J.H., Obermaier B., Urrestarazu L.A., Aert R., Albermann K.,
RA Altmann R., Andre B., Baladron V., Ballesta J.P.G., Becam A.-M.,
RA Beinhauer J.D., Boskovic J., Buitrago M.J., Bussereau F., Coster F.,
RA Crouzet M., D'Angelo M., Dal Pero F., De Antoni A., del Rey F., Doignon F.,
RA Domdey H., Dubois E., Fiedler T.A., Fleig U., Floeth M., Fritz C.,
RA Gaillardin C., Garcia-Cantalejo J.M., Glansdorff N., Goffeau A.,
RA Gueldener U., Herbert C.J., Heumann K., Heuss-Neitzel D., Hilbert H.,
RA Hinni K., Iraqui Houssaini I., Jacquet M., Jimenez A., Jonniaux J.-L.,
RA Karpfinger-Hartl L., Lanfranchi G., Lepingle A., Levesque H., Lyck R.,
RA Maftahi M., Mallet L., Maurer C.T.C., Messenguy F., Mewes H.-W., Moestl D.,
RA Nasr F., Nicaud J.-M., Niedenthal R.K., Pandolfo D., Pierard A.,
RA Piravandi E., Planta R.J., Pohl T.M., Purnelle B., Rebischung C.,
RA Remacha M.A., Revuelta J.L., Rinke M., Saiz J.E., Sartorello F.,
RA Scherens B., Sen-Gupta M., Soler-Mira A., Urbanus J.H.M., Valle G.,
RA Van Dyck L., Verhasselt P., Vierendeels F., Vissers S., Voet M.,
RA Volckaert G., Wach A., Wambutt R., Wedler H., Zollner A., Hani J.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome XIV and its
RT evolutionary implications.";
RL Nature 387:93-98(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 NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-50.
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=8619318; DOI=10.1002/yea.320111210;
RA Mallet L., Bussereau F., Jacquet M.;
RT "A 43.5 kb segment of yeast chromosome XIV, which contains MFA2, MEP2,
RT CAP/SRV2, NAM9, FKB1/FPR1/RBP1, MOM22 and CPT1, predicts an adenosine
RT deaminase gene and 14 new open reading frames.";
RL Yeast 11:1195-1209(1995).
RN [5]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 371-492, AND VARIANTS ALA-378;
RP ILE-423; SER-424; ALA-426 AND ASN-480.
RC STRAIN=ATCC 200060 / W303, S103, SK1, V1-09, YJM 1129, YJM 269, YJM 270,
RC YJM 320, YJM 326, YJM 339, YJM 627, and YJM230;
RX PubMed=18780730; DOI=10.1534/genetics.108.092932;
RA Sinha H., David L., Pascon R.C., Clauder-Muenster S., Krishnakumar S.,
RA Nguyen M., Shi G., Dean J., Davis R.W., Oefner P.J., McCusker J.H.,
RA Steinmetz L.M.;
RT "Sequential elimination of major-effect contributors identifies additional
RT quantitative trait loci conditioning high-temperature growth in yeast.";
RL Genetics 180:1661-1670(2008).
RN [6]
RP FUNCTION, SUBCELLULAR LOCATION, AND INTERACTION WITH CBF5; SHQ1 AND NHP2.
RX PubMed=12228251; DOI=10.1074/jbc.m207669200;
RA Yang P.K., Rotondo G., Porras T., Legrain P., Chanfreau G.;
RT "The Shq1p.Naf1p complex is required for box H/ACA small nucleolar
RT ribonucleoprotein particle biogenesis.";
RL J. Biol. Chem. 277:45235-45242(2002).
RN [7]
RP FUNCTION, AND SUBCELLULAR LOCATION.
RX PubMed=12242285; DOI=10.1128/mcb.22.20.7053-7065.2002;
RA Dez C., Noaillac-Depeyre J., Caizergues-Ferrer M., Henry Y.;
RT "Naf1p, an essential nucleoplasmic factor specifically required for
RT accumulation of box H/ACA small nucleolar RNPs.";
RL Mol. Cell. Biol. 22:7053-7065(2002).
RN [8]
RP FUNCTION, RNA-BINDING, SUBCELLULAR LOCATION, AND INTERACTION WITH CBF5;
RP NHP2 AND RPB1.
