RIBA1_ARATH
ID RIBA1_ARATH Reviewed; 543 AA.
AC P47924; Q9SBA8;
DT 01-FEB-1996, integrated into UniProtKB/Swiss-Prot.
DT 10-JAN-2003, sequence version 2.
DT 03-AUG-2022, entry version 151.
DE RecName: Full=Bifunctional riboflavin biosynthesis protein RIBA 1, chloroplastic;
DE Short=AtRIBA1;
DE Includes:
DE RecName: Full=3,4-dihydroxy-2-butanone 4-phosphate synthase;
DE Short=DHBP synthase;
DE EC=4.1.99.12;
DE Includes:
DE RecName: Full=GTP cyclohydrolase-2;
DE EC=3.5.4.25;
DE AltName: Full=GTP cyclohydrolase II;
DE Flags: Precursor;
GN Name=RIBA1; Synonyms=RIBBA; OrderedLocusNames=At5g64300; ORFNames=MSJ1.14;
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 [GENOMIC DNA].
RX PubMed=10783978; DOI=10.1016/s0031-9422(00)00013-3;
RA Herz S.W., Eberhardt S., Bacher A.;
RT "Biosynthesis of riboflavin in plants. The ribA gene of Arabidopsis
RT thaliana specifies a bifunctional GTP cyclohydrolase II/3,4-dihydroxy-2-
RT butanone 4-phosphate synthase.";
RL Phytochemistry 53:723-731(2000).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=9501997; DOI=10.1093/dnares/4.6.401;
RA Nakamura Y., Sato S., Kaneko T., Kotani H., Asamizu E., Miyajima N.,
RA Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 5. III. Sequence
RT features of the regions of 1,191,918 bp covered by seventeen physically
RT assigned P1 clones.";
RL DNA Res. 4:401-414(1997).
RN [3]
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 [4]
RP NUCLEOTIDE SEQUENCE [MRNA] OF 279-543.
RX PubMed=7642114; DOI=10.1016/0378-1119(95)00246-3;
RA Kobayashi M., Sugiyama M., Yamamoto K.;
RT "Isolation of cDNAs encoding GTP cyclohydrolase II from Arabidopsis
RT thaliana.";
RL Gene 160:303-304(1995).
RN [5]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=19376835; DOI=10.1104/pp.109.138677;
RA Reiland S., Messerli G., Baerenfaller K., Gerrits B., Endler A.,
RA Grossmann J., Gruissem W., Baginsky S.;
RT "Large-scale Arabidopsis phosphoproteome profiling reveals novel
RT chloroplast kinase substrates and phosphorylation networks.";
RL Plant Physiol. 150:889-903(2009).
RN [6]
RP FUNCTION, CATALYTIC ACTIVITY, TISSUE SPECIFICITY, AND SUBCELLULAR LOCATION.
RX PubMed=23203051; DOI=10.3390/ijms131114086;
RA Hiltunen H.M., Illarionov B., Hedtke B., Fischer M., Grimm B.;
RT "Arabidopsis RIBA Proteins: two out of three isoforms have lost their
RT bifunctional activity in riboflavin biosynthesis.";
RL Int. J. Mol. Sci. 13:14086-14105(2012).
RN [7]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=22081402; DOI=10.1007/s11103-011-9846-1;
RA Hedtke B., Alawady A., Albacete A., Kobayashi K., Melzer M., Roitsch T.,
RA Masuda T., Grimm B.;
RT "Deficiency in riboflavin biosynthesis affects tetrapyrrole biosynthesis in
RT etiolated Arabidopsis tissue.";
RL Plant Mol. Biol. 78:77-93(2012).
