RIBRX_ARATH
ID RIBRX_ARATH Reviewed; 599 AA.
AC Q9STY4;
DT 26-JUN-2013, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-2000, sequence version 1.
DT 03-AUG-2022, entry version 126.
DE RecName: Full=Riboflavin biosynthesis protein PYRR, chloroplastic;
DE Includes:
DE RecName: Full=Inactive diaminohydroxyphosphoribosylaminopyrimidine deaminase;
DE Short=DRAP deaminase;
DE AltName: Full=Riboflavin-specific deaminase;
DE Includes:
DE RecName: Full=5-amino-6-(5-phosphoribosylamino)uracil reductase;
DE EC=1.1.1.193;
DE AltName: Full=HTP reductase;
DE Includes:
DE RecName: Full=Riboflavin biosynthesis intermediates N-glycosidase {ECO:0000305|PubMed:25431972};
DE EC=3.2.2.- {ECO:0000269|PubMed:25431972};
DE Flags: Precursor;
GN Name=PYRR; Synonyms=PHS1; OrderedLocusNames=At3g47390; ORFNames=T21L8.140;
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130713; DOI=10.1038/35048706;
RA Salanoubat M., Lemcke K., Rieger M., Ansorge W., Unseld M., Fartmann B.,
RA Valle G., Bloecker H., Perez-Alonso M., Obermaier B., Delseny M.,
RA Boutry M., Grivell L.A., Mache R., Puigdomenech P., De Simone V.,
RA Choisne N., Artiguenave F., Robert C., Brottier P., Wincker P.,
RA Cattolico L., Weissenbach J., Saurin W., Quetier F., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Benes V., Wurmbach E., Drzonek H.,
RA Erfle H., Jordan N., Bangert S., Wiedelmann R., Kranz H., Voss H.,
RA Holland R., Brandt P., Nyakatura G., Vezzi A., D'Angelo M., Pallavicini A.,
RA Toppo S., Simionati B., Conrad A., Hornischer K., Kauer G., Loehnert T.-H.,
RA Nordsiek G., Reichelt J., Scharfe M., Schoen O., Bargues M., Terol J.,
RA Climent J., Navarro P., Collado C., Perez-Perez A., Ottenwaelder B.,
RA Duchemin D., Cooke R., Laudie M., Berger-Llauro C., Purnelle B., Masuy D.,
RA de Haan M., Maarse A.C., Alcaraz J.-P., Cottet A., Casacuberta E.,
RA Monfort A., Argiriou A., Flores M., Liguori R., Vitale D., Mannhaupt G.,
RA Haase D., Schoof H., Rudd S., Zaccaria P., Mewes H.-W., Mayer K.F.X.,
RA Kaul S., Town C.D., Koo H.L., Tallon L.J., Jenkins J., Rooney T., Rizzo M.,
RA Walts A., Utterback T., Fujii C.Y., Shea T.P., Creasy T.H., Haas B.,
RA Maiti R., Wu D., Peterson J., Van Aken S., Pai G., Militscher J.,
RA Sellers P., Gill J.E., Feldblyum T.V., Preuss D., Lin X., Nierman W.C.,
RA Salzberg S.L., White O., Venter J.C., Fraser C.M., Kaneko T., Nakamura Y.,
RA Sato S., Kato T., Asamizu E., Sasamoto S., Kimura T., Idesawa K.,
RA Kawashima K., Kishida Y., Kiyokawa C., Kohara M., Matsumoto M., Matsuno A.,
RA Muraki A., Nakayama S., Nakazaki N., Shinpo S., Takeuchi C., Wada T.,
RA Watanabe A., Yamada M., Yasuda M., Tabata S.;
RT "Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana.";
RL Nature 408:820-822(2000).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [3]
RP IDENTIFICATION, FUNCTION, AND MUTAGENESIS OF 416-PRO--ALA-599.
RC STRAIN=cv. Columbia;
RX PubMed=20580123; DOI=10.1016/j.jplph.2010.05.005;
RA Ouyang M., Ma J., Zou M., Guo J., Wang L., Lu C., Zhang L.;
RT "The photosensitive phs1 mutant is impaired in the riboflavin biogenesis
RT pathway.";
RL J. Plant Physiol. 167:1466-1476(2010).
RN [4]
RP FUNCTION, CATALYTIC ACTIVITY, AND SUBCELLULAR LOCATION.
RX PubMed=23150645; DOI=10.1104/pp.112.208488;
RA Hasnain G., Frelin O., Roje S., Ellens K.W., Ali K., Guan J.C.,
RA Garrett T.J., de Crecy-Lagard V., Gregory J.F. III, McCarty D.R.,
RA Hanson A.D.;
RT "Identification and characterization of the missing pyrimidine reductase in
RT the plant riboflavin biosynthesis pathway.";
RL Plant Physiol. 161:48-56(2013).
