ID A0A108T1Y2_BACSE Unreviewed; 404 AA.
AC A0A108T1Y2;
DT 13-APR-2016, integrated into UniProtKB/TrEMBL.
DT 13-APR-2016, sequence version 1.
DT 27-MAR-2024, entry version 49.
DE RecName: Full=Riboflavin biosynthesis protein RibBA {ECO:0000256|HAMAP-Rule:MF_01283};
DE Includes:
DE RecName: Full=3,4-dihydroxy-2-butanone 4-phosphate synthase {ECO:0000256|HAMAP-Rule:MF_01283};
DE Short=DHBP synthase {ECO:0000256|HAMAP-Rule:MF_01283};
DE EC=4.1.99.12 {ECO:0000256|HAMAP-Rule:MF_01283};
DE Includes:
DE RecName: Full=GTP cyclohydrolase-2 {ECO:0000256|HAMAP-Rule:MF_01283};
DE EC=3.5.4.25 {ECO:0000256|HAMAP-Rule:MF_01283};
DE AltName: Full=GTP cyclohydrolase II {ECO:0000256|HAMAP-Rule:MF_01283};
GN Name=ribBA {ECO:0000256|HAMAP-Rule:MF_01283,
GN ECO:0000313|EMBL:KWR51788.1};
GN ORFNames=AA415_03164 {ECO:0000313|EMBL:KWR51788.1}, DW668_07515
GN {ECO:0000313|EMBL:RHF76107.1}, DW853_18590
GN {ECO:0000313|EMBL:RHC22532.1}, DW889_12110
GN {ECO:0000313|EMBL:RHB27286.1}, DWV41_16060
GN {ECO:0000313|EMBL:RGW92851.1}, DWV77_12740
GN {ECO:0000313|EMBL:RGW32771.1}, DWY58_18230
GN {ECO:0000313|EMBL:RGR25325.1}, DWY65_15990
GN {ECO:0000313|EMBL:RGR07674.1}, DWZ78_16905
GN {ECO:0000313|EMBL:RHM15269.1}, DXC34_17815
GN {ECO:0000313|EMBL:RGM09267.1}, F9958_17145
GN {ECO:0000313|EMBL:KAB5308501.1};
OS Bacteroides stercoris.
OC Bacteria; Bacteroidota; Bacteroidia; Bacteroidales; Bacteroidaceae;
OC Bacteroides.
OX NCBI_TaxID=46506 {ECO:0000313|EMBL:KWR51788.1, ECO:0000313|Proteomes:UP000056419};
RN [1] {ECO:0000313|EMBL:KWR51788.1, ECO:0000313|Proteomes:UP000056419}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=CL09T03C01 {ECO:0000313|EMBL:KWR51788.1,
RC ECO:0000313|Proteomes:UP000056419};
RX PubMed=26768901; DOI=10.1186/s12864-016-2377-z;
RA Coyne M.J., Roelofs K.G., Comstock L.E.;
RT "Type VI secretion systems of human gut Bacteroidales segregate into three
RT genetic architectures, two of which are contained on mobile genetic
RT elements.";
RL BMC Genomics 17:58-58(2016).
RN [2] {ECO:0000313|EMBL:KWR51788.1}
RP NUCLEOTIDE SEQUENCE.
RC STRAIN=CL09T03C01 {ECO:0000313|EMBL:KWR51788.1};
RA McClelland M., Jain A., Saraogi P., Mendelson R., Westerman R.,
RA SanMiguel P., Csonka L.;
RL Submitted (JAN-2016) to the EMBL/GenBank/DDBJ databases.
