RIBA2_ARATH
ID RIBA2_ARATH Reviewed; 476 AA.
AC Q6NLQ7; Q9SJY9;
DT 26-JUN-2013, integrated into UniProtKB/Swiss-Prot.
DT 05-JUL-2004, sequence version 1.
DT 03-AUG-2022, entry version 123.
DE RecName: Full=Monofunctional riboflavin biosynthesis protein RIBA 2, chloroplastic;
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=Inactive GTP cyclohydrolase-2;
DE AltName: Full=GTP cyclohydrolase II;
DE Flags: Precursor;
GN Name=RIBA2; OrderedLocusNames=At2g22450; ORFNames=F14M13.15;
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=10617197; DOI=10.1038/45471;
RA Lin X., Kaul S., Rounsley S.D., Shea T.P., Benito M.-I., Town C.D.,
RA Fujii C.Y., Mason T.M., Bowman C.L., Barnstead M.E., Feldblyum T.V.,
RA Buell C.R., Ketchum K.A., Lee J.J., Ronning C.M., Koo H.L., Moffat K.S.,
RA Cronin L.A., Shen M., Pai G., Van Aken S., Umayam L., Tallon L.J.,
RA Gill J.E., Adams M.D., Carrera A.J., Creasy T.H., Goodman H.M.,
RA Somerville C.R., Copenhaver G.P., Preuss D., Nierman W.C., White O.,
RA Eisen J.A., Salzberg S.L., Fraser C.M., Venter J.C.;
RT "Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana.";
RL Nature 402:761-768(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].
RA Cheuk R., Chen H., Kim C.J., Shinn P., Ecker J.R.;
RT "Arabidopsis ORF clones.";
RL Submitted (MAR-2004) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RA Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A.,
RA Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y.,
RA Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.,
RA Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y.,
RA Shinozaki K.;
RT "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs.";
RL Submitted (JUL-2006) to the EMBL/GenBank/DDBJ databases.
RN [5]
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 [6]
RP FUNCTION.
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 the conversion
CC of D-ribulose 5-phosphate to formate and 3,4-dihydroxy-2-butanone 4-
CC phosphate. RIBA2 and RIBA3 together are not able to complement the loss
CC 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 -!- 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 -!- PATHWAY: Cofactor biosynthesis; riboflavin biosynthesis; 2-hydroxy-3-
CC oxobutyl phosphate from D-ribulose 5-phosphate: step 1/1.
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 -!- 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 -!- CAUTION: The substrate-binding sites for the inactive GTP
CC cyclohydrolase-2 activity are conserved while several cofactor-binding
CC sites are lost. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAD22355.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AC006592; AAD22355.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002685; AEC07307.1; -; Genomic_DNA.
DR EMBL; BT011627; AAS47633.1; -; mRNA.
DR EMBL; BT012273; AAS76760.1; -; mRNA.
DR EMBL; AK228961; BAF00850.1; -; mRNA.
DR PIR; G84612; G84612.
DR RefSeq; NP_179831.2; NM_127810.4.
DR AlphaFoldDB; Q6NLQ7; -.
DR SMR; Q6NLQ7; -.
DR STRING; 3702.AT2G22450.1; -.
DR iPTMnet; Q6NLQ7; -.
DR PaxDb; Q6NLQ7; -.
DR PRIDE; Q6NLQ7; -.
DR ProMEX; Q6NLQ7; -.
DR ProteomicsDB; 234889; -.
DR EnsemblPlants; AT2G22450.1; AT2G22450.1; AT2G22450.
DR GeneID; 816777; -.
DR Gramene; AT2G22450.1; AT2G22450.1; AT2G22450.
DR KEGG; ath:AT2G22450; -.
DR Araport; AT2G22450; -.
DR TAIR; locus:2041253; AT2G22450.
DR eggNOG; KOG1284; Eukaryota.
DR HOGENOM; CLU_020273_1_1_1; -.