CC -!- FUNCTION: Involved in riboflavin biosynthesis. Catalyzes both the
CC conversion of D-ribulose 5-phosphate to formate and 3,4-dihydroxy-2-
CC butanone 4-phosphate and the conversion of GTP to 2,5-diamino-6-
CC ribosylamino-4(3H)-pyrimidinone 5'-phosphate (DARP), formate and
CC pyrophosphate. RIBA2 and RIBA3 together are not able to complement the
CC loss of function of RIBA1. {ECO:0000269|PubMed:22081402,
CC ECO:0000269|PubMed:23203051}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=D-ribulose 5-phosphate = (2S)-2-hydroxy-3-oxobutyl phosphate +
CC formate + H(+); Xref=Rhea:RHEA:18457, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:15740, ChEBI:CHEBI:58121, ChEBI:CHEBI:58830;
CC EC=4.1.99.12; Evidence={ECO:0000269|PubMed:23203051};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=GTP + 4 H2O = 2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)-
CC pyrimidine + formate + 3 H(+) + 2 phosphate; Xref=Rhea:RHEA:23704,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:15740,
CC ChEBI:CHEBI:37565, ChEBI:CHEBI:43474, ChEBI:CHEBI:58614; EC=3.5.4.25;
CC Evidence={ECO:0000269|PubMed:23203051};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000250};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035; Evidence={ECO:0000250};
CC Note=Binds 2 divalent metal cations per subunit. Magnesium or
CC manganese. {ECO:0000250};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105; Evidence={ECO:0000250};
CC Note=Binds 1 zinc ion per subunit. {ECO:0000250};
CC -!- PATHWAY: Cofactor biosynthesis; riboflavin biosynthesis; 2-hydroxy-3-
CC oxobutyl phosphate from D-ribulose 5-phosphate: step 1/1.
CC -!- PATHWAY: Cofactor biosynthesis; riboflavin biosynthesis; 5-amino-6-(D-
CC ribitylamino)uracil from GTP: step 1/4.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast
CC {ECO:0000269|PubMed:23203051}.
CC -!- TISSUE SPECIFICITY: Expressed in leaves, shoots, roots, flowers and
CC siliques. {ECO:0000269|PubMed:23203051}.
CC -!- DISRUPTION PHENOTYPE: No visible phenotype when heterozygous. Bleached
CC phenotype and no viable seeds produced when homozygous.
CC {ECO:0000269|PubMed:22081402}.
CC -!- SIMILARITY: In the N-terminal section; belongs to the DHBP synthase
CC family. {ECO:0000305}.
CC -!- SIMILARITY: In the C-terminal section; belongs to the GTP
CC cyclohydrolase II family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAA08113.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
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DR EMBL; AJ000053; CAA03884.1; -; Genomic_DNA.
DR EMBL; AB008268; BAB09861.1; -; Genomic_DNA.
DR EMBL; CP002688; AED97867.1; -; Genomic_DNA.
DR EMBL; D45165; BAA08113.1; ALT_INIT; mRNA.
DR PIR; JC4209; JC4209.
DR RefSeq; NP_201235.4; NM_125826.5.
DR AlphaFoldDB; P47924; -.
DR SMR; P47924; -.
DR BioGRID; 21793; 2.
DR STRING; 3702.AT5G64300.1; -.
DR iPTMnet; P47924; -.
DR PaxDb; P47924; -.
DR PRIDE; P47924; -.
DR ProteomicsDB; 236579; -.
DR EnsemblPlants; AT5G64300.1; AT5G64300.1; AT5G64300.
DR GeneID; 836551; -.
DR Gramene; AT5G64300.1; AT5G64300.1; AT5G64300.
DR KEGG; ath:AT5G64300; -.
DR Araport; AT5G64300; -.
DR TAIR; locus:2173373; AT5G64300.
DR eggNOG; KOG1284; Eukaryota.
DR HOGENOM; CLU_020273_1_1_1; -.
DR InParanoid; P47924; -.
DR OMA; WISAHGL; -.
DR OrthoDB; 916311at2759; -.
DR PhylomeDB; P47924; -.
DR BioCyc; ARA:AT5G64300-MON; -.
DR BioCyc; MetaCyc:AT5G64300-MON; -.
DR BRENDA; 4.1.99.12; 399.
DR UniPathway; UPA00275; UER00399.
DR UniPathway; UPA00275; UER00400.
DR PRO; PR:P47924; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; P47924; baseline and differential.
DR Genevisible; P47924; AT.
DR GO; GO:0009507; C:chloroplast; IDA:UniProtKB.
DR GO; GO:0009570; C:chloroplast stroma; HDA:TAIR.
DR GO; GO:0008686; F:3,4-dihydroxy-2-butanone-4-phosphate synthase activity; IDA:UniProtKB.
DR GO; GO:0005525; F:GTP binding; IEA:UniProtKB-KW.
DR GO; GO:0003935; F:GTP cyclohydrolase II activity; IDA:UniProtKB.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0009231; P:riboflavin biosynthetic process; IMP:UniProtKB.
DR CDD; cd00641; GTP_cyclohydro2; 1.
