RIBA3_ARATH
ID RIBA3_ARATH Reviewed; 509 AA.
AC Q9FN89;
DT 26-JUN-2013, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2001, sequence version 1.
DT 03-AUG-2022, entry version 135.
DE RecName: Full=Monofunctional riboflavin biosynthesis protein RIBA 3, chloroplastic;
DE Includes:
DE RecName: Full=Inactive 3,4-dihydroxy-2-butanone 4-phosphate synthase;
DE Short=DHBP synthase;
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=RIBA3; OrderedLocusNames=At5g59750; ORFNames=MTH12.13, MTH12.150;
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=9405937; DOI=10.1093/dnares/4.4.291;
RA Kotani H., Nakamura Y., Sato S., Kaneko T., Asamizu E., Miyajima N.,
RA Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 5. II. Sequence
RT features of the regions of 1,044,062 bp covered by thirteen physically
RT assigned P1 clones.";
RL DNA Res. 4:291-300(1997).
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=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 [4]
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 [5]
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 GTP to 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate
CC (DARP), formate and pyrophosphate. RIBA2 and RIBA3 together are not
CC able to complement the loss of function of RIBA1.
CC {ECO:0000269|PubMed:22081402, 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=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; 5-amino-6-(D-
CC ribitylamino)uracil from GTP: step 1/4.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast
CC {ECO:0000269|PubMed:23203051}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=1;
CC Comment=A number of isoforms are produced.;
CC Name=1;
CC IsoId=Q9FN89-1; Sequence=Displayed;
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 DHBP synthase
CC activity are conserved while several cofactor-binding sites are lost.
CC {ECO:0000305}.
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DR EMBL; AB006705; BAB09512.1; -; Genomic_DNA.
DR EMBL; CP002688; AED97227.1; -; Genomic_DNA.
DR EMBL; AF361835; AAK32847.1; -; mRNA.
DR EMBL; AY050405; AAK91421.1; -; mRNA.
DR EMBL; BT002730; AAO11646.1; -; mRNA.
DR RefSeq; NP_568913.1; NM_125367.6. [Q9FN89-1]
DR AlphaFoldDB; Q9FN89; -.
DR SMR; Q9FN89; -.
DR STRING; 3702.AT5G59750.2; -.
DR PRIDE; Q9FN89; -.
DR ProteomicsDB; 234693; -. [Q9FN89-1]
DR EnsemblPlants; AT5G59750.1; AT5G59750.1; AT5G59750. [Q9FN89-1]
DR GeneID; 836096; -.
DR Gramene; AT5G59750.1; AT5G59750.1; AT5G59750. [Q9FN89-1]
DR KEGG; ath:AT5G59750; -.
DR Araport; AT5G59750; -.
DR eggNOG; KOG1284; Eukaryota.
DR OMA; GGVHMAM; -.
DR PhylomeDB; Q9FN89; -.
DR BioCyc; ARA:AT5G59750-MON; -.
DR UniPathway; UPA00275; UER00400.
DR PRO; PR:Q9FN89; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q9FN89; baseline and differential.
DR Genevisible; Q9FN89; AT.
DR GO; GO:0009507; C:chloroplast; IBA:GO_Central.
DR GO; GO:0008686; F:3,4-dihydroxy-2-butanone-4-phosphate synthase activity; IBA:GO_Central.
DR GO; GO:0005525; F:GTP binding; IEA:UniProtKB-KW.
DR GO; GO:0003935; F:GTP cyclohydrolase II activity; IEA:UniProtKB-EC.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0009231; P:riboflavin biosynthetic process; IBA:GO_Central.
DR CDD; cd00641; GTP_cyclohydro2; 1.
DR Gene3D; 3.40.50.10990; -; 1.
DR HAMAP; MF_00179; RibA; 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 Alternative splicing; Chloroplast; GTP-binding; Hydrolase; Metal-binding;
KW Nucleotide-binding; Plastid; Reference proteome; Riboflavin biosynthesis;
KW Transit peptide; Zinc.
FT TRANSIT 1..43
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN 44..509
FT /note="Monofunctional riboflavin biosynthesis protein RIBA
FT 3, chloroplastic"
FT /id="PRO_0000422709"
FT REGION 44..302
FT /note="Inactive DHBP synthase"
FT REGION 303..509
FT /note="GTP cyclohydrolase II"
FT ACT_SITE 431
FT /note="Proton acceptor; for GTP cyclohydrolase activity"
FT /evidence="ECO:0000255"
FT ACT_SITE 433
FT /note="Nucleophile; for GTP cyclohydrolase activity"
FT /evidence="ECO:0000250"
FT BINDING 125..126
FT /ligand="D-ribulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:58121"
FT /evidence="ECO:0000250"
FT BINDING 240..244
FT /ligand="D-ribulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:58121"
FT /evidence="ECO:0000250"
FT BINDING 353..357
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000250"
FT BINDING 358
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250"
FT BINDING 369
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250"
FT BINDING 371
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250"
FT BINDING 374
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000250"
FT BINDING 397..399
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000250"
FT BINDING 419
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000250"
FT BINDING 454
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000250"
FT BINDING 459
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000250"
SQ SEQUENCE 509 AA; 56146 MW; D9E56782486E4D10 CRC64;
MMDSALYHPR IFFAHSFING LYSSPRFANT CWRLVSRSSW EIKASENSDR NVFDENPVRK
TDGSLFDSAS FETVDAEITP ETDDFFVSDA EGDPDCPTQG YSSIELALQA LRKGKFVIVV
DDETGDVEGN LIMAATLTSP KDIAFLIKNG SGIVSVGMKK ENLERLSLTL MSPEMEDEDS
SAPTFTITVD AKSGTSTGVS ASDRAMTVLA LSSLDAKPDD FRRPGHVFPL KYRDGGVLRR
AGHTEASVDL MILAGLRPLS VLSAILDQED GSMASLPYMK KLATEHDIPI VSLTDLIRYR
RKRDKLVERI TVSRLPTKWG LFQAYCYRSK LDGTENIALV KGNVGNGEDI LVRVHSECLT
GDIFGSARCD CGNQLDLAME LIEKEGRGVV VYLRGHEGRG IGLGHKLRAY NLQDEGHDTV
QANVELGLSI DSREYGIGAQ MLRDIGVRTM RLMTNNPAKF TGLKGYGLAV VGRVPVVTPI
TKENRRYMET KRKKMGHIYI SDNNDQPLA
