RIB2_YEAST
ID RIB2_YEAST Reviewed; 591 AA.
AC Q12362; D6W201;
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1997, sequence version 1.
DT 03-AUG-2022, entry version 172.
DE RecName: Full=Bifunctional protein RIB2;
DE Includes:
DE RecName: Full=tRNA pseudouridine(32) synthase, cytoplasmic;
DE EC=5.4.99.28;
DE AltName: Full=tRNA pseudouridine synthase 8;
DE AltName: Full=tRNA pseudouridylate synthase 8;
DE AltName: Full=tRNA-uridine isomerase 8;
DE Includes:
DE RecName: Full=Diaminohydroxyphosphoribosylaminopyrimidine deaminase;
DE Short=DRAP deaminase;
DE EC=3.5.4.26;
DE AltName: Full=Riboflavin-specific deaminase;
GN Name=RIB2; Synonyms=PUS8; OrderedLocusNames=YOL066C;
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].
RA Gonzalez G.A., Santos M.A., Garcia-Ramirez J.J., Revuelta J.L.;
RT "Cloning and sequencing of the RIB2 gene from Saccharomyces cerevisiae.";
RL Submitted (JAN-1995) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=9178509;
RX DOI=10.1002/(sici)1097-0061(199705)13:6<583::aid-yea111>3.0.co;2-y;
RA Tzermia M., Katsoulou C., Alexandraki D.;
RT "Sequence analysis of a 33.2 kb segment from the left arm of yeast
RT chromosome XV reveals eight known genes and ten new open reading frames
RT including homologues of ABC transporters, inositol phosphatases and human
RT expressed sequence tags.";
RL Yeast 13:583-589(1997).
RN [3]
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 [4]
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 [5]
RP FUNCTION.
RX PubMed=11947306; DOI=10.1016/0014-5793(69)80345-5;
RA Bacher A., Baur R., Oltmanns O., Lingens F.;
RT "Biosynthesis of riboflavin. Mutants accumulating 6-hydroxy-2,4,5-
RT triaminopyrimidine.";
RL FEBS Lett. 5:316-318(1969).
RN [6]
RP FUNCTION.
RX PubMed=4555411; DOI=10.1128/jb.110.3.818-822.1972;
RA Oltmanns O., Bacher A.;
RT "Biosynthesis of riboflavine in Saccharomyces cerevisiae: the role of genes
RT rib 1 and rib 7.";
RL J. Bacteriol. 110:818-822(1972).
RN [7]
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 [8]
RP FUNCTION, CATALYTIC ACTIVITY, AND SUBCELLULAR LOCATION.
RX PubMed=15466869; DOI=10.1074/jbc.m409581200;
RA Behm-Ansmant I., Grosjean H., Massenet S., Motorin Y., Branlant C.;
RT "Pseudouridylation at position 32 of mitochondrial and cytoplasmic tRNAs
RT requires two distinct enzymes in Saccharomyces cerevisiae.";
RL J. Biol. Chem. 279:52998-53006(2004).
CC -!- FUNCTION: Responsible for synthesis of pseudouridine from uracil-32 in
CC cytoplasmic transfer RNAs.
CC -!- FUNCTION: Involved in riboflavin biosynthesis. Converts 2,5-diamino-6-
CC (ribosylamino)-4(3H)-pyrimidinone 5'-phosphate into 5-amino-6-
CC (ribosylamino)-2,4(1H,3H)-pyrimidinedione 5'-phosphate.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=uridine(32) in tRNA = pseudouridine(32) in tRNA;
CC Xref=Rhea:RHEA:42544, Rhea:RHEA-COMP:10107, Rhea:RHEA-COMP:10108,
CC ChEBI:CHEBI:65314, ChEBI:CHEBI:65315; EC=5.4.99.28;
CC Evidence={ECO:0000269|PubMed:15466869};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)-pyrimidine +
CC H(+) + H2O = 5-amino-6-(5-phospho-D-ribosylamino)uracil + NH4(+);
CC Xref=Rhea:RHEA:21868, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:28938, ChEBI:CHEBI:58453, ChEBI:CHEBI:58614; EC=3.5.4.26;
CC Evidence={ECO:0000269|PubMed:15466869};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105; Evidence={ECO:0000250};
CC Note=Binds 1 zinc ion. {ECO:0000250};
CC -!- PATHWAY: Cofactor biosynthesis; riboflavin biosynthesis; 5-amino-6-(D-
CC ribitylamino)uracil from GTP: step 2/4.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:15466869}.
CC -!- MISCELLANEOUS: Present with 1540 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: In the N-terminal section; belongs to the pseudouridine
CC synthase RluA family. {ECO:0000305}.
CC -!- SIMILARITY: In the C-terminal section; belongs to the cytidine and
CC deoxycytidylate deaminase family. {ECO:0000305}.
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DR EMBL; Z21618; CAA79742.1; -; Genomic_DNA.
DR EMBL; Z74808; CAA99076.1; -; Genomic_DNA.
DR EMBL; BK006948; DAA10717.1; -; Genomic_DNA.
DR PIR; S50972; S50972.
DR RefSeq; NP_014575.1; NM_001183321.1.
DR AlphaFoldDB; Q12362; -.
DR SMR; Q12362; -.
DR BioGRID; 34335; 175.
DR DIP; DIP-3840N; -.
DR STRING; 4932.YOL066C; -.