RN [3] {ECO:0000313|Proteomes:UP000261223, ECO:0000313|Proteomes:UP000283310}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=AF05-4 {ECO:0000313|EMBL:RGW92851.1,
RC ECO:0000313|Proteomes:UP000284777}, AF12-7
RC {ECO:0000313|EMBL:RGW32771.1, ECO:0000313|Proteomes:UP000285150},
RC AF25-6 {ECO:0000313|EMBL:RGR25325.1,
RC ECO:0000313|Proteomes:UP000284161}, AF26-20BH
RC {ECO:0000313|EMBL:RGR07674.1, ECO:0000313|Proteomes:UP000283310},
RC AF35-20 {ECO:0000313|EMBL:RHM15269.1,
RC ECO:0000313|Proteomes:UP000284604}, AM25-16
RC {ECO:0000313|EMBL:RHF76107.1, ECO:0000313|Proteomes:UP000283762},
RC AM36-9BH {ECO:0000313|EMBL:RHC22532.1,
RC ECO:0000313|Proteomes:UP000285305}, AM40-34
RC {ECO:0000313|EMBL:RHB27286.1, ECO:0000313|Proteomes:UP000283482}, and
RC TF03-6 {ECO:0000313|EMBL:RGM09267.1,
RC ECO:0000313|Proteomes:UP000261223};
RA Zou Y., Xue W., Luo G.;
RT "A genome reference for cultivated species of the human gut microbiota.";
RL Submitted (AUG-2018) to the EMBL/GenBank/DDBJ databases.
RN [4] {ECO:0000313|EMBL:KAB5308501.1, ECO:0000313|Proteomes:UP000467334}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=BIOML-A6 {ECO:0000313|EMBL:KAB5308501.1,
RC ECO:0000313|Proteomes:UP000467334};
RX PubMed=31477907; DOI=.1038/s41591-019-0559-3;
RA Poyet M., Groussin M., Gibbons S.M., Avila-Pacheco J., Jiang X.,
RA Kearney S.M., Perrotta A.R., Berdy B., Zhao S., Lieberman T.D.,
RA Swanson P.K., Smith M., Roesemann S., Alexander J.E., Rich S.A., Livny J.,
RA Vlamakis H., Clish C., Bullock K., Deik A., Scott J., Pierce K.A.,
RA Xavier R.J., Alm E.J.;
RT "A library of human gut bacterial isolates paired with longitudinal
RT multiomics data enables mechanistic microbiome research.";
RL Nat. Med. 25:1442-1452(2019).
CC -!- FUNCTION: Catalyzes the conversion of D-ribulose 5-phosphate to formate
CC and 3,4-dihydroxy-2-butanone 4-phosphate.
CC {ECO:0000256|ARBA:ARBA00002284, ECO:0000256|HAMAP-Rule:MF_01283}.
CC -!- FUNCTION: Catalyzes the conversion of GTP to 2,5-diamino-6-
CC ribosylamino-4(3H)-pyrimidinone 5'-phosphate (DARP), formate and
CC pyrophosphate. {ECO:0000256|HAMAP-Rule:MF_01283}.
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:0000256|ARBA:ARBA00000141,
CC ECO:0000256|HAMAP-Rule:MF_01283};
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:0000256|ARBA:ARBA00029293, ECO:0000256|HAMAP-
CC Rule:MF_01283};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000256|HAMAP-Rule:MF_01283};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000256|HAMAP-Rule:MF_01283};
CC Note=Binds 2 divalent metal cations per subunit. Magnesium or
CC manganese. {ECO:0000256|HAMAP-Rule:MF_01283};
CC -!- COFACTOR:
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000256|ARBA:ARBA00001936};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000256|HAMAP-Rule:MF_01283};
CC Note=Binds 1 zinc ion per subunit. {ECO:0000256|HAMAP-Rule:MF_01283};
CC -!- PATHWAY: Cofactor biosynthesis; riboflavin biosynthesis; 2-hydroxy-3-
CC oxobutyl phosphate from D-ribulose 5-phosphate: step 1/1.
CC {ECO:0000256|ARBA:ARBA00004904, ECO:0000256|HAMAP-Rule:MF_01283}.
CC -!- PATHWAY: Cofactor biosynthesis; riboflavin biosynthesis; 5-amino-6-(D-
CC ribitylamino)uracil from GTP: step 1/4. {ECO:0000256|ARBA:ARBA00004853,
CC ECO:0000256|HAMAP-Rule:MF_01283}.