RX PubMed=12515383;
RA Fatica A., Dlakic M., Tollervey D.;
RT "Naf1 p is a box H/ACA snoRNP assembly factor.";
RL RNA 8:1502-1514(2002).
RN [9]
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 [10]
RP SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
RX PubMed=14562095; DOI=10.1038/nature02026;
RA Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W.,
RA Weissman J.S., O'Shea E.K.;
RT "Global analysis of protein localization in budding yeast.";
RL Nature 425:686-691(2003).
RN [11]
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 [12]
RP FUNCTION, AND INTERACTION WITH CBF5.
RX PubMed=15798213; DOI=10.1128/mcb.25.8.3295-3304.2005;
RA Yang P.K., Hoareau C., Froment C., Monsarrat B., Henry Y., Chanfreau G.;
RT "Cotranscriptional recruitment of the pseudouridylsynthetase Cbf5p and of
RT the RNA binding protein Naf1p during H/ACA snoRNP assembly.";
RL Mol. Cell. Biol. 25:3295-3304(2005).
RN [13]
RP FUNCTION, AND INTERACTION WITH CBF5 AND NHP2.
RX PubMed=15964797; DOI=10.1128/mcb.25.13.5396-5403.2005;
RA Ballarino M., Morlando M., Pagano F., Fatica A., Bozzoni I.;
RT "The cotranscriptional assembly of snoRNPs controls the biosynthesis of
RT H/ACA snoRNAs in Saccharomyces cerevisiae.";
RL Mol. Cell. Biol. 25:5396-5403(2005).
RN [14]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-255, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=ADR376;
RX PubMed=17330950; DOI=10.1021/pr060559j;
RA Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J.,
RA Elias J.E., Gygi S.P.;
RT "Large-scale phosphorylation analysis of alpha-factor-arrested
RT Saccharomyces cerevisiae.";
RL J. Proteome Res. 6:1190-1197(2007).
RN [15]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-255, 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).
RN [16]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-255, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=19779198; DOI=10.1126/science.1172867;
RA Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.;
RT "Global analysis of Cdk1 substrate phosphorylation sites provides insights
RT into evolution.";
RL Science 325:1682-1686(2009).
RN [17]
RP X-RAY CRYSTALLOGRAPHY (2.74 ANGSTROMS) OF 109-234, AND DOMAIN.
RX PubMed=17612558; DOI=10.1016/j.jmb.2007.06.031;
RA Leulliot N., Godin K.S., Hoareau-Aveilla C., Quevillon-Cheruel S.,
RA Varani G., Henry Y., Van Tilbeurgh H.;
RT "The box H/ACA RNP assembly factor Naf1p contains a domain homologous to
RT Gar1p mediating its interaction with Cbf5p.";
RL J. Mol. Biol. 371:1338-1353(2007).
CC -!- FUNCTION: RNA-binding protein required for the maturation of box H/ACA
CC snoRNPs complex and ribosome biogenesis. During assembly of the H/ACA
CC snoRNPs complex, it associates with the complex and disappears during
CC maturation of the complex and is replaced by GAR1 to yield mature H/ACA
CC snoRNPs complex. Acts as a competitive binder for CBF5 probably
CC required to prevent non-cognate RNAs from being loaded during transport
CC of the particle by inducing a non-productive conformation of CBF5.
CC {ECO:0000269|PubMed:12228251, ECO:0000269|PubMed:12242285,
CC ECO:0000269|PubMed:12515383, ECO:0000269|PubMed:15798213,
CC ECO:0000269|PubMed:15964797}.
CC -!- SUBUNIT: During assembly of the complex, component of the small
CC nucleolar ribonucleoprotein particles containing H/ACA-type snoRNAs
CC (H/ACA snoRNPs) which contains CBF5, NAF1, NHP2 and NOP10 proteins.
CC Interacts with SHQ1. Interacts directly with CBF5. Interacts with
CC hyperphosphorylated C-terminal domain (CTD) of RNA polymerase II large
CC subunit (RPB1). {ECO:0000269|PubMed:12228251,
CC ECO:0000269|PubMed:12515383, ECO:0000269|PubMed:15798213,
CC ECO:0000269|PubMed:15964797}.
