ID T0HE36_9SPHN Unreviewed; 429 AA.
AC T0HE36;
DT 16-OCT-2013, integrated into UniProtKB/TrEMBL.
DT 16-OCT-2013, sequence version 1.
DT 27-MAR-2024, entry version 47.
DE RecName: Full=3,4-dihydroxy-2-butanone 4-phosphate synthase {ECO:0000256|ARBA:ARBA00018836, ECO:0000256|HAMAP-Rule:MF_00180};
DE Short=DHBP synthase {ECO:0000256|HAMAP-Rule:MF_00180};
DE EC=4.1.99.12 {ECO:0000256|ARBA:ARBA00012153, ECO:0000256|HAMAP-Rule:MF_00180};
GN Name=ribB {ECO:0000256|HAMAP-Rule:MF_00180};
GN ORFNames=RLDS_12910 {ECO:0000313|EMBL:EQB14631.1};
OS Sphingobium lactosutens DS20.
OC Bacteria; Pseudomonadota; Alphaproteobacteria; Sphingomonadales;
OC Sphingomonadaceae; Sphingobium.
OX NCBI_TaxID=1331060 {ECO:0000313|EMBL:EQB14631.1, ECO:0000313|Proteomes:UP000015531};
RN [1] {ECO:0000313|EMBL:EQB14631.1, ECO:0000313|Proteomes:UP000015531}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DS20 {ECO:0000313|EMBL:EQB14631.1,
RC ECO:0000313|Proteomes:UP000015531};
RX PubMed=24051323;
RA Kumar R., Dwivedi V., Negi V., Khurana J.P., Lal R.;
RT "Draft Genome Sequence of Sphingobium lactosutens Strain DS20T, Isolated
RT from a Hexachlorocyclohexane Dumpsite.";
RL Genome Announc. 1:e00753-13(2013).
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_00180}.
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_00180};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000256|HAMAP-Rule:MF_00180};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000256|HAMAP-Rule:MF_00180};
CC Note=Binds 2 divalent metal cations per subunit. Magnesium or
CC manganese. {ECO:0000256|HAMAP-Rule:MF_00180};
CC -!- COFACTOR:
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000256|ARBA:ARBA00001936};
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_00180}.
CC -!- SUBUNIT: Homodimer. {ECO:0000256|HAMAP-Rule:MF_00180}.
CC -!- SIMILARITY: Belongs to the DHBP synthase family. {ECO:0000256|HAMAP-
CC Rule:MF_00180}.
CC -!- SIMILARITY: In the C-terminal section; belongs to the GTP
CC cyclohydrolase II family. {ECO:0000256|ARBA:ARBA00008976}.
CC -!- SIMILARITY: In the N-terminal section; belongs to the DHBP synthase
CC family. {ECO:0000256|ARBA:ARBA00005520}.
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:EQB14631.1}.
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DR EMBL; ATDP01000090; EQB14631.1; -; Genomic_DNA.
DR RefSeq; WP_021226250.1; NZ_ATDP01000090.1.
DR AlphaFoldDB; T0HE36; -.
DR PATRIC; fig|1331060.3.peg.2452; -.
DR eggNOG; COG0108; Bacteria.
DR eggNOG; COG0807; Bacteria.
DR OrthoDB; 9793111at2; -.
DR UniPathway; UPA00275; UER00399.
DR Proteomes; UP000015531; Unassembled WGS sequence.
DR GO; GO:0008686; F:3,4-dihydroxy-2-butanone-4-phosphate synthase 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:0009231; P:riboflavin biosynthetic process; IEA:UniProtKB-UniRule.
DR Gene3D; 3.90.870.10; DHBP synthase; 1.
DR Gene3D; 3.40.50.10990; GTP cyclohydrolase II; 1.
DR HAMAP; MF_00180; RibB; 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; IPR036144; RibA-like_sf.
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 Lyase {ECO:0000256|HAMAP-Rule:MF_00180};
KW Magnesium {ECO:0000256|HAMAP-Rule:MF_00180};
KW Manganese {ECO:0000256|HAMAP-Rule:MF_00180};
KW Metal-binding {ECO:0000256|ARBA:ARBA00022723, ECO:0000256|HAMAP-
KW Rule:MF_00180};
KW Riboflavin biosynthesis {ECO:0000256|ARBA:ARBA00022619, ECO:0000256|HAMAP-
KW Rule:MF_00180}.
FT DOMAIN 270..426
FT /note="GTP cyclohydrolase II"
FT /evidence="ECO:0000259|Pfam:PF00925"
FT BINDING 89..90
FT /ligand="D-ribulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:58121"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00180"
FT BINDING 90
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00180"
FT BINDING 90
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00180"
FT BINDING 94
FT /ligand="D-ribulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:58121"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00180"
FT BINDING 202..206
FT /ligand="D-ribulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:58121"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00180"
FT BINDING 205
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00180"
FT SITE 188
FT /note="Essential for catalytic activity"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00180"
FT SITE 226
FT /note="Essential for catalytic activity"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00180"
SQ SEQUENCE 429 AA; 46475 MW; 499C8A3162B01402 CRC64;
MSSALLDTVR NLVNEGGMSR SGLARAAGLH ANSLRKLGEA DWNPTAETLG KLEAYLLKRE
GGTALASPEE IINEARNGRM FILVDDEDRE NEGDLVIPAQ MATPDAINFM ATHGRGLICL
AMTRDRVDHL GLELMSRNNG TRHETAFTVS IEAREGVTTG ISAADRARTI SVAIDGSKGR
ADIVTPGHVF PLVAKDGGVL VRTGHTEAAV DVARLAGLNP SGVICEVMKD DGTMARLDDL
IPFARKHRMK IGTIRDLIAY RRRHDHMVER RAETSFTSKW GGEWKAISFY NRATRTEQMV
LQKGHVVPDQ PTLVRMHQLS LMDDIYGAQG KRSDLLARSM EMIGREGAGL IVLLAGSDAG
DFLSTSIARY AAKGAATGDM DELRDYGVGA QLLAELGVHD MILLTNSQHS LVALDGYDLA
VVGQRPITV
//
