RIBRX_MAIZE
ID RIBRX_MAIZE Reviewed; 623 AA.
AC K7WIZ6;
DT 26-JUN-2013, integrated into UniProtKB/Swiss-Prot.
DT 06-FEB-2013, sequence version 1.
DT 03-AUG-2022, entry version 58.
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; ORFNames=GRMZM2G090068 {ECO:0000305};
OS Zea mays (Maize).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; PACMAD clade;
OC Panicoideae; Andropogonodae; Andropogoneae; Tripsacinae; Zea.
OX NCBI_TaxID=4577;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, CATALYTIC ACTIVITY, SUBCELLULAR
RP LOCATION, AND DISRUPTION PHENOTYPE.
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 [2]
RP FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, AND BIOPHYSICOCHEMICAL
RP PROPERTIES.
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. 39% activity
CC when NADH replaces NADPH. No evidence for a phosphatase activity
CC conferred by the N-terminal domain. {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. Has no activity against GTP, nucleoside monophosphates or ADP-
CC 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 -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.94 mM for 2,5-diamino-6-hydroxy-4-(5-phospho-D-
CC ribosylamino)pyrimidine {ECO:0000269|PubMed:25431972};
CC KM=0.19 mM for 5-amino-6-(5-phospho-D-ribosylamino)uracil
CC {ECO:0000269|PubMed:25431972};
CC Note=kcat is 5.0 sec(-1) with 2,5-diamino-6-hydroxy-4-(5-phospho-D-
CC ribosylamino)pyrimidine as substrate. kcat is 9.39 sec(-1) with 5-
CC amino-6-(5-phospho-D-ribosylamino)uracil as substrate.
CC {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 -!- DISRUPTION PHENOTYPE: Lethal when homozygous. Required for both
CC endosperm and embryo formation in the seed.
CC {ECO:0000269|PubMed:23150645}.
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; JX838796; AFX59276.1; -; mRNA.
DR RefSeq; NP_001266474.1; NM_001279545.1.
DR AlphaFoldDB; K7WIZ6; -.
DR SMR; K7WIZ6; -.
DR STRING; 4577.GRMZM2G090068_P01; -.
DR PaxDb; K7WIZ6; -.
DR PRIDE; K7WIZ6; -.
DR EnsemblPlants; Zm00001eb240960_T002; Zm00001eb240960_P002; Zm00001eb240960.
DR GeneID; 101202729; -.
DR Gramene; Zm00001eb240960_T002; Zm00001eb240960_P002; Zm00001eb240960.
DR KEGG; zma:101202729; -.
DR eggNOG; KOG1018; Eukaryota.
DR HOGENOM; CLU_486092_0_0_1; -.
DR OMA; YRAIKCK; -.
DR OrthoDB; 824208at2759; -.
DR UniPathway; UPA00275; UER00402.
DR Proteomes; UP000007305; Chromosome 5.
DR ExpressionAtlas; K7WIZ6; baseline and differential.
DR GO; GO:0009507; C:chloroplast; IDA:CACAO.
DR GO; GO:0008703; F:5-amino-6-(5-phosphoribosylamino)uracil reductase activity; IEA:UniProtKB-EC.
DR GO; GO:0008835; F:diaminohydroxyphosphoribosylaminopyrimidine deaminase activity; IBA:GO_Central.
DR GO; GO:0004159; F:dihydropyrimidine dehydrogenase (NAD+) activity; IDA:CACAO.
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; IEA:EnsemblPlants.
DR GO; GO:0046443; P:FAD metabolic process; IEA:EnsemblPlants.
DR GO; GO:0009644; P:response to high light intensity; IEA:EnsemblPlants.
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; 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 Chloroplast; Glycosidase; Hydrolase; Multifunctional enzyme; NADP;
KW Oxidoreductase; Plastid; Reference proteome; Transit peptide.
FT TRANSIT 1..45
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN 46..623
FT /note="Riboflavin biosynthesis protein PYRR, chloroplastic"
FT /id="PRO_0000422707"
FT DOMAIN 52..181
FT /note="CMP/dCMP-type deaminase"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01083"
SQ SEQUENCE 623 AA; 67802 MW; F503D4AAD6713CB9 CRC64;
MPLPQPLLGG ASPAPARAAS SFLHPLLHTR HRVSTAPAAA SSFVPASHSS HANDAMLLRR
AADVADRSAG LTSPHPNFGC VIARPQLNTD SADSWVVGEG FLYAQGTPCA ELLASQEAGE
HARGGTAYLN LEPGDCFGDN TAVGSLVQAG ITRVVVGLRH PLKHLRGKAI QALRNEGIQV
DVVGEDLQSK LFKEALKSCL TVNAPLLYRA AFHVPFSVLK YAMTADGKIA ASSGHASWIS
GKASRGRVFE LRGRSDAVIV GGNTVRFDDP RLTARHVKGH VPVRIVMSQS LNLPEEANLW
NLNDAYTIVA TQRGARRDFQ RKLAMKGVEV VEFDMLNPRA VMSYCYDRGY LAVLWECGGT
LAASAISASV IHKVYAFWAP KIIGGLNAPT PVGELGMSQM TQAINLIDVS YEQIDRDMLM
SGFIEPIPDL SPVIPSVEEI PSIDPEVSPY ETNIISFYKT WDIFGAFSNF SPHSIQMPDE
NGDYFTWPTV EHYYQAHKFV GVDNPQARDI VQEIKLAKSP EEAARIGRTR QKGFPELVRT
DWESTKIDVM YRAIKCKFST YPHLTNMLLS TAGSVLVEAS PHDLFWGGGR EGEGLNYLGR
LLMQLRSEIL GTVPASAEVG EAD
