RIBA3_ORYSJ
ID RIBA3_ORYSJ Reviewed; 536 AA.
AC Q6L506; A0A0P0WNE0; Q84PC2;
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=Probable 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=Os05g0460600;
GN ORFNames=OJ1281_H05.8, OsJ_18816;
OS Oryza sativa subsp. japonica (Rice).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade;
OC Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa.
OX NCBI_TaxID=39947;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16261349; DOI=10.1007/s00438-005-0039-y;
RA Cheng C.-H., Chung M.C., Liu S.-M., Chen S.-K., Kao F.Y., Lin S.-J.,
RA Hsiao S.-H., Tseng I.C., Hsing Y.-I.C., Wu H.-P., Chen C.-S., Shaw J.-F.,
RA Wu J., Matsumoto T., Sasaki T., Chen H.-C., Chow T.-Y.;
RT "A fine physical map of the rice chromosome 5.";
RL Mol. Genet. Genomics 274:337-345(2005).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16100779; DOI=10.1038/nature03895;
RG International rice genome sequencing project (IRGSP);
RT "The map-based sequence of the rice genome.";
RL Nature 436:793-800(2005).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=18089549; DOI=10.1093/nar/gkm978;
RG The rice annotation project (RAP);
RT "The rice annotation project database (RAP-DB): 2008 update.";
RL Nucleic Acids Res. 36:D1028-D1033(2008).
RN [4]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=24280374; DOI=10.1186/1939-8433-6-4;
RA Kawahara Y., de la Bastide M., Hamilton J.P., Kanamori H., McCombie W.R.,
RA Ouyang S., Schwartz D.C., Tanaka T., Wu J., Zhou S., Childs K.L.,
RA Davidson R.M., Lin H., Quesada-Ocampo L., Vaillancourt B., Sakai H.,
RA Lee S.S., Kim J., Numa H., Itoh T., Buell C.R., Matsumoto T.;
RT "Improvement of the Oryza sativa Nipponbare reference genome using next
RT generation sequence and optical map data.";
RL Rice 6:4-4(2013).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=15685292; DOI=10.1371/journal.pbio.0030038;
RA Yu J., Wang J., Lin W., Li S., Li H., Zhou J., Ni P., Dong W., Hu S.,
RA Zeng C., Zhang J., Zhang Y., Li R., Xu Z., Li S., Li X., Zheng H., Cong L.,
RA Lin L., Yin J., Geng J., Li G., Shi J., Liu J., Lv H., Li J., Wang J.,
RA Deng Y., Ran L., Shi X., Wang X., Wu Q., Li C., Ren X., Wang J., Wang X.,
RA Li D., Liu D., Zhang X., Ji Z., Zhao W., Sun Y., Zhang Z., Bao J., Han Y.,
RA Dong L., Ji J., Chen P., Wu S., Liu J., Xiao Y., Bu D., Tan J., Yang L.,
RA Ye C., Zhang J., Xu J., Zhou Y., Yu Y., Zhang B., Zhuang S., Wei H.,
RA Liu B., Lei M., Yu H., Li Y., Xu H., Wei S., He X., Fang L., Zhang Z.,
RA Zhang Y., Huang X., Su Z., Tong W., Li J., Tong Z., Li S., Ye J., Wang L.,
RA Fang L., Lei T., Chen C.-S., Chen H.-C., Xu Z., Li H., Huang H., Zhang F.,
RA Xu H., Li N., Zhao C., Li S., Dong L., Huang Y., Li L., Xi Y., Qi Q.,
RA Li W., Zhang B., Hu W., Zhang Y., Tian X., Jiao Y., Liang X., Jin J.,
RA Gao L., Zheng W., Hao B., Liu S.-M., Wang W., Yuan L., Cao M.,
RA McDermott J., Samudrala R., Wang J., Wong G.K.-S., Yang H.;
RT "The genomes of Oryza sativa: a history of duplications.";
RL PLoS Biol. 3:266-281(2005).
RN [6]
RP NUCLEOTIDE SEQUENCE [MRNA] OF 77-536.
RX PubMed=12684538; DOI=10.1073/pnas.0737574100;
RA Cooper B., Clarke J.D., Budworth P., Kreps J., Hutchison D., Park S.,
RA Guimil S., Dunn M., Luginbuehl P., Ellero C., Goff S.A., Glazebrook J.;
RT "A network of rice genes associated with stress response and seed
RT development.";
RL Proc. Natl. Acad. Sci. U.S.A. 100:4945-4950(2003).
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 (By similarity). {ECO:0000250}.
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 -!- 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 {ECO:0000305}.
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; AC117265; AAT39168.1; -; Genomic_DNA.
