RIBD_ARATH
ID RIBD_ARATH Reviewed; 426 AA.
AC Q8GWP5; Q8L8N0; Q9SUB7;
DT 26-JUN-2013, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2003, sequence version 1.
DT 03-AUG-2022, entry version 129.
DE RecName: Full=Riboflavin biosynthesis protein PYRD, chloroplastic;
DE Includes:
DE RecName: Full=Diaminohydroxyphosphoribosylaminopyrimidine deaminase;
DE Short=DRAP deaminase;
DE EC=3.5.4.26;
DE AltName: Full=Riboflavin-specific deaminase;
DE Includes:
DE RecName: Full=Inactive 5-amino-6-(5-phosphoribosylamino)uracil reductase;
DE AltName: Full=HTP reductase;
DE Flags: Precursor;
GN Name=PYRD; OrderedLocusNames=At4g20960; ORFNames=T13K14.120;
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=10617198; DOI=10.1038/47134;
RA Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G., Pohl T.,
RA Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N., Harris B.,
RA Ansorge W., Brandt P., Grivell L.A., Rieger M., Weichselgartner M.,
RA de Simone V., Obermaier B., Mache R., Mueller M., Kreis M., Delseny M.,
RA Puigdomenech P., Watson M., Schmidtheini T., Reichert B., Portetelle D.,
RA Perez-Alonso M., Boutry M., Bancroft I., Vos P., Hoheisel J.,
RA Zimmermann W., Wedler H., Ridley P., Langham S.-A., McCullagh B.,
RA Bilham L., Robben J., van der Schueren J., Grymonprez B., Chuang Y.-J.,
RA Vandenbussche F., Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R.,
RA Defoor E., Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M.,
RA Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W., Mooijman P.,
RA Klein Lankhorst R., Rose M., Hauf J., Koetter P., Berneiser S., Hempel S.,
RA Feldpausch M., Lamberth S., Van den Daele H., De Keyser A., Buysshaert C.,
RA Gielen J., Villarroel R., De Clercq R., van Montagu M., Rogers J.,
RA Cronin A., Quail M.A., Bray-Allen S., Clark L., Doggett J., Hall S.,
RA Kay M., Lennard N., McLay K., Mayes R., Pettett A., Rajandream M.A.,
RA Lyne M., Benes V., Rechmann S., Borkova D., Bloecker H., Scharfe M.,
RA Grimm M., Loehnert T.-H., Dose S., de Haan M., Maarse A.C., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D.,
RA Herzl A., Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E.,
RA Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R., Schnabl S.,
RA Hiller R., Schmidt W., Lecharny A., Aubourg S., Chefdor F., Cooke R.,
RA Berger C., Monfort A., Casacuberta E., Gibbons T., Weber N., Vandenbol M.,
RA Bargues M., Terol J., Torres A., Perez-Perez A., Purnelle B., Bent E.,
RA Johnson S., Tacon D., Jesse T., Heijnen L., Schwarz S., Scholler P.,
RA Heber S., Francs P., Bielke C., Frishman D., Haase D., Lemcke K.,
RA Mewes H.-W., Stocker S., Zaccaria P., Bevan M., Wilson R.K.,
RA de la Bastide M., Habermann K., Parnell L., Dedhia N., Gnoj L., Schutz K.,
RA Huang E., Spiegel L., Sekhon M., Murray J., Sheet P., Cordes M.,
RA Abu-Threideh J., Stoneking T., Kalicki J., Graves T., Harmon G.,
RA Edwards J., Latreille P., Courtney L., Cloud J., Abbott A., Scott K.,
RA Johnson D., Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K.,
RA Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W.,
RA Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D., Du H.,
RA Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C., Antonoiu B.,
RA Zidanic M., Strong C., Sun H., Lamar B., Yordan C., Ma P., Zhong J.,
RA Preston R., Vil D., Shekher M., Matero A., Shah R., Swaby I.K.,
RA O'Shaughnessy A., Rodriguez M., Hoffman J., Till S., Granat S., Shohdy N.,
RA Hasegawa A., Hameed A., Lodhi M., Johnson A., Chen E., Marra M.A.,
RA Martienssen R., McCombie W.R.;
RT "Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana.";
RL Nature 402:769-777(1999).
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 NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=11910074; DOI=10.1126/science.1071006;
RA Seki M., Narusaka M., Kamiya A., Ishida J., Satou M., Sakurai T.,
RA Nakajima M., Enju A., Akiyama K., Oono Y., Muramatsu M., Hayashizaki Y.,
RA Kawai J., Carninci P., Itoh M., Ishii Y., Arakawa T., Shibata K.,
RA Shinagawa A., Shinozaki K.;
RT "Functional annotation of a full-length Arabidopsis cDNA collection.";
RL Science 296:141-145(2002).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RA Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B.,
RA Feldmann K.A.;
RT "Full-length cDNA from Arabidopsis thaliana.";
RL Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases.
RN [6]
RP FUNCTION, CATALYTIC ACTIVITY, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES, AND
RP DOMAIN.
RX PubMed=15208317; DOI=10.1074/jbc.m404406200;
RA Fischer M., Roemisch W., Saller S., Illarionov B., Richter G., Rohdich F.,
RA Eisenreich W., Bacher A.;
RT "Evolution of vitamin B2 biosynthesis: structural and functional similarity
RT between pyrimidine deaminases of eubacterial and plant origin.";
RL J. Biol. Chem. 279:36299-36308(2004).
RN [7]
RP FUNCTION, 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).
CC -!- FUNCTION: Monofunctional pyrimidine deaminase involved in the
CC riboflavin biosynthesis pathway. Has also a reductase domain that lacks
CC catalytically essential substrate-binding residues.