RN [5]
RP FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, AND MUTAGENESIS OF
RP 416-PRO--ALA-599.
RX PubMed=25431972; DOI=10.1042/bj20141237;
RA Frelin O., Huang L., Hasnain G., Jeffryes J.G., Ziemak M.J., Rocca J.R.,
RA Wang B., Rice J., Roje S., Yurgel S.N., Gregory J.F. III, Edison A.S.,
RA Henry C.S., de Crecy-Lagard V., Hanson A.D.;
RT "A directed-overflow and damage-control N-glycosidase in riboflavin
RT biosynthesis.";
RL Biochem. J. 466:137-145(2015).
CC -!- FUNCTION: Pyrimidine reductase involved in the riboflavin biosynthesis
CC pathway. Has also a non-functional N-terminal deaminase domain that
CC lacks the catalytically essential zinc-binding residues.
CC {ECO:0000269|PubMed:20580123, ECO:0000269|PubMed:23150645}.
CC -!- FUNCTION: Catalyzes the hydrolysis of the N-glycosidic bond in the
CC first two intermediates of riboflavin biosynthesis, which are highly
CC reactive metabolites, yielding relatively innocuous products. Thus, can
CC divert a surplus of harmful intermediates into relatively harmless
CC products and pre-empt the damage these intermediates would otherwise
CC do. Helps maintain flavin levels. Has no activity against GTP,
CC nucleoside monophosphates or ADP-ribose. {ECO:0000269|PubMed:25431972}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=5-amino-6-(5-phospho-D-ribitylamino)uracil + NADP(+) = 5-
CC amino-6-(5-phospho-D-ribosylamino)uracil + H(+) + NADPH;
CC Xref=Rhea:RHEA:17845, ChEBI:CHEBI:15378, ChEBI:CHEBI:57783,
CC ChEBI:CHEBI:58349, ChEBI:CHEBI:58421, ChEBI:CHEBI:58453;
CC EC=1.1.1.193; Evidence={ECO:0000269|PubMed:23150645};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)-pyrimidine +
CC H2O = 2,5,6-triamino-4-hydroxypyrimidine + D-ribose 5-phosphate;
CC Xref=Rhea:RHEA:23436, ChEBI:CHEBI:15377, ChEBI:CHEBI:58614,
CC ChEBI:CHEBI:78346, ChEBI:CHEBI:137796;
CC Evidence={ECO:0000269|PubMed:25431972};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=5-amino-6-(5-phospho-D-ribosylamino)uracil + H2O = 5,6-
CC diaminouracil + D-ribose 5-phosphate; Xref=Rhea:RHEA:55020,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:46252, ChEBI:CHEBI:58453,
CC ChEBI:CHEBI:78346; Evidence={ECO:0000269|PubMed:25431972};
CC -!- PATHWAY: Cofactor biosynthesis; riboflavin biosynthesis; 5-amino-6-(D-
CC ribitylamino)uracil from GTP: step 3/4.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast
CC {ECO:0000269|PubMed:23150645}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=1;
CC Comment=A number of isoforms are produced. According to EST
CC sequences.;
CC Name=1;
CC IsoId=Q9STY4-1; Sequence=Displayed;
CC -!- DOMAIN: The C-terminal domain (416-599) is not required for the
CC reductase activity while the non-functional deaminase domain (21-150)
CC is necessary.
CC -!- MISCELLANEOUS: Unlike bacteria that have a bifunctional, two-domain
CC RibD enzyme, plants have a monofunctional reductase and a
CC monofunctional deaminase, each having an enzymatically inactive domain.
CC -!- SIMILARITY: In the C-terminal section; belongs to the YbiA family.
CC {ECO:0000305}.
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DR EMBL; AL096860; CAB51211.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE78275.1; -; Genomic_DNA.
DR PIR; T12994; T12994.
DR RefSeq; NP_190323.1; NM_114607.3. [Q9STY4-1]
DR AlphaFoldDB; Q9STY4; -.
DR SMR; Q9STY4; -.
DR STRING; 3702.AT3G47390.1; -.
DR PaxDb; Q9STY4; -.
DR PRIDE; Q9STY4; -.
DR EnsemblPlants; AT3G47390.1; AT3G47390.1; AT3G47390. [Q9STY4-1]
DR GeneID; 823893; -.
DR Gramene; AT3G47390.1; AT3G47390.1; AT3G47390. [Q9STY4-1]
DR KEGG; ath:AT3G47390; -.
DR Araport; AT3G47390; -.
DR TAIR; locus:2099555; AT3G47390.
DR eggNOG; KOG1018; Eukaryota.
DR InParanoid; Q9STY4; -.
DR OrthoDB; 824208at2759; -.
DR PhylomeDB; Q9STY4; -.
DR BioCyc; ARA:AT3G47390-MON; -.
DR UniPathway; UPA00275; UER00402.
DR PRO; PR:Q9STY4; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q9STY4; baseline and differential.
