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Protein

Bifunctional protein RIB2

Gene

RIB2

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Responsible for synthesis of pseudouridine from uracil-32 in cytoplasmic transfer RNAs.
Involved in riboflavin biosynthesis. Converts 2,5-diamino-6-(ribosylamino)-4(3H)-pyrimidinone 5'-phosphate into 5-amino-6-(ribosylamino)-2,4(1H,3H)-pyrimidinedione 5'-phosphate.

Catalytic activityi

tRNA uridine(32) = tRNA pseudouridine(32).1 Publication
2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine + H2O = 5-amino-6-(5-phosphoribosylamino)uracil + NH3.1 Publication

Cofactori

Zn2+By similarityNote: Binds 1 zinc ion.By similarity

Pathwayi: riboflavin biosynthesis

This protein is involved in step 2 of the subpathway that synthesizes 5-amino-6-(D-ribitylamino)uracil from GTP.
Proteins known to be involved in the 4 steps of the subpathway in this organism are:
  1. GTP cyclohydrolase-2 (RIB1)
  2. Bifunctional protein RIB2 (RIB2)
  3. no protein annotated in this organism
  4. no protein annotated in this organism
This subpathway is part of the pathway riboflavin biosynthesis, which is itself part of Cofactor biosynthesis.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes 5-amino-6-(D-ribitylamino)uracil from GTP, the pathway riboflavin biosynthesis and in Cofactor biosynthesis.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei211 – 2111By similarity
Metal bindingi482 – 4821Zinc; catalyticBy similarity
Active sitei484 – 4841Proton donorBy similarity
Metal bindingi515 – 5151Zinc; catalyticBy similarity
Metal bindingi525 – 5251Zinc; catalyticBy similarity

GO - Molecular functioni

GO - Biological processi

  • riboflavin biosynthetic process Source: SGD
  • tRNA pseudouridine synthesis Source: SGD
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase, Isomerase

Keywords - Biological processi

Riboflavin biosynthesis, tRNA processing

Keywords - Ligandi

Metal-binding, RNA-binding, Zinc

Enzyme and pathway databases

BioCyciMetaCyc:YOL066C-MONOMER.
YEAST:YOL066C-MONOMER.
BRENDAi5.4.99.28. 984.
UniPathwayiUPA00275; UER00401.

Names & Taxonomyi

Protein namesi
Recommended name:
Bifunctional protein RIB2
Including the following 2 domains:
tRNA pseudouridine(32) synthase, cytoplasmic (EC:5.4.99.28)
Alternative name(s):
tRNA pseudouridine synthase 8
tRNA pseudouridylate synthase 8
tRNA-uridine isomerase 8
Diaminohydroxyphosphoribosylaminopyrimidine deaminase (EC:3.5.4.26)
Short name:
DRAP deaminase
Alternative name(s):
Riboflavin-specific deaminase
Gene namesi
Name:RIB2
Synonyms:PUS8
Ordered Locus Names:YOL066C
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome XV

Organism-specific databases

EuPathDBiFungiDB:YOL066C.
SGDiS000005427. RIB2.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 591591Bifunctional protein RIB2PRO_0000162725Add
BLAST

Proteomic databases

MaxQBiQ12362.
PRIDEiQ12362.

Interactioni

Protein-protein interaction databases

BioGridi34335. 31 interactions.
DIPiDIP-3840N.
MINTiMINT-495231.

Structurei

3D structure databases

ProteinModelPortaliQ12362.
SMRiQ12362. Positions 163-334.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini99 – 16870S4 RNA-bindingPROSITE-ProRule annotationAdd
BLAST
Domaini433 – 552120CMP/dCMP-type deaminasePROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni1 – 432432tRNA pseudouridine synthaseAdd
BLAST
Regioni433 – 591159DRAP deaminaseAdd
BLAST

Sequence similaritiesi

In the N-terminal section; belongs to the pseudouridine synthase RluA family.Curated
In the C-terminal section; belongs to the cytidine and deoxycytidylate deaminase family.Curated
Contains 1 CMP/dCMP-type deaminase domain.PROSITE-ProRule annotation
Contains 1 S4 RNA-binding domain.PROSITE-ProRule annotation

Phylogenomic databases

GeneTreeiENSGT00420000029802.
HOGENOMiHOG000167783.
InParanoidiQ12362.
KOiK14655.
OMAiQCALEKY.
OrthoDBiEOG7M0P19.

