RIBA1_ORYSJ
ID RIBA1_ORYSJ Reviewed; 538 AA.
AC Q6Z234; B9G1G3;
DT 26-JUN-2013, integrated into UniProtKB/Swiss-Prot.
DT 05-JUL-2004, sequence version 1.
DT 03-AUG-2022, entry version 99.
DE RecName: Full=Probable bifunctional riboflavin biosynthesis protein RIBA 1, chloroplastic;
DE Short=OsRIBA1;
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; OrderedLocusNames=Os08g0481950, LOC_Os08g37605;
GN ORFNames=OJ1111_H02.5, OsJ_27700, OSJNBb0092C08.34;
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=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 [3]
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 [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Nipponbare;
RG The rice full-length cDNA consortium;
RT "Oryza sativa full length cDNA.";
RL Submitted (OCT-2006) to the EMBL/GenBank/DDBJ databases.
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}.
CC -!- SEQUENCE CAUTION:
CC Sequence=EEE68880.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AP004213; BAD09287.1; -; Genomic_DNA.
DR EMBL; AP005391; BAD10288.1; -; Genomic_DNA.
DR EMBL; AP014964; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; CM000145; EEE68880.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AK241452; -; NOT_ANNOTATED_CDS; mRNA.
DR AlphaFoldDB; Q6Z234; -.
DR SMR; Q6Z234; -.
DR STRING; 4530.OS08T0481950-01; -.
DR PaxDb; Q6Z234; -.
DR PRIDE; Q6Z234; -.
DR eggNOG; KOG1284; Eukaryota.
DR HOGENOM; CLU_020273_1_1_1; -.
DR InParanoid; Q6Z234; -.
DR UniPathway; UPA00275; UER00399.
DR UniPathway; UPA00275; UER00400.
DR Proteomes; UP000000763; Chromosome 8.
DR Proteomes; UP000007752; Chromosome 8.
DR Proteomes; UP000059680; Chromosome 8.
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..73
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN 74..538
FT /note="Probable bifunctional riboflavin biosynthesis
FT protein RIBA 1, chloroplastic"
FT /id="PRO_0000422710"
FT REGION 1..29
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 46..311
FT /note="DHBP synthase"
FT /evidence="ECO:0000250"
FT REGION 312..530
FT /note="GTP cyclohydrolase II"
FT /evidence="ECO:0000250"
FT REGION 506..538
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 440
FT /note="Proton acceptor; for GTP cyclohydrolase activity"
FT /evidence="ECO:0000255"
FT ACT_SITE 442
FT /note="Nucleophile; for GTP cyclohydrolase activity"
FT /evidence="ECO:0000250"
FT BINDING 134..135
FT /ligand="D-ribulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:58121"
FT /evidence="ECO:0000250"
FT BINDING 135
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 135
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 139
FT /ligand="D-ribulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:58121"
FT /evidence="ECO:0000250"
FT BINDING 249..253
FT /ligand="D-ribulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:58121"
FT /evidence="ECO:0000250"
FT BINDING 252
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 273
FT /ligand="D-ribulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:58121"
FT /evidence="ECO:0000250"
FT BINDING 362..366
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000250"
FT BINDING 367
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250"
FT BINDING 378
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250"
FT BINDING 380
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250"
FT BINDING 383
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000250"
FT BINDING 406..408
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000250"
FT BINDING 428
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000250"
FT BINDING 463
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000250"
FT BINDING 468
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000250"
FT SITE 235
FT /note="Essential for DHBP synthase activity"
FT /evidence="ECO:0000250"
FT SITE 273
FT /note="Essential for DHBP synthase activity"
FT /evidence="ECO:0000250"
SQ SEQUENCE 538 AA; 58884 MW; D677674377B11767 CRC64;
MSRLSSIYSQ HRTSGLRSDR SIMPNSTSNS LRTISSVHLP YNHRARNFHI SHAVGDSSEH
VIINGQASPS KVVQADAAAL GTIAADMAPV VDGFSADDDE LDLDSPTEGF SSIPEAIEDI
RQGKYVIVVD DEDRENEGDL IMAASKVTPE AMAFIVRHGT GIVCVSMKED DLERLELPLM
VTTKENEEKL RTAFTVSVDA KEGTTTGVSA KDRANTVLAL ASPNSKPEDF NRPGHIFPLK
YREGGVLKRA GHTEASVDLA MLAGLPPAAV LCEIVDDDDG SMALLPKLQD FARRENLKII
SIADLIRYRR KRDRLVERVC VTPLQLQWGS FQSYCYRSLI DGMEHIAMVK GDVGDGQDIL
VRVHSECLTG DIFGSARCDC GNQLALAMTM IEKTGRGVVV YLRGHEGRGI GLGHKLRAYN
LQDDGRDTVE ANEDLGLPVD SREYGIGAQI LRDLGVRTMR LMTNNPAKYT GLKGYGLSVL
GRVPLLTPIT NENRRYMETK RLKMGHVYGT RPSGNTSTLA DGGIKKEQDQ IDSASEQE