DR Genevisible; Q9STY4; AT.
DR GO; GO:0009507; C:chloroplast; IDA:TAIR.
DR GO; GO:0008703; F:5-amino-6-(5-phosphoribosylamino)uracil reductase activity; IDA:TAIR.
DR GO; GO:0008835; F:diaminohydroxyphosphoribosylaminopyrimidine deaminase activity; IBA:GO_Central.
DR GO; GO:0016799; F:hydrolase activity, hydrolyzing N-glycosyl compounds; IDA:UniProtKB.
DR GO; GO:0050661; F:NADP binding; IEA:InterPro.
DR GO; GO:1901135; P:carbohydrate derivative metabolic process; IDA:UniProtKB.
DR GO; GO:0009658; P:chloroplast organization; IMP:TAIR.
DR GO; GO:0046443; P:FAD metabolic process; IMP:TAIR.
DR GO; GO:0009644; P:response to high light intensity; IMP:TAIR.
DR GO; GO:0009231; P:riboflavin biosynthetic process; IEA:UniProtKB-UniPathway.
DR CDD; cd15457; NADAR; 1.
DR Gene3D; 1.10.357.40; -; 1.
DR Gene3D; 3.40.430.10; -; 1.
DR InterPro; IPR002125; CMP_dCMP_dom.
DR InterPro; IPR016193; Cytidine_deaminase-like.
DR InterPro; IPR024072; DHFR-like_dom_sf.
DR InterPro; IPR004794; Eubact_RibD.
DR InterPro; IPR012816; NADAR.
DR InterPro; IPR011549; RibD_C.
DR InterPro; IPR002734; RibDG_C.
DR InterPro; IPR037238; YbiA-like_sf.
DR Pfam; PF00383; dCMP_cyt_deam_1; 1.
DR Pfam; PF08719; NADAR; 1.
DR Pfam; PF01872; RibD_C; 1.
DR SUPFAM; SSF143990; SSF143990; 1.
DR SUPFAM; SSF53597; SSF53597; 1.
DR SUPFAM; SSF53927; SSF53927; 1.
DR TIGRFAMs; TIGR00326; eubact_ribD; 1.
DR TIGRFAMs; TIGR00227; ribD_Cterm; 1.
DR TIGRFAMs; TIGR02464; ribofla_fusion; 1.
DR PROSITE; PS51747; CYT_DCMP_DEAMINASES_2; 1.
PE 1: Evidence at protein level;
KW Alternative splicing; Chloroplast; Glycosidase; Hydrolase;
KW Multifunctional enzyme; NADP; Oxidoreductase; Plastid; Reference proteome;
KW Transit peptide.
FT TRANSIT 1..17
FT /note="Chloroplast"
FT /evidence="ECO:0000305"
FT CHAIN 18..599
FT /note="Riboflavin biosynthesis protein PYRR, chloroplastic"
FT /id="PRO_0000422706"
FT DOMAIN 30..152
FT /note="CMP/dCMP-type deaminase"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01083"
FT MUTAGEN 416..599
FT /note="Missing: In phs1; Photosensitive phenotype under
FT high light. In leaves grown in normal light, the FAD and
FT FMN contents of the mutant are significantly lower (by 16%
FT and 20% respectively) than the wild-type."
FT /evidence="ECO:0000269|PubMed:20580123,
FT ECO:0000269|PubMed:25431972"
SQ SEQUENCE 599 AA; 65502 MW; 11829D0332046797 CRC64;
MALSFRISSS SPLICRATLS NGDNSRNYHT TDAAFIRRAA DLSEMSAGLT SPHPNFGCVI
ATSSGKVAGE GYLYAQGTKP AEALAVEAAG EFSRGATAYL NMEPGDCHGD HTAVSALVQA
GIERVVVGIR HPLQHLRGSA IRELRSHGIE VNVLGEDFES KVLEDARKSC LLVNAPLIHR
ACSRVPFSVL KYAMTLDGKI AASSGHAAWI SSKLSRTRVF ELRGGSDAVI VGGNTVRQDD
PRLTARHGQG HTPTRIVMTQ SLDLPEKANL WDVSEVSTIV VTQRGARKSF QKLLASKGVE
VVEFDMLNPR EVMEYFHLRG YLSILWECGG TLAASAISSS VIHKVVAFVA PKIIGGSKAP
SPVGDLGMVE MTQALNLIDV CYEQVGPDML VSGFLQPIPD LLPVIPSEDA TVEIDPSVDP
FEPSIIFFYK TWDLYGMWNI TIRYHTTVHV KWYLALSKKH NLLILHPKTL KANKFVGVEN
PKAYDCVEKI RTARSPEEAA LIGRSTLRQK PELVRNDWED VKIEVMYKAL KCKFSTYPHL
KSMLLSTIGT VLVEASPHDL FWGGGREGEG LNYLGRLLMQ LRSEYLGESS VSAEKTSSA