Family and domain databases

InterProiIPR002125. CMP_dCMP_Zn-bd.
IPR016193. Cytidine_deaminase-like.
IPR020103. PsdUridine_synth_cat_dom.
IPR006225. PsdUridine_synth_RluC/D.
IPR006224. PsdUridine_synth_RluC/D_CS.
IPR006145. PsdUridine_synth_RsuA/RluD.
IPR002942. S4_RNA-bd.
[Graphical view]
PfamiPF00383. dCMP_cyt_deam_1. 1 hit.
PF00849. PseudoU_synth_2. 1 hit.
[Graphical view]
SUPFAMiSSF53927. SSF53927. 1 hit.
SSF55120. SSF55120. 2 hits.
TIGRFAMsiTIGR00005. rluA_subfam. 1 hit.
PROSITEiPS51747. CYT_DCMP_DEAMINASES_2. 1 hit.
PS01129. PSI_RLU. 1 hit.
PS50889. S4. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q12362-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MEDSNNEASD DFNNLLNKEI ESAKEVKLRK FANRNNNRNE NSSKVKDASG
60 70 80 90 100
FRLRVIQTDG HKTKKTDPDY EVTIDGPLRK IEPYFFTYKT FCKERWRDRK
110 120 130 140 150
LVDVFVSEFR DREPSYYSKT IAEGKVYLND EPANLDTIIR DGDLITHKVH
160 170 180 190 200
RHEPPVTSKP IDIVFEDEDI LVIDKPSSIP VHPTGRYRFN TITKMLERQL
210 220 230 240 250
GYSVHPCNRL DKPTSGLMFL AKTPLGADRM GDQMKAREVT KEYVARVKGE
260 270 280 290 300
FPIGIVEVDK PVRSVNPKVA LNAVCEMSDE NAKHAKTVFQ RVSYDGQTSI
310 320 330 340 350
VKCKPLTGRT HQIRVHLQYL GFPIANDPIY SNPDIWGPDL GRGGLQNYDD
360 370 380 390 400
IVLKLDAIGK TNPAESWIHP HSEGEYLLGR QCEECEAEMY TDPGTNDLDL
410 420 430 440 450
WLHAFRYESL ERNSDTQKPL WSYRTKYPEW ALEPHRRYME MAVKEAGKCG
460 470 480 490 500
PTKTAFSVGA VLVHGTQVLA TGYSRELPGN THAEQCALIK YSQLHPNCPT
510 520 530 540 550
IVPMGTVLYT TMEPCSFRLS GNEPCCDRIL ATQGAIGTVF VGVMEPDTFV
560 570 580 590
KNNTSLNKLE SHGVNYIQIP GYEEECTIIA FKGHDNSDDK A
Length:591
Mass (Da):67,036
Last modified:November 1, 1997 - v1
Checksum:i5C625500C997ED83
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z21618 Genomic DNA. Translation: CAA79742.1.
Z74808 Genomic DNA. Translation: CAA99076.1.
BK006948 Genomic DNA. Translation: DAA10717.1.
PIRiS50972.
RefSeqiNP_014575.1. NM_001183321.1.

Genome annotation databases

EnsemblFungiiYOL066C; YOL066C; YOL066C.
GeneIDi854088.
KEGGisce:YOL066C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z21618 Genomic DNA. Translation: CAA79742.1.
Z74808 Genomic DNA. Translation: CAA99076.1.
BK006948 Genomic DNA. Translation: DAA10717.1.
PIRiS50972.
RefSeqiNP_014575.1. NM_001183321.1.

3D structure databases

ProteinModelPortaliQ12362.
SMRiQ12362. Positions 163-334.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi34335. 31 interactions.
DIPiDIP-3840N.
MINTiMINT-495231.

Proteomic databases

MaxQBiQ12362.
PRIDEiQ12362.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYOL066C; YOL066C; YOL066C.
GeneIDi854088.
KEGGisce:YOL066C.

Organism-specific databases

EuPathDBiFungiDB:YOL066C.
SGDiS000005427. RIB2.

Phylogenomic databases

GeneTreeiENSGT00420000029802.
HOGENOMiHOG000167783.
InParanoidiQ12362.
KOiK14655.
OMAiQCALEKY.
OrthoDBiEOG7M0P19.

Enzyme and pathway databases

UniPathwayiUPA00275; UER00401.
BioCyciMetaCyc:YOL066C-MONOMER.
YEAST:YOL066C-MONOMER.
BRENDAi5.4.99.28. 984.

Miscellaneous databases

PROiQ12362.