DR Gene3D; 3.40.50.10990; -; 1.
DR HAMAP; MF_00179; RibA; 1.
DR HAMAP; MF_00180; RibB; 1.
DR HAMAP; MF_01283; RibBA; 1.
DR InterPro; IPR017945; DHBP_synth_RibB-like_a/b_dom.
DR InterPro; IPR000422; DHBP_synthase_RibB.
DR InterPro; IPR032677; GTP_cyclohydro_II.
DR InterPro; IPR000926; RibA.
DR InterPro; IPR036144; RibA-like_sf.
DR InterPro; IPR016299; Riboflavin_synth_RibBA.
DR Pfam; PF00926; DHBP_synthase; 1.
DR Pfam; PF00925; GTP_cyclohydro2; 1.
DR SUPFAM; SSF142695; SSF142695; 1.
DR SUPFAM; SSF55821; SSF55821; 1.
DR TIGRFAMs; TIGR00505; ribA; 1.
DR TIGRFAMs; TIGR00506; ribB; 1.
PE 1: Evidence at protein level;
KW Chloroplast; GTP-binding; Hydrolase; Lyase; Magnesium; Manganese;
KW Metal-binding; Multifunctional enzyme; Nucleotide-binding; Plastid;
KW Reference proteome; Riboflavin biosynthesis; Transit peptide; Zinc.
FT TRANSIT 1..56
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN 57..543
FT /note="Bifunctional riboflavin biosynthesis protein RIBA 1,
FT chloroplastic"
FT /id="PRO_0000030436"
FT REGION 57..328
FT /note="DHBP synthase"
FT REGION 329..543
FT /note="GTP cyclohydrolase II"
FT ACT_SITE 457
FT /note="Proton acceptor; for GTP cyclohydrolase activity"
FT /evidence="ECO:0000255"
FT ACT_SITE 459
FT /note="Nucleophile; for GTP cyclohydrolase activity"
FT /evidence="ECO:0000250"
FT BINDING 152..153
FT /ligand="D-ribulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:58121"
FT /evidence="ECO:0000250"
FT BINDING 153
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 153
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 157
FT /ligand="D-ribulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:58121"
FT /evidence="ECO:0000250"
FT BINDING 267..271
FT /ligand="D-ribulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:58121"
FT /evidence="ECO:0000250"
FT BINDING 270
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 291
FT /ligand="D-ribulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:58121"
FT /evidence="ECO:0000250"
FT BINDING 379..383
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000250"
FT BINDING 384
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250"
FT BINDING 395
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250"
FT BINDING 397
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250"
FT BINDING 400
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000250"
FT BINDING 423..425
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000250"
FT BINDING 445
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000250"
FT BINDING 480
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000250"
FT BINDING 485
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000250"
FT SITE 253
FT /note="Essential for DHBP synthase activity"
FT /evidence="ECO:0000250"
FT SITE 291
FT /note="Essential for DHBP synthase activity"
FT /evidence="ECO:0000250"
SQ SEQUENCE 543 AA; 59056 MW; 31D89A500E42BF81 CRC64;
MSSINLSSSS PSTISLSRSR LSQSSTTLLH GLHRVTLPSN HPLSTFSIKT NTGKVKAAVI
SREDDLLSFT NGNTPLSNGS LIDDRTEEPL EADSVSLGTL AADSAPAPAN GFVAEDDDFE
LDLPTPGFSS IPEAIEDIRQ GKLVVVVDDE DRENEGDLVM AAQLATPEAM AFIVRHGTGI
VCVSMKEDDL ERLHLPLMVN QKENEEKLST AFTVTVDAKH GTTTGVSARD RATTILSLAS
RDSKPEDFNR PGHIFPLKYR EGGVLKRAGH TEASVDLTVL AGLDPVGVLC EIVDDDGSMA
RLPKLREFAA ENNLKVVSIA DLIRYRRKRD KLVERASAAR IPTMWGPFTA YCYRSILDGI
EHIAMVKGEI GDGQDILVRV HSECLTGDIF GSARCDCGNQ LALSMQQIEA TGRGVLVYLR
GHEGRGIGLG HKLRAYNLQD AGRDTVEANE ELGLPVDSRE YGIGAQIIRD LGVRTMKLMT
NNPAKYVGLK GYGLAIVGRV PLLSLITKEN KRYLETKRTK MGHMYGLKFK GDVVEKIESE
SES