DR InParanoid; Q6NLQ7; -.
DR OMA; CDSTHLL; -.
DR OrthoDB; 916311at2759; -.
DR PhylomeDB; Q6NLQ7; -.
DR BioCyc; ARA:AT2G22450-MON; -.
DR BRENDA; 4.1.99.12; 399.
DR UniPathway; UPA00275; UER00399.
DR PRO; PR:Q6NLQ7; -.
DR Proteomes; UP000006548; Chromosome 2.
DR ExpressionAtlas; Q6NLQ7; baseline and differential.
DR Genevisible; Q6NLQ7; AT.
DR GO; GO:0009507; C:chloroplast; IDA:UniProtKB.
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:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0009231; P:riboflavin biosynthetic process; IBA:GO_Central.
DR Gene3D; 3.40.50.10990; -; 1.
DR HAMAP; MF_00180; RibB; 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; IPR036144; RibA-like_sf.
DR Pfam; PF00926; DHBP_synthase; 1.
DR Pfam; PF00925; GTP_cyclohydro2; 1.
DR SUPFAM; SSF142695; SSF142695; 1.
DR SUPFAM; SSF55821; SSF55821; 1.
DR TIGRFAMs; TIGR00506; ribB; 1.
PE 1: Evidence at protein level;
KW Chloroplast; GTP-binding; Lyase; Magnesium; Metal-binding;
KW Nucleotide-binding; Plastid; Reference proteome; Riboflavin biosynthesis;
KW Transit peptide.
FT TRANSIT 1..54
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN 55..476
FT /note="Monofunctional riboflavin biosynthesis protein RIBA
FT 2, chloroplastic"
FT /id="PRO_0000422708"
FT REGION 44..306
FT /note="DHBP synthase"
FT REGION 307..476
FT /note="Inactive GTP cyclohydrolase II"
FT BINDING 130..131
FT /ligand="D-ribulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:58121"
FT /evidence="ECO:0000250"
FT BINDING 131
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 131
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 135
FT /ligand="D-ribulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:58121"
FT /evidence="ECO:0000250"
FT BINDING 245..249
FT /ligand="D-ribulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:58121"
FT /evidence="ECO:0000250"
FT BINDING 248
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 269
FT /ligand="D-ribulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:58121"
FT /evidence="ECO:0000250"
FT BINDING 357..361
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000250"
FT BINDING 376
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000250"
FT BINDING 399..401
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000250"
FT BINDING 450
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000250"
FT SITE 231
FT /note="Essential for DHBP synthase activity"
FT /evidence="ECO:0000250"
FT SITE 269
FT /note="Essential for DHBP synthase activity"
FT /evidence="ECO:0000250"
SQ SEQUENCE 476 AA; 52200 MW; 4F5BFEE0F8356CAC CRC64;
MASLTLRCDS THLLPSRDVV KGTKPFGTSL VYPRIISKKF NVRMRVIPEE GDVFSSSKSN
GSSMGIELQP DLVSFGTLAA EMIPTTMDSP EVEDEEFDLD RPTDGFASIP QAIEDIRHGK
MVVVVDDEDR ENEGDLIMAA SLATPEAMAF VVKHGTGIVC VSMKGEDLER LELPLMVTRK
DNEEKLRTAF TVSVDAKKGT STGVSARDRA QTILTLASKD SKPEDFNRPG HIFPLRYREG
GVLKRAGHTE ASVDLTVLAG LEPVSVLCEI VDDDGSMARL PRLRQFAQEN NLKLISIADL
IRYRRKRERL VEFTAVAPIP TMWGPFKAHC FKSLLDGVEH IAMVKGEIGD GKDILVRVHA
ECITDDIFGN SSGGKQLAIA MRLIEENGRG VFVYLRGPES KGIDLSHKPR TYNTNSDQAE
GVSFPVASRE YGIGAQILRD LGVREMKVMT NNPAHYVGLK GYGLSISGKV PLITTP
