ID A0A0S1SSE5_9BACT Unreviewed; 427 AA.
AC A0A0S1SSE5; A0A0S1SG70; A0A0S1SJW0; A0A0S1SNM2; A0A0S1STS9;
DT 17-FEB-2016, integrated into UniProtKB/TrEMBL.
DT 17-FEB-2016, sequence version 1.
DT 27-MAR-2024, entry version 46.
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 ORFNames=PeribacterD1_0150 {ECO:0000313|EMBL:ALM12852.1};
OS Candidatus Peribacter riflensis.
OC Bacteria; Candidatus Peregrinibacteria; Candidatus Peribacteria;
OC Candidatus Peribacterales; Candidatus Peribacteraceae; Peribacter.
OX NCBI_TaxID=1735162 {ECO:0000313|EMBL:ALM12852.1, ECO:0000313|Proteomes:UP000069135};
RN [1] {ECO:0000313|Proteomes:UP000069135}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RA Anantharaman K., Brown C.T., Burstein D., Castelle C.J., Probst A.J.,
RA Thomas B.C., Williams K.H., Banfield J.F.;
RT "Analysis of five complete genome sequences for members of the class
RT Peribacteria in the recently recognized Peregrinibacteria bacterial
RT phylum.";
RL Submitted (OCT-2015) to the EMBL/GenBank/DDBJ databases.
RN [2] {ECO:0000313|EMBL:ALM12852.1, ECO:0000313|Proteomes:UP000069135}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=RIFOXYD1_FULL_PER-ii_59_16 {ECO:0000313|EMBL:ALM12852.1};
RX PubMed=26844018;
RA Anantharaman K., Brown C.T., Burstein D., Castelle C.J., Probst A.J.,
RA Thomas B.C., Williams K.H., Banfield J.F.;
RT "Analysis of five complete genome sequences for members of the class
RT Peribacteria in the recently recognized Peregrinibacteria bacterial
RT phylum.";
RL PeerJ 4:E1607-E1607(2016).
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|ARBA:ARBA00043932, ECO:0000256|HAMAP-
CC 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|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=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}.
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DR EMBL; CP013065; ALM12852.1; -; Genomic_DNA.
DR AlphaFoldDB; A0A0S1SSE5; -.
DR STRING; 1735162.PeribacterB2_0150; -.
DR KEGG; prf:PeribacterA2_0150; -.
DR PATRIC; fig|1735161.3.peg.149; -.
DR UniPathway; UPA00275; UER00399.
DR Proteomes; UP000069135; Chromosome.
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:SF18; 3,4-DIHYDROXY-2-BUTANONE 4-PHOSPHATE SYNTHASE; 1.
DR PANTHER; PTHR21327; GTP CYCLOHYDROLASE II-RELATED; 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|HAMAP-Rule:MF_01283};
KW Magnesium {ECO:0000256|HAMAP-Rule:MF_01283};
KW Manganese {ECO:0000256|HAMAP-Rule:MF_01283};
KW Metal-binding {ECO:0000256|ARBA:ARBA00022723, ECO:0000256|HAMAP-
KW Rule:MF_01283}; Multifunctional enzyme {ECO:0000256|HAMAP-Rule:MF_01283};
KW Nucleotide-binding {ECO:0000256|ARBA:ARBA00022741, ECO:0000256|HAMAP-
KW Rule:MF_01283};
KW Riboflavin biosynthesis {ECO:0000256|ARBA:ARBA00022619, ECO:0000256|HAMAP-
KW Rule:MF_01283}; Zinc {ECO:0000256|HAMAP-Rule:MF_01283}.
FT DOMAIN 236..399
FT /note="GTP cyclohydrolase II"
FT /evidence="ECO:0000259|Pfam:PF00925"
FT REGION 1..226
FT /note="DHBP synthase"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01283"
FT REGION 227..427
FT /note="GTP cyclohydrolase II"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01283"
FT ACT_SITE 355
FT /note="Proton acceptor; for GTP cyclohydrolase activity"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01283"
FT ACT_SITE 357
FT /note="Nucleophile; for GTP cyclohydrolase activity"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01283"
FT BINDING 52..53
FT /ligand="D-ribulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:58121"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01283"
FT BINDING 53
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01283"
FT BINDING 53
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01283"
FT BINDING 57
FT /ligand="D-ribulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:58121"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01283"
FT BINDING 165..169
FT /ligand="D-ribulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:58121"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01283"
FT BINDING 168
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01283"
FT BINDING 189
FT /ligand="D-ribulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:58121"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01283"
FT BINDING 277..281
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01283"
FT BINDING 282
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01283"
FT BINDING 293
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01283"
FT BINDING 295
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01283"
FT BINDING 298
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01283"
FT BINDING 320..322
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01283"
FT BINDING 343
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01283"
FT BINDING 378
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01283"
FT BINDING 383
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01283"
FT SITE 151
FT /note="Essential for DHBP synthase activity"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01283"
FT SITE 189
FT /note="Essential for DHBP synthase activity"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01283"
SQ SEQUENCE 427 AA; 46654 MW; D32AFE816401BC8B CRC64;
MPPFDSAQGK PFDPAFADAT VGRQGTPFAT VPEALEALKA GRMIIVVDDE ARENEGDLVF
AAEHITEETM AFIIRHTGGV VCLSLSNAIA DRLRLPPMVS ENSSKRQTPF TVSIEAVEGV
DTGISAHDRA RTVRAAIDPD ARPSDLARPG HVFPLRAQDG GVLVRAGHTE AAVDLCRLAN
LREAAVLSEL MHDDGTMMRL PSLQEFSAAH GLSILRIADL IAYRRRIETL VRSEARSLLQ
TETGEWTIHV YRDLLQNGEH VALTKGDVSG GAPVLVRVHS ECFTGDTLHS LRCDCGHQLH
TAMQMIQGEG RGILLYLKQE GRGIGLTNKI RAYQIQQEQG LDTVEANEQL GFAPDLREYG
IGAQILRDLG AGNIRLLTNN PRKIVGLEGH GLTVVERIPI ELSQGTPEQH RYLMTKQKKL
GHTIHIA
//
