ID NOB1_YEAST Reviewed; 459 AA.
AC Q08444; D6W2B9; O00021;
DT 09-JAN-2007, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 27-MAR-2024, entry version 172.
DE RecName: Full=20S-pre-rRNA D-site endonuclease NOB1;
DE EC=3.1.-.-;
DE AltName: Full=NIN1-binding protein;
DE AltName: Full=Pre-rRNA-processing endonuclease NOB1;
GN Name=NOB1; OrderedLocusNames=YOR056C; ORFNames=YOR29-07;
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=9133743;
RX DOI=10.1002/(sici)1097-0061(19970330)13:4<379::aid-yea85>3.0.co;2-g;
RA Valens M., Bohn C., Daignan-Fornier B., Dang V.-D., Bolotin-Fukuhara M.;
RT "The sequence of a 54.7 kb fragment of yeast chromosome XV reveals the
RT presence of two tRNAs and 24 new open reading frames.";
RL Yeast 13:379-390(1997).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169874;
RA Dujon B., Albermann K., Aldea M., Alexandraki D., Ansorge W., Arino J.,
RA Benes V., Bohn C., Bolotin-Fukuhara M., Bordonne R., Boyer J., Camasses A.,
RA Casamayor A., Casas C., Cheret G., Cziepluch C., Daignan-Fornier B.,
RA Dang V.-D., de Haan M., Delius H., Durand P., Fairhead C., Feldmann H.,
RA Gaillon L., Galisson F., Gamo F.-J., Gancedo C., Goffeau A., Goulding S.E.,
RA Grivell L.A., Habbig B., Hand N.J., Hani J., Hattenhorst U., Hebling U.,
RA Hernando Y., Herrero E., Heumann K., Hiesel R., Hilger F., Hofmann B.,
RA Hollenberg C.P., Hughes B., Jauniaux J.-C., Kalogeropoulos A.,
RA Katsoulou C., Kordes E., Lafuente M.J., Landt O., Louis E.J., Maarse A.C.,
RA Madania A., Mannhaupt G., Marck C., Martin R.P., Mewes H.-W., Michaux G.,
RA Paces V., Parle-McDermott A.G., Pearson B.M., Perrin A., Pettersson B.,
RA Poch O., Pohl T.M., Poirey R., Portetelle D., Pujol A., Purnelle B.,
RA Ramezani Rad M., Rechmann S., Schwager C., Schweizer M., Sor F., Sterky F.,
RA Tarassov I.A., Teodoru C., Tettelin H., Thierry A., Tobiasch E.,
RA Tzermia M., Uhlen M., Unseld M., Valens M., Vandenbol M., Vetter I.,
RA Vlcek C., Voet M., Volckaert G., Voss H., Wambutt R., Wedler H.,
RA Wiemann S., Winsor B., Wolfe K.H., Zollner A., Zumstein E., Kleine K.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome XV.";
RL Nature 387:98-102(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 INTERACTION WITH PNO1, SUBCELLULAR LOCATION, AND MUTAGENESIS OF LEU-279;
RP GLN-280 AND MET-281.
RX PubMed=12502737; DOI=10.1101/gad.1025602;
RA Tone Y., Toh-e A.;
RT "Nob1p is required for biogenesis of the 26S proteasome and degraded upon
RT its maturation in Saccharomyces cerevisiae.";
RL Genes Dev. 16:3142-3157(2002).
RN [5]
RP SUBCELLULAR LOCATION.
RX PubMed=12628929; DOI=10.1093/emboj/cdg121;
RA Schaefer T., Strauss D., Petfalski E., Tollervey D., Hurt E.;
RT "The path from nucleolar 90S to cytoplasmic 40S pre-ribosomes.";
RL EMBO J. 22:1370-1380(2003).
RN [6]
RP FUNCTION, AND SUBCELLULAR LOCATION.
RX PubMed=12588997; DOI=10.1128/mcb.23.5.1798-1807.2003;
RA Fatica A., Oeffinger M., Dlakic M., Tollervey D.;
RT "Nob1p is required for cleavage of the 3' end of 18S rRNA.";
RL Mol. Cell. Biol. 23:1798-1807(2003).
RN [7]
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 [8]
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 [9]
RP SUBUNIT.
RX PubMed=15037774; DOI=10.1261/rna.5162204;
RA Vanrobays E., Gelugne J.-P., Caizergues-Ferrer M., Lafontaine D.L.J.;
RT "Dim2p, a KH-domain protein required for small ribosomal subunit
RT synthesis.";
RL RNA 10:645-656(2004).
RN [10]
RP FUNCTION, AND MUTAGENESIS OF ASP-92 AND ASP-110.
RX PubMed=15388878; DOI=10.1261/rna.7123504;
RA Fatica A., Tollervey D., Dlakic M.;
RT "PIN domain of Nob1p is required for D-site cleavage in 20S pre-rRNA.";
RL RNA 10:1698-1701(2004).
RN [11]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=22814378; DOI=10.1073/pnas.1210303109;
RA Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A.,
RA Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E., Timmerman E.,
RA Prieto J., Arnesen T., Sherman F., Gevaert K., Aldabe R.;
RT "N-terminal acetylome analyses and functional insights of the N-terminal
RT acetyltransferase NatB.";
RL Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012).