CC -!- SIMILARITY: In the C-terminal section; belongs to the GTP
CC cyclohydrolase II family. {ECO:0000256|HAMAP-Rule:MF_01283}.
CC -!- SIMILARITY: In the N-terminal section; belongs to the DHBP synthase
CC family. {ECO:0000256|ARBA:ARBA00005520, ECO:0000256|HAMAP-
CC Rule:MF_01283}.
CC -!- CAUTION: The sequence shown here is derived from an EMBL/GenBank/DDBJ
CC whole genome shotgun (WGS) entry which is preliminary data.
CC {ECO:0000313|EMBL:KWR51788.1}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; WCLE01000064; KAB5308501.1; -; Genomic_DNA.
DR EMBL; LRGC01000029; KWR51788.1; -; Genomic_DNA.
DR EMBL; QSSV01000037; RGM09267.1; -; Genomic_DNA.
DR EMBL; QRTW01000054; RGR07674.1; -; Genomic_DNA.
DR EMBL; QRUB01000039; RGR25325.1; -; Genomic_DNA.
DR EMBL; QSAF01000016; RGW32771.1; -; Genomic_DNA.
DR EMBL; QSBD01000044; RGW92851.1; -; Genomic_DNA.
DR EMBL; QSGN01000031; RHB27286.1; -; Genomic_DNA.
DR EMBL; QSHQ01000086; RHC22532.1; -; Genomic_DNA.
DR EMBL; QRHJ01000016; RHF76107.1; -; Genomic_DNA.
DR EMBL; QRPN01000038; RHM15269.1; -; Genomic_DNA.
DR RefSeq; WP_005652360.1; NZ_WCLN01000066.1.
DR AlphaFoldDB; A0A108T1Y2; -.
DR STRING; 46506.AA415_03164; -.
DR GeneID; 31795978; -.
DR PATRIC; fig|46506.5.peg.3405; -.
DR UniPathway; UPA00275; UER00399.
DR Proteomes; UP000056419; Unassembled WGS sequence.
DR Proteomes; UP000261223; Unassembled WGS sequence.
DR Proteomes; UP000283310; Unassembled WGS sequence.
DR Proteomes; UP000283482; Unassembled WGS sequence.
DR Proteomes; UP000283762; Unassembled WGS sequence.
DR Proteomes; UP000284161; Unassembled WGS sequence.
DR Proteomes; UP000284604; Unassembled WGS sequence.
DR Proteomes; UP000284777; Unassembled WGS sequence.
DR Proteomes; UP000285150; Unassembled WGS sequence.
DR Proteomes; UP000285305; Unassembled WGS sequence.
DR Proteomes; UP000467334; Unassembled WGS sequence.
DR GO; GO:0008686; F:3,4-dihydroxy-2-butanone-4-phosphate synthase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0005525; F:GTP binding; IEA:UniProtKB-KW.
DR GO; GO:0003935; F:GTP cyclohydrolase II activity; IEA:UniProtKB-UniRule.
DR GO; GO:0000287; F:magnesium ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0030145; F:manganese ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0008270; F:zinc ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0009231; P:riboflavin biosynthetic process; IEA:UniProtKB-UniRule.
DR CDD; cd00641; GTP_cyclohydro2; 1.
DR Gene3D; 3.90.870.10; DHBP synthase; 1.
DR Gene3D; 3.40.50.10990; GTP cyclohydrolase II; 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 NCBIfam; TIGR00505; ribA; 1.
DR NCBIfam; TIGR00506; ribB; 1.
DR PANTHER; PTHR21327; GTP CYCLOHYDROLASE II-RELATED; 1.
DR PANTHER; PTHR21327:SF48; RIBOFLAVIN BIOSYNTHESIS PROTEIN RIBBA; 1.
DR Pfam; PF00926; DHBP_synthase; 1.
DR Pfam; PF00925; GTP_cyclohydro2; 1.
DR PIRSF; PIRSF001259; RibA; 1.
DR SUPFAM; SSF142695; RibA-like; 1.
DR SUPFAM; SSF55821; YrdC/RibB; 1.