CC -!- INTERACTION:
CC P53919; P33322: CBF5; NbExp=6; IntAct=EBI-28887, EBI-4105;
CC P53919; P32495: NHP2; NbExp=3; IntAct=EBI-28887, EBI-12014;
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:12228251,
CC ECO:0000269|PubMed:12242285, ECO:0000269|PubMed:12515383,
CC ECO:0000269|PubMed:14562095}. Note=Mostly present in the nucleoplasm.
CC Absent from the nucleolus.
CC -!- DOMAIN: The central region (136-221) reveals a striking structural
CC homology with the core domain of GAR1. {ECO:0000269|PubMed:17612558}.
CC -!- MISCELLANEOUS: Present with 1810 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the NAF1 family. {ECO:0000305}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; Z69382; CAA93381.1; -; Genomic_DNA.
DR EMBL; Z71400; CAA96005.1; -; Genomic_DNA.
DR EMBL; EF125216; ABN58535.1; -; Genomic_DNA.
DR EMBL; EF125217; ABN58543.1; -; Genomic_DNA.
DR EMBL; EF125218; ABN58552.1; -; Genomic_DNA.
DR EMBL; EF125219; ABN58561.1; -; Genomic_DNA.
DR EMBL; EF125220; ABN58570.1; -; Genomic_DNA.
DR EMBL; EF125221; ABN58579.1; -; Genomic_DNA.
DR EMBL; EF125222; ABN58588.1; -; Genomic_DNA.
DR EMBL; EF125223; ABN58597.1; -; Genomic_DNA.
DR EMBL; EF125224; ABN58606.1; -; Genomic_DNA.
DR EMBL; EF125225; ABN58615.1; -; Genomic_DNA.
DR EMBL; EF125226; ABN58624.1; -; Genomic_DNA.
DR EMBL; EF125228; ABN58642.1; -; Genomic_DNA.
DR EMBL; BK006947; DAA10425.1; -; Genomic_DNA.
DR PIR; S63065; S63065.
DR RefSeq; NP_014275.3; NM_001182962.3.
DR PDB; 2V3M; X-ray; 2.74 A; A/B/C/D/E/F=109-232.
DR PDBsum; 2V3M; -.
DR AlphaFoldDB; P53919; -.
DR SMR; P53919; -.
DR BioGRID; 35703; 214.
DR DIP; DIP-4345N; -.
DR IntAct; P53919; 257.
DR MINT; P53919; -.
DR STRING; 4932.YNL124W; -.
DR iPTMnet; P53919; -.
DR MaxQB; P53919; -.
DR PaxDb; P53919; -.
DR PRIDE; P53919; -.
DR EnsemblFungi; YNL124W_mRNA; YNL124W; YNL124W.
DR GeneID; 855599; -.
DR KEGG; sce:YNL124W; -.
DR SGD; S000005068; NAF1.
DR VEuPathDB; FungiDB:YNL124W; -.
DR eggNOG; KOG2236; Eukaryota.
DR GeneTree; ENSGT01040000244168; -.
DR HOGENOM; CLU_025072_1_0_1; -.
DR InParanoid; P53919; -.
DR OMA; PSVNMGW; -.
DR BioCyc; YEAST:G3O-33145-MON; -.
DR EvolutionaryTrace; P53919; -.
DR PRO; PR:P53919; -.
DR Proteomes; UP000002311; Chromosome XIV.
DR RNAct; P53919; protein.
DR GO; GO:0005654; C:nucleoplasm; IDA:SGD.
DR GO; GO:0005634; C:nucleus; IDA:SGD.
DR GO; GO:0005732; C:sno(s)RNA-containing ribonucleoprotein complex; IBA:GO_Central.
DR GO; GO:0003723; F:RNA binding; IPI:SGD.
DR GO; GO:0000493; P:box H/ACA snoRNP assembly; IMP:SGD.
DR GO; GO:0001522; P:pseudouridine synthesis; IEA:InterPro.
DR GO; GO:0042254; P:ribosome biogenesis; IBA:GO_Central.
DR GO; GO:0006364; P:rRNA processing; IEA:UniProtKB-KW.
DR Gene3D; 2.40.10.230; -; 1.
DR InterPro; IPR038664; Gar1/Naf1_Cbf5-bd_sf.