Family and domain databases

InterProiIPR002125. CMP_dCMP_Zn-bd.
IPR016193. Cytidine_deaminase-like.
IPR020103. PsdUridine_synth_cat_dom.
IPR006225. PsdUridine_synth_RluC/D.
IPR006224. PsdUridine_synth_RluC/D_CS.
IPR006145. PsdUridine_synth_RsuA/RluD.
IPR002942. S4_RNA-bd.
[Graphical view]
PfamiPF00383. dCMP_cyt_deam_1. 1 hit.
PF00849. PseudoU_synth_2. 1 hit.
[Graphical view]
SUPFAMiSSF53927. SSF53927. 1 hit.
SSF55120. SSF55120. 2 hits.
TIGRFAMsiTIGR00005. rluA_subfam. 1 hit.
PROSITEiPS51747. CYT_DCMP_DEAMINASES_2. 1 hit.
PS01129. PSI_RLU. 1 hit.
PS50889. S4. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Cloning and sequencing of the RIB2 gene from Saccharomyces cerevisiae."
    Gonzalez G.A., Santos M.A., Garcia-Ramirez J.J., Revuelta J.L.
    Submitted (JAN-1995) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "Sequence analysis of a 33.2 kb segment from the left arm of yeast chromosome XV reveals eight known genes and ten new open reading frames including homologues of ABC transporters, inositol phosphatases and human expressed sequence tags."
    Tzermia M., Katsoulou C., Alexandraki D.
    Yeast 13:583-589(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  3. "The nucleotide sequence of Saccharomyces cerevisiae chromosome XV."
    Dujon B., Albermann K., Aldea M., Alexandraki D., Ansorge W., Arino J., Benes V., Bohn C., Bolotin-Fukuhara M., Bordonne R., Boyer J., Camasses A., Casamayor A., Casas C., Cheret G., Cziepluch C., Daignan-Fornier B., Dang V.-D.
    , de Haan M., Delius H., Durand P., Fairhead C., Feldmann H., Gaillon L., Galisson F., Gamo F.-J., Gancedo C., Goffeau A., Goulding S.E., Grivell L.A., Habbig B., Hand N.J., Hani J., Hattenhorst U., Hebling U., Hernando Y., Herrero E., Heumann K., Hiesel R., Hilger F., Hofmann B., Hollenberg C.P., Hughes B., Jauniaux J.-C., Kalogeropoulos A., Katsoulou C., Kordes E., Lafuente M.J., Landt O., Louis E.J., Maarse A.C., Madania A., Mannhaupt G., Marck C., Martin R.P., Mewes H.-W., Michaux G., Paces V., Parle-McDermott A.G., Pearson B.M., Perrin A., Pettersson B., Poch O., Pohl T.M., Poirey R., Portetelle D., Pujol A., Purnelle B., Ramezani Rad M., Rechmann S., Schwager C., Schweizer M., Sor F., Sterky F., Tarassov I.A., Teodoru C., Tettelin H., Thierry A., Tobiasch E., Tzermia M., Uhlen M., Unseld M., Valens M., Vandenbol M., Vetter I., Vlcek C., Voet M., Volckaert G., Voss H., Wambutt R., Wedler H., Wiemann S., Winsor B., Wolfe K.H., Zollner A., Zumstein E., Kleine K.
    Nature 387:98-102(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  4. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  5. "Biosynthesis of riboflavin. Mutants accumulating 6-hydroxy-2,4,5-triaminopyrimidine."
    Bacher A., Baur R., Oltmanns O., Lingens F.
    FEBS Lett. 5:316-318(1969) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  6. "Biosynthesis of riboflavine in Saccharomyces cerevisiae: the role of genes rib 1 and rib 7."
    Oltmanns O., Bacher A.
    J. Bacteriol. 110:818-822(1972) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  7. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  8. "Pseudouridylation at position 32 of mitochondrial and cytoplasmic tRNAs requires two distinct enzymes in Saccharomyces cerevisiae."
    Behm-Ansmant I., Grosjean H., Massenet S., Motorin Y., Branlant C.
    J. Biol. Chem. 279:52998-53006(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY, SUBCELLULAR LOCATION.

Entry informationi

Entry nameiRIB2_YEAST
AccessioniPrimary (citable) accession number: Q12362
Secondary accession number(s): D6W201
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: November 1, 1997
Last modified: July 6, 2016
This is version 137 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 1540 molecules/cell in log phase SD medium.1 Publication

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. SIMILARITY comments
    Index of protein domains and families
  3. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  4. Yeast chromosome XV
    Yeast (Saccharomyces cerevisiae) chromosome XV: entries and gene names

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.