RIBA2_ORYSJ
ID RIBA2_ORYSJ Reviewed; 553 AA.
AC Q0E079; A0A0P0VKQ6;
DT 26-JUN-2013, integrated into UniProtKB/Swiss-Prot.
DT 17-OCT-2006, sequence version 1.
DT 03-AUG-2022, entry version 106.
DE RecName: Full=Probable bifunctional riboflavin biosynthesis protein RIBA 2, chloroplastic;
DE Short=OsRIBA2;
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=RIBA2; OrderedLocusNames=Os02g0572400; ORFNames=J023020F21, OsJ_07218;
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=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 [2]
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 [3]
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 [4]
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 [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=12869764; DOI=10.1126/science.1081288;
RG The rice full-length cDNA consortium;
RT "Collection, mapping, and annotation of over 28,000 cDNA clones from
RT japonica rice.";
RL Science 301:376-379(2003).
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 (By similarity). {ECO:0000250}.
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;
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=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 {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}.
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DR EMBL; AP008208; BAF09109.1; -; Genomic_DNA.
DR EMBL; AP014958; BAS79355.1; -; Genomic_DNA.
DR EMBL; CM000139; EAZ23521.1; -; Genomic_DNA.
DR EMBL; AK069475; BAG91454.1; -; mRNA.
DR RefSeq; XP_015626297.1; XM_015770811.1.
DR AlphaFoldDB; Q0E079; -.
DR SMR; Q0E079; -.
DR STRING; 4530.OS02T0572400-01; -.
DR PaxDb; Q0E079; -.
DR PRIDE; Q0E079; -.
DR EnsemblPlants; Os02t0572400-01; Os02t0572400-01; Os02g0572400.
DR GeneID; 4329733; -.
DR Gramene; Os02t0572400-01; Os02t0572400-01; Os02g0572400.
DR KEGG; osa:4329733; -.
DR eggNOG; KOG1284; Eukaryota.
DR HOGENOM; CLU_020273_1_0_1; -.
DR InParanoid; Q0E079; -.
DR OMA; ECRGLIC; -.
DR OrthoDB; 916311at2759; -.
DR PlantReactome; R-OSA-1119379; Flavin biosynthesis.
DR UniPathway; UPA00275; UER00399.
DR UniPathway; UPA00275; UER00400.
DR Proteomes; UP000000763; Chromosome 2.
DR Proteomes; UP000007752; Chromosome 2.
DR Proteomes; UP000059680; Chromosome 2.
DR ExpressionAtlas; Q0E079; baseline and differential.
DR Genevisible; Q0E079; 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_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 2: Evidence at transcript 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..553
FT /note="Probable bifunctional riboflavin biosynthesis
FT protein RIBA 2, chloroplastic"
FT /id="PRO_0000422711"
FT REGION 62..336
FT /note="DHBP synthase"
FT /evidence="ECO:0000250"
FT REGION 70..90
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 337..553
FT /note="GTP cyclohydrolase II"
FT /evidence="ECO:0000250"
FT COMPBIAS 74..89
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 465
FT /note="Proton acceptor; for GTP cyclohydrolase activity"
FT /evidence="ECO:0000255"
FT ACT_SITE 467
FT /note="Nucleophile; for GTP cyclohydrolase activity"
FT /evidence="ECO:0000250"
FT BINDING 160..161
FT /ligand="D-ribulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:58121"
FT /evidence="ECO:0000250"
FT BINDING 161
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 161
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 165
FT /ligand="D-ribulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:58121"
FT /evidence="ECO:0000250"
FT BINDING 275..279
FT /ligand="D-ribulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:58121"
FT /evidence="ECO:0000250"
FT BINDING 278
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 299
FT /ligand="D-ribulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:58121"
FT /evidence="ECO:0000250"
FT BINDING 387..391
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000250"
FT BINDING 392
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250"
FT BINDING 403
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250"
FT BINDING 405
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250"
FT BINDING 408
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000250"
FT BINDING 431..433
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000250"
FT BINDING 453
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000250"
FT BINDING 488
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000250"
FT BINDING 493
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000250"
FT SITE 261
FT /note="Essential for DHBP synthase activity"
FT /evidence="ECO:0000250"
FT SITE 299
FT /note="Essential for DHBP synthase activity"
FT /evidence="ECO:0000250"
SQ SEQUENCE 553 AA; 59590 MW; 173D0EF102FF34AA CRC64;
MASISPTSSS VAALRGHPVQ FVKGGAVSKE AKGSISFSPV ANSNNANVKF TGLRVAASLK
RDGAFPGDGY SGNDNTVLPK STSVRGQDYP TADSVLPTES IIVPEISNAG LKCVADMFSD
EDKDTEQDLD SPTEGFSSIS EAIKDIQQGK LVIVVDDESR ENEGDLIMAA SLVTPEAMAF
VVRYGTGIVC VSMKEEDLER LNLPLMVATK ENEEKLCTAF TVTVDAKEGT TTGVSAKDRA
KTVMTLASPD SKPEDFNRPG HIFPLKYREG GVLKRAGHTE ASVDLAMLAG LPPAAVLCEI
VDEDGSMARL PKLRVFAERE NLKIVSIADL IRYRRKRDRL VERSSVARLP LRWGNVRAYC
YRSVIDGIEH IAMVKGEIGD GQGVLVRVHS ECLTGDIFGS ARCDCGDQLA MAMEMIEKAG
RGVLVYLRGH EGRGIGLGHK LRAYNLQDDG RDTVEANEDL GLPVDSREYG IGAQILRDLG
VRSMKLMTNN PAKYGGLKGY GLSIVGRVPL VTPITSENRR YLETKRTKMG HVYGLANGQA
SHQTGSNGAK GEH