DR EMBL; AP008211; BAF17671.1; -; Genomic_DNA.
DR EMBL; AP014961; BAS94403.1; -; Genomic_DNA.
DR EMBL; CM000142; EEE63987.1; -; Genomic_DNA.
DR EMBL; AY224441; AAO72560.1; -; mRNA.
DR RefSeq; XP_015637605.1; XM_015782119.1.
DR AlphaFoldDB; Q6L506; -.
DR SMR; Q6L506; -.
DR BioGRID; 808054; 1.
DR IntAct; Q6L506; 1.
DR STRING; 4530.OS05T0460600-01; -.
DR PaxDb; Q6L506; -.
DR PRIDE; Q6L506; -.
DR EnsemblPlants; Os05t0460600-01; Os05t0460600-01; Os05g0460600.
DR GeneID; 4339017; -.
DR Gramene; Os05t0460600-01; Os05t0460600-01; Os05g0460600.
DR KEGG; osa:4339017; -.
DR eggNOG; KOG1284; Eukaryota.
DR HOGENOM; CLU_020273_1_1_1; -.
DR InParanoid; Q6L506; -.
DR OMA; GGVHMAM; -.
DR OrthoDB; 916311at2759; -.
DR PlantReactome; R-OSA-1119379; Flavin biosynthesis.
DR UniPathway; UPA00275; UER00400.
DR Proteomes; UP000000763; Chromosome 5.
DR Proteomes; UP000007752; Chromosome 5.
DR Proteomes; UP000059680; Chromosome 5.
DR ExpressionAtlas; Q6L506; baseline and differential.
DR Genevisible; Q6L506; OS.
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 2: Evidence at transcript level;
KW Chloroplast; GTP-binding; Hydrolase; Metal-binding; Nucleotide-binding;
KW Plastid; Reference proteome; Riboflavin biosynthesis; Transit peptide;
KW Zinc.
FT TRANSIT 1..43
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN 44..536
FT /note="Probable monofunctional riboflavin biosynthesis
FT protein RIBA 3, chloroplastic"
FT /id="PRO_0000422712"
FT REGION 44..310
FT /note="Inactive DHBP synthase"
FT /evidence="ECO:0000250"
FT REGION 311..536
FT /note="GTP cyclohydrolase II"
FT /evidence="ECO:0000250"
FT REGION 507..536
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 439
FT /note="Proton acceptor; for GTP cyclohydrolase activity"
FT /evidence="ECO:0000255"
FT ACT_SITE 441
FT /note="Nucleophile; for GTP cyclohydrolase activity"
FT /evidence="ECO:0000250"
FT BINDING 133..134
FT /ligand="D-ribulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:58121"
FT /evidence="ECO:0000250"
FT BINDING 138
FT /ligand="D-ribulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:58121"
FT /evidence="ECO:0000250"
FT BINDING 248..252
FT /ligand="D-ribulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:58121"
FT /evidence="ECO:0000250"
FT BINDING 361..365
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000250"
FT BINDING 366
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250"
FT BINDING 377
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250"
FT BINDING 379
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250"
FT BINDING 382
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000250"
FT BINDING 405..407
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000250"
FT BINDING 427
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000250"
FT BINDING 462
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000250"
FT BINDING 467
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000250"
SQ SEQUENCE 536 AA; 57327 MW; 563F9C7C0A4B4A05 CRC64;
MDRVLLSSQL SSQTVVNTRV QQGSGGINSI GFAVIRKGSL KLRCYAIGGL GGGENLNDPL
KESNNGPVLQ GFNGSSASFR TVGAKITQET GDFFVSDAEG DPDKPTDGFS SIDEAIGALH
EGKFVIAVDD ESGDNEGDLV MAATLADPES IAFMIRNGSG IISVGMKEED LTRLMIPMMS
PIAEIEDISA AASTVTVDAR VGISTGVSAA DRAKTIFTLA SPDSKPTDLR RPGHIFPLKY
RNGGVLKRAG HTEASVDLVA LAGLRPVSVL STVINPVDGS MAGMPVLKQM ALEHDIPIVS
IADLIRYRRK REKLVELIAV SRLPTKWGLF RAYCYQSKLD GTEHIAVAKG DIGDGEDVLV
RVHSECLTGD ILGSARCDCG NQLDLAMQLI DKAGRGVLVY LRGHEGRGIG LGQKLRAYNL
QDDGHDTVQA NVELGLAVDS REYGIGAQIL RDMGVRTMRL MTNNPAKFVG LKGYGLAVVG
RVPVISPITK ENQRYLETKR TKMGHVYGSD LPGNVPEEFL NPDDIAGDQD EDDTHN