CC {ECO:0000269|PubMed:15208317, ECO:0000269|PubMed:23150645}.
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:15208317};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000269|PubMed:15208317};
CC Note=Binds 1 zinc ion. {ECO:0000269|PubMed:15208317};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC Vmax=0.9 umol/min/mg enzyme {ECO:0000269|PubMed:15208317};
CC -!- PATHWAY: Cofactor biosynthesis; riboflavin biosynthesis; 5-amino-6-(D-
CC ribitylamino)uracil from GTP: step 2/4.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast
CC {ECO:0000269|PubMed:23150645}.
CC -!- DOMAIN: The N-terminal domain (64-250) is required for the deaminase
CC activity. {ECO:0000269|PubMed:15208317}.
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 -!- SEQUENCE CAUTION:
CC Sequence=CAB45891.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
CC Sequence=CAB79096.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
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DR EMBL; AL080282; CAB45891.1; ALT_INIT; Genomic_DNA.
DR EMBL; AL161554; CAB79096.1; ALT_INIT; Genomic_DNA.
DR EMBL; CP002687; AEE84379.1; -; Genomic_DNA.
DR EMBL; AK118717; BAC43311.1; -; mRNA.
DR EMBL; BT006051; AAP04036.1; -; mRNA.
DR EMBL; AY088903; AAM67209.1; -; mRNA.
DR PIR; T10638; T10638.
DR RefSeq; NP_567618.1; NM_118214.4.
DR AlphaFoldDB; Q8GWP5; -.
DR SMR; Q8GWP5; -.
DR STRING; 3702.AT4G20960.1; -.
DR PaxDb; Q8GWP5; -.
DR PRIDE; Q8GWP5; -.
DR ProteomicsDB; 236185; -.
DR EnsemblPlants; AT4G20960.1; AT4G20960.1; AT4G20960.
DR GeneID; 827843; -.
DR Gramene; AT4G20960.1; AT4G20960.1; AT4G20960.
DR KEGG; ath:AT4G20960; -.
DR Araport; AT4G20960; -.
DR TAIR; locus:2133074; AT4G20960.
DR eggNOG; KOG1018; Eukaryota.
DR HOGENOM; CLU_036590_2_0_1; -.
DR InParanoid; Q8GWP5; -.
DR OMA; GHYMRRC; -.
DR OrthoDB; 752608at2759; -.
DR PhylomeDB; Q8GWP5; -.
DR BioCyc; ARA:AT4G20960-MON; -.
DR BioCyc; MetaCyc:AT4G20960-MON; -.
DR UniPathway; UPA00275; UER00401.
DR PRO; PR:Q8GWP5; -.
DR Proteomes; UP000006548; Chromosome 4.
DR ExpressionAtlas; Q8GWP5; baseline and differential.
DR Genevisible; Q8GWP5; AT.
DR GO; GO:0009507; C:chloroplast; HDA:TAIR.
DR GO; GO:0009570; C:chloroplast stroma; HDA:TAIR.
DR GO; GO:0008835; F:diaminohydroxyphosphoribosylaminopyrimidine deaminase activity; IBA:GO_Central.
DR GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
DR GO; GO:0009231; P:riboflavin biosynthetic process; IDA:TAIR.
DR Gene3D; 3.40.430.10; -; 1.
DR InterPro; IPR016192; APOBEC/CMP_deaminase_Zn-bd.
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 Pfam; PF00383; dCMP_cyt_deam_1; 1.
DR SUPFAM; SSF53597; SSF53597; 1.
DR SUPFAM; SSF53927; SSF53927; 1.
DR TIGRFAMs; TIGR00326; eubact_ribD; 1.
DR PROSITE; PS00903; CYT_DCMP_DEAMINASES_1; 1.
DR PROSITE; PS51747; CYT_DCMP_DEAMINASES_2; 1.
PE 1: Evidence at protein level;
KW Chloroplast; Hydrolase; Metal-binding; Plastid; Reference proteome;
KW Transit peptide; Zinc.
FT TRANSIT 1..61
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN 62..426
FT /note="Riboflavin biosynthesis protein PYRD, chloroplastic"
FT /id="PRO_0000422704"
FT DOMAIN 72..194
FT /note="CMP/dCMP-type deaminase"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01083"
FT ACT_SITE 123
FT /note="Proton donor"
FT /evidence="ECO:0000250"
FT BINDING 121
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250"
FT BINDING 146
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250"
FT BINDING 155
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250"
FT CONFLICT 65
FT /note="R -> K (in Ref. 5; AAM67209)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 426 AA; 46674 MW; EAC7581555AD0F99 CRC64;
MQISCLPISI PSITPRTSIP LLPSLSSNPR RIFNLTSLQS PNHCFFKRLH KSQTGFSNPV
LAAMRREEDV EVDDSFYMRK CVELAKRAIG CTSPNPMVGC VIVKDGDIVG QGFHPKAGQP
HAEVFALRDA GELAENATAY VSLEPCNHYG RTPPCTEALI KAKVRRVVIG MVDPNPIVFS
SGISRLKDAG IDVTVSVEEE LCKKMNEGFI HRMLTGKPFL ALRYSMSVNG CLLDKIGQGA
SDSGGYYSKL LQEYDAIILS SSLSDELSSI SSQEAINVSI QPIQIIVASN AQQSHILASS
HTVEESGPKV VVFTAKESVA ESGISSSGVE TVVLEKINLD SILDYCYNRG LCSVLLDLRG
NVKDLEVLLR DGFEQKLLQK VIIEVLPEWS TKDERQIASM KWLESKHVKD LQSKQLGGSV
LLEGYF