CC -!- FUNCTION: Required for the synthesis of 40S ribosome subunits. Has a
CC role in processing 20S pre-rRNA into the mature 18S rRNA, where it is
CC required for cleavage at the 3' end of the mature 18S rRNA (D-site).
CC Accompanies the 20S pre-rRNA from the nucleus to the cytoplasm. In
CC association with NIN1, may promote the recruitment of the proteasome to
CC the ribosomal subunits stalled in maturation.
CC {ECO:0000269|PubMed:12588997, ECO:0000269|PubMed:15388878}.
CC -!- SUBUNIT: Component of the small ribosomal subunit, ribosomal RNA
CC processing complex (SSU RRP complex). Interacts with PNO1.
CC {ECO:0000269|PubMed:12502737, ECO:0000269|PubMed:15037774}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm. Nucleus, nucleolus. Endoplasmic
CC reticulum.
CC -!- MISCELLANEOUS: Present with 4490 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the NOB1 family. {ECO:0000305}.
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DR EMBL; Z70678; CAA94541.1; -; Genomic_DNA.
DR EMBL; Z74964; CAA99249.1; -; Genomic_DNA.
DR EMBL; BK006948; DAA10835.1; -; Genomic_DNA.
DR PIR; S66939; S66939.
DR RefSeq; NP_014699.1; NM_001183475.1.
DR PDB; 8C01; EM; 2.70 A; o=1-459.
DR PDBsum; 8C01; -.
DR AlphaFoldDB; Q08444; -.
DR SMR; Q08444; -.
DR BioGRID; 34454; 258.
DR DIP; DIP-6440N; -.
DR IntAct; Q08444; 35.
DR MINT; Q08444; -.
DR STRING; 4932.YOR056C; -.
DR iPTMnet; Q08444; -.
DR MaxQB; Q08444; -.
DR PaxDb; 4932-YOR056C; -.
DR PeptideAtlas; Q08444; -.
DR EnsemblFungi; YOR056C_mRNA; YOR056C; YOR056C.
DR GeneID; 854221; -.
DR KEGG; sce:YOR056C; -.
DR AGR; SGD:S000005582; -.
DR SGD; S000005582; NOB1.
DR VEuPathDB; FungiDB:YOR056C; -.
DR eggNOG; KOG2463; Eukaryota.
DR GeneTree; ENSGT00390000015857; -.
DR HOGENOM; CLU_024666_2_1_1; -.
DR InParanoid; Q08444; -.
DR OMA; GYELECE; -.
DR OrthoDB; 5473723at2759; -.
DR BioCyc; YEAST:G3O-33596-MONOMER; -.
DR Reactome; R-SCE-6791226; Major pathway of rRNA processing in the nucleolus and cytosol.
DR BioGRID-ORCS; 854221; 0 hits in 10 CRISPR screens.
DR PRO; PR:Q08444; -.
DR Proteomes; UP000002311; Chromosome XV.
DR RNAct; Q08444; Protein.
DR GO; GO:0005737; C:cytoplasm; IDA:MGI.
DR GO; GO:0005783; C:endoplasmic reticulum; IEA:UniProtKB-SubCell.
DR GO; GO:0005730; C:nucleolus; IDA:MGI.
DR GO; GO:0005634; C:nucleus; IDA:SGD.
DR GO; GO:0030688; C:preribosome, small subunit precursor; IDA:SGD.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0004521; F:RNA endonuclease activity; IDA:SGD.
DR GO; GO:0070181; F:small ribosomal subunit rRNA binding; IDA:SGD.
DR GO; GO:0030490; P:maturation of SSU-rRNA; IDA:MGI.
DR GO; GO:0000462; P:maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA); IMP:SGD.
DR GO; GO:0043248; P:proteasome assembly; IMP:SGD.
DR GO; GO:0042274; P:ribosomal small subunit biogenesis; IDA:MGI.
DR CDD; cd09876; PIN_Nob1-like; 1.
DR Gene3D; 3.40.50.1010; 5'-nuclease; 1.
DR Gene3D; 6.20.210.10; Nin one binding (NOB1), Zn-ribbon-like; 1.
DR InterPro; IPR039907; NOB1.
DR InterPro; IPR017117; Nob1_euk.
DR InterPro; IPR036283; NOB1_Zf-like_sf.
DR InterPro; IPR014881; NOB1_Zn-bd.
DR InterPro; IPR002716; PIN_dom.
DR InterPro; IPR033411; Ribonuclease_PIN.
DR PANTHER; PTHR12814; RNA-BINDING PROTEIN NOB1; 1.
DR PANTHER; PTHR12814:SF2; RNA-BINDING PROTEIN NOB1; 1.
DR Pfam; PF08772; NOB1_Zn_bind; 1.
DR Pfam; PF17146; PIN_6; 1.
DR PIRSF; PIRSF037125; D-site_20S_pre-rRNA_nuclease; 1.
DR SMART; SM00670; PINc; 1.