DR MaxQB; Q12362; -.
DR PaxDb; Q12362; -.
DR PRIDE; Q12362; -.
DR EnsemblFungi; YOL066C_mRNA; YOL066C; YOL066C.
DR GeneID; 854088; -.
DR KEGG; sce:YOL066C; -.
DR SGD; S000005427; RIB2.
DR VEuPathDB; FungiDB:YOL066C; -.
DR eggNOG; KOG1018; Eukaryota.
DR eggNOG; KOG1919; Eukaryota.
DR GeneTree; ENSGT00420000029802; -.
DR HOGENOM; CLU_016902_12_4_1; -.
DR InParanoid; Q12362; -.
DR OMA; RYRYNTI; -.
DR BioCyc; MetaCyc:YOL066C-MON; -.
DR BioCyc; YEAST:YOL066C-MON; -.
DR BRENDA; 5.4.99.28; 984.
DR UniPathway; UPA00275; UER00401.
DR PRO; PR:Q12362; -.
DR Proteomes; UP000002311; Chromosome XV.
DR RNAct; Q12362; protein.
DR GO; GO:0005737; C:cytoplasm; HDA:SGD.
DR GO; GO:0043723; F:2,5-diamino-6-ribitylamino-4(3H)-pyrimidinone 5'-phosphate deaminase activity; IMP:SGD.
DR GO; GO:0008835; F:diaminohydroxyphosphoribosylaminopyrimidine deaminase activity; IEA:UniProtKB-EC.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0009982; F:pseudouridine synthase activity; IDA:SGD.
DR GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
DR GO; GO:0106029; F:tRNA pseudouridine synthase activity; IEA:UniProtKB-EC.
DR GO; GO:0000455; P:enzyme-directed rRNA pseudouridine synthesis; IBA:GO_Central.
DR GO; GO:0009231; P:riboflavin biosynthetic process; IMP:SGD.
DR GO; GO:0031119; P:tRNA pseudouridine synthesis; IDA:SGD.
DR InterPro; IPR002125; CMP_dCMP_dom.
DR InterPro; IPR016193; Cytidine_deaminase-like.
DR InterPro; IPR020103; PsdUridine_synth_cat_dom_sf.
DR InterPro; IPR006225; PsdUridine_synth_RluC/D.
DR InterPro; IPR006224; PsdUridine_synth_RluC/D_CS.
DR InterPro; IPR006145; PsdUridine_synth_RsuA/RluA.
DR Pfam; PF00849; PseudoU_synth_2; 1.
DR SUPFAM; SSF53927; SSF53927; 1.
DR SUPFAM; SSF55120; SSF55120; 1.
DR TIGRFAMs; TIGR00005; rluA_subfam; 1.
DR PROSITE; PS51747; CYT_DCMP_DEAMINASES_2; 1.
DR PROSITE; PS01129; PSI_RLU; 1.
DR PROSITE; PS50889; S4; 1.
PE 1: Evidence at protein level;
KW Cytoplasm; Hydrolase; Isomerase; Metal-binding; Reference proteome;
KW Riboflavin biosynthesis; RNA-binding; tRNA processing; Zinc.
FT CHAIN 1..591
FT /note="Bifunctional protein RIB2"
FT /id="PRO_0000162725"
FT DOMAIN 99..168
FT /note="S4 RNA-binding"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00182"
FT DOMAIN 433..552
FT /note="CMP/dCMP-type deaminase"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01083"
FT REGION 1..432
FT /note="tRNA pseudouridine synthase"
FT REGION 433..591
FT /note="DRAP deaminase"
FT ACT_SITE 211
FT /evidence="ECO:0000250"
FT ACT_SITE 484
FT /note="Proton donor"
FT /evidence="ECO:0000250"
FT BINDING 482
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250"
FT BINDING 515
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250"
FT BINDING 525
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250"
SQ SEQUENCE 591 AA; 67036 MW; 5C625500C997ED83 CRC64;
MEDSNNEASD DFNNLLNKEI ESAKEVKLRK FANRNNNRNE NSSKVKDASG FRLRVIQTDG
HKTKKTDPDY EVTIDGPLRK IEPYFFTYKT FCKERWRDRK LVDVFVSEFR DREPSYYSKT
IAEGKVYLND EPANLDTIIR DGDLITHKVH RHEPPVTSKP IDIVFEDEDI LVIDKPSSIP
VHPTGRYRFN TITKMLERQL GYSVHPCNRL DKPTSGLMFL AKTPLGADRM GDQMKAREVT
KEYVARVKGE FPIGIVEVDK PVRSVNPKVA LNAVCEMSDE NAKHAKTVFQ RVSYDGQTSI
VKCKPLTGRT HQIRVHLQYL GFPIANDPIY SNPDIWGPDL GRGGLQNYDD IVLKLDAIGK
TNPAESWIHP HSEGEYLLGR QCEECEAEMY TDPGTNDLDL WLHAFRYESL ERNSDTQKPL
WSYRTKYPEW ALEPHRRYME MAVKEAGKCG PTKTAFSVGA VLVHGTQVLA TGYSRELPGN
THAEQCALIK YSQLHPNCPT IVPMGTVLYT TMEPCSFRLS GNEPCCDRIL ATQGAIGTVF
VGVMEPDTFV KNNTSLNKLE SHGVNYIQIP GYEEECTIIA FKGHDNSDDK A