DR InterPro; IPR007504; H/ACA_rnp_Gar1/Naf1.
DR InterPro; IPR040309; Naf1.
DR InterPro; IPR009000; Transl_B-barrel_sf.
DR PANTHER; PTHR31633; PTHR31633; 1.
DR Pfam; PF04410; Gar1; 1.
DR SUPFAM; SSF50447; SSF50447; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Nucleus; Phosphoprotein; Reference proteome;
KW Ribonucleoprotein; Ribosome biogenesis; RNA-binding; rRNA processing.
FT CHAIN 1..492
FT /note="H/ACA ribonucleoprotein complex non-core subunit
FT NAF1"
FT /id="PRO_0000203428"
FT REGION 1..117
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 172..230
FT /note="RNA-binding"
FT REGION 237..351
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 472..492
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 17..46
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 51..72
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 73..106
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 277..293
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 334..351
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 255
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:17330950,
FT ECO:0007744|PubMed:18407956, ECO:0007744|PubMed:19779198"
FT VARIANT 378
FT /note="P -> A (in strain: YJM269, YJM270, YJM326 and
FT YJM1129)"
FT /evidence="ECO:0000269|PubMed:18780730"
FT VARIANT 423
FT /note="M -> I (in strain: YJM627)"
FT /evidence="ECO:0000269|PubMed:18780730"
FT VARIANT 424
FT /note="P -> S (in strain: YJM269, YJM270, YJM326 and
FT YJM1129)"
FT /evidence="ECO:0000269|PubMed:18780730"
FT VARIANT 426
FT /note="T -> A (in strain: SK1, V1-09, YJM269, YJM270,
FT YJM280, YJM320, YJM326, YJM339, YJM627, YJM789 and
FT YJM1129)"
FT /evidence="ECO:0000269|PubMed:18780730"
FT VARIANT 480
FT /note="H -> N (in strain: V1-09 and YJM627)"
FT /evidence="ECO:0000269|PubMed:18780730"
FT STRAND 137..147
FT /evidence="ECO:0007829|PDB:2V3M"
FT STRAND 150..155
FT /evidence="ECO:0007829|PDB:2V3M"
FT STRAND 169..172
FT /evidence="ECO:0007829|PDB:2V3M"
FT STRAND 177..180
FT /evidence="ECO:0007829|PDB:2V3M"
FT STRAND 183..186
FT /evidence="ECO:0007829|PDB:2V3M"
FT STRAND 188..190
FT /evidence="ECO:0007829|PDB:2V3M"
FT STRAND 192..196
FT /evidence="ECO:0007829|PDB:2V3M"
FT HELIX 199..201
FT /evidence="ECO:0007829|PDB:2V3M"
FT HELIX 202..209
FT /evidence="ECO:0007829|PDB:2V3M"
FT TURN 210..213
FT /evidence="ECO:0007829|PDB:2V3M"
FT STRAND 214..219
FT /evidence="ECO:0007829|PDB:2V3M"
SQ SEQUENCE 492 AA; 54949 MW; 5A496278070F6255 CRC64;
MSDDLFSKAL ENPDQDLNVE LPKDDVDLGL LGDGGNERKT DEPVADAERS TGLGSGSSES
ESDSGSDSDS DSGSSGSEDD SADQDVEGED EGGDAIENED EDEDPSPSGP ILSKNEILEE
TVPELPEDYE ISEKTIITPI GVLKSAFENN IIIHATMSGE KRVLKEGSIF CLEDRTLIGM
LTEVFGPLQN PFYRIKLPDS KKNLFDELKV RLGEKAFIVT PDAHWIDTFE LKRNKGTDAS
NGYDEELPEE EQEFSDDEKE ALFKKMKKQQ RQRKKRDNRK LANDSDNVKV KRARQPKANS
LPKLVPPLGM SSNAPMQHGY KSRNARENIK RESSATSNRN GSSPVPITQH HQQQFSANNY
PFPQQPNGMP YPPYSPFPQP TNFQYPPPPF GQATPAQFSN TVPYGSLPPA YNNMSPPTQQ
SFMPMTQSQP PLPYGVPPMN QMQNPMYIQP PPQAPPQGNG NFQQVMELHQ ILLQQQQQQH
QYQHQHQQDP RT