PE 3: Inferred from homology;
KW GTP-binding {ECO:0000256|ARBA:ARBA00023134, ECO:0000256|HAMAP-
KW Rule:MF_01283};
KW Hydrolase {ECO:0000256|ARBA:ARBA00022801, ECO:0000256|HAMAP-Rule:MF_01283};
KW Lyase {ECO:0000256|ARBA:ARBA00023239, ECO:0000256|HAMAP-Rule:MF_01283};
KW Magnesium {ECO:0000256|ARBA:ARBA00022842, ECO:0000256|HAMAP-Rule:MF_01283};
KW Manganese {ECO:0000256|ARBA:ARBA00023211, ECO:0000256|HAMAP-Rule:MF_01283};
KW Metal-binding {ECO:0000256|ARBA:ARBA00022723, ECO:0000256|HAMAP-
KW Rule:MF_01283};
KW Multifunctional enzyme {ECO:0000256|ARBA:ARBA00023268, ECO:0000256|HAMAP-
KW Rule:MF_01283};
KW Nucleotide-binding {ECO:0000256|ARBA:ARBA00022741, ECO:0000256|HAMAP-
KW Rule:MF_01283}; Reference proteome {ECO:0000313|Proteomes:UP000056419};
KW Riboflavin biosynthesis {ECO:0000256|ARBA:ARBA00022619, ECO:0000256|HAMAP-
KW Rule:MF_01283}; Zinc {ECO:0000256|HAMAP-Rule:MF_01283}.
FT DOMAIN 212..376
FT /note="GTP cyclohydrolase II"
FT /evidence="ECO:0000259|Pfam:PF00925"
FT REGION 1..204
FT /note="DHBP synthase"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01283"
FT REGION 205..404
FT /note="GTP cyclohydrolase II"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01283"
FT ACT_SITE 332
FT /note="Proton acceptor; for GTP cyclohydrolase activity"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01283"
FT ACT_SITE 334
FT /note="Nucleophile; for GTP cyclohydrolase activity"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01283"
FT BINDING 30..31
FT /ligand="D-ribulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:58121"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01283"
FT BINDING 31
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01283"
FT BINDING 31
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01283"
FT BINDING 35
FT /ligand="D-ribulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:58121"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01283"
FT BINDING 143..147
FT /ligand="D-ribulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:58121"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01283"
FT BINDING 146
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01283"
FT BINDING 167
FT /ligand="D-ribulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:58121"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01283"
FT BINDING 255..259
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01283"
FT BINDING 260
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01283"
FT BINDING 271
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01283"
FT BINDING 273
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01283"
FT BINDING 276
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01283"
FT BINDING 298..300
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01283"
FT BINDING 320
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01283"
FT BINDING 355
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01283"
FT BINDING 360
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01283"
FT SITE 129
FT /note="Essential for DHBP synthase activity"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01283"
FT SITE 167
FT /note="Essential for DHBP synthase activity"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01283"
SQ SEQUENCE 404 AA; 44949 MW; 8A183EA924910602 CRC64;
MEKVKLNTIE EAIEDFKAGN FVIVVDDEDR ENEGDLIIAA EKITSEKVNF MLKHARGVLC
APITVSRCKE LDLPHQVTDN TSVLGTPFTV TVDKLEGCTT GVSAADRAAT IQALADPLST
PATFGRPGHI NPLYAQEKGV LRRAGHTEAT IDMCRLSGFY PAGALMEIMN EDGTMARLPE
LRKMADEFNL KLISIRDMIA YRLQQESIVE KGVEVDMPTE HGHFRLIPFR QKSNGLEHVA
LFKGTWAPDE PVLVRVHSSC ATGDIFGSMR CDCGEQLHKA MEVIEKAGKG VIVYLNQEGR
GIGLMEKMRA YKLQEDGMDT VDANICLGHL ADERDYGVGA QILRELGVHK MRLLTNNPVK
RVGLEAYGLE IVENVPVETT PNQYNERYLR TKKERMGHTL HFSK
//