DR SUPFAM; SSF144206; NOB1 zinc finger-like; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Endoplasmic reticulum; Hydrolase; Metal-binding;
KW Nuclease; Nucleus; Reference proteome; Ribosome biogenesis; Zinc.
FT CHAIN 1..459
FT /note="20S-pre-rRNA D-site endonuclease NOB1"
FT /id="PRO_0000270554"
FT DOMAIN 10..115
FT /note="PINc"
FT REGION 120..205
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 366..385
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 120..152
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 164..205
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 304
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250"
FT BINDING 307
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250"
FT BINDING 323
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250"
FT BINDING 326
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250"
FT MUTAGEN 92
FT /note="D->N: No 20S cleavage."
FT /evidence="ECO:0000269|PubMed:15388878"
FT MUTAGEN 110
FT /note="D->N: No change in activity or growth."
FT /evidence="ECO:0000269|PubMed:15388878"
FT MUTAGEN 279
FT /note="L->R: Temperature-sensitive."
FT /evidence="ECO:0000269|PubMed:12502737"
FT MUTAGEN 280
FT /note="Q->G: Temperature-sensitive."
FT /evidence="ECO:0000269|PubMed:12502737"
FT MUTAGEN 281
FT /note="M->G: Temperature-sensitive."
FT /evidence="ECO:0000269|PubMed:12502737"
FT STRAND 9..14
FT /evidence="ECO:0007829|PDB:8C01"
FT HELIX 16..21
FT /evidence="ECO:0007829|PDB:8C01"
FT HELIX 24..27
FT /evidence="ECO:0007829|PDB:8C01"
FT TURN 28..30
FT /evidence="ECO:0007829|PDB:8C01"
FT STRAND 34..36
FT /evidence="ECO:0007829|PDB:8C01"
FT HELIX 38..43
FT /evidence="ECO:0007829|PDB:8C01"
FT HELIX 47..58
FT /evidence="ECO:0007829|PDB:8C01"
FT STRAND 62..64
FT /evidence="ECO:0007829|PDB:8C01"
FT HELIX 69..82
FT /evidence="ECO:0007829|PDB:8C01"
FT HELIX 84..86
FT /evidence="ECO:0007829|PDB:8C01"
FT HELIX 90..106
FT /evidence="ECO:0007829|PDB:8C01"
FT STRAND 107..110
FT /evidence="ECO:0007829|PDB:8C01"
FT TURN 226..228
FT /evidence="ECO:0007829|PDB:8C01"
FT HELIX 229..235
FT /evidence="ECO:0007829|PDB:8C01"
FT TURN 236..238
FT /evidence="ECO:0007829|PDB:8C01"
FT STRAND 241..243
FT /evidence="ECO:0007829|PDB:8C01"
FT STRAND 266..268
FT /evidence="ECO:0007829|PDB:8C01"
FT HELIX 272..280
FT /evidence="ECO:0007829|PDB:8C01"
FT TURN 288..290
FT /evidence="ECO:0007829|PDB:8C01"
FT STRAND 296..304
FT /evidence="ECO:0007829|PDB:8C01"
FT TURN 305..307
FT /evidence="ECO:0007829|PDB:8C01"
FT TURN 324..326
FT /evidence="ECO:0007829|PDB:8C01"
FT STRAND 332..340
FT /evidence="ECO:0007829|PDB:8C01"
FT TURN 341..343
FT /evidence="ECO:0007829|PDB:8C01"
FT STRAND 346..349
FT /evidence="ECO:0007829|PDB:8C01"
FT HELIX 371..377
FT /evidence="ECO:0007829|PDB:8C01"
FT STRAND 379..382
FT /evidence="ECO:0007829|PDB:8C01"
FT STRAND 384..386
FT /evidence="ECO:0007829|PDB:8C01"
FT HELIX 398..418
FT /evidence="ECO:0007829|PDB:8C01"
FT TURN 450..453
FT /evidence="ECO:0007829|PDB:8C01"
SQ SEQUENCE 459 AA; 51742 MW; 96DEB818BB490A98 CRC64;
MTENQTAHVR ALILDATPLI TQSYTHYQNY AQSFYTTPTV FQEIKDAQAR KNLEIWQSLG
TLKLVHPSEN SIAKVSTFAK LTGDYSVLSA NDLHILALTY ELEIKLNNGD WRLRKKPGDA
LDASKADVGT DGKQKLTEDN KKEEDSESVP KKKNKRRGGK KQKAKREARE AREAENANLE
LESKAEEHVE EAGSKEQICN DENIKESSDL NEVFEDADDD GDWITPENLT EAIIKDSGED
TTGSLGVEAS EEDRHVALNR PENQVALATG DFAVQNVALQ MNLNLMNFMS GLKIKRIRNY
MLRCHACFKI FPLPKDGKPK HFCASCGGQG TLLRCAVSVD SRTGNVTPHL KSNFQWNNRG
NRYSVASPLS KNSQKRYGKK GHVHSKPQEN VILREDQKEY EKVIKQEEWT RRHNEKILNN
WIGGGSADNY ISPFAITGLK QHNVRIGKGR YVNSSKRRS
//
