ID Q13UE0_PARXL Unreviewed; 244 AA.
AC Q13UE0;
DT 22-AUG-2006, integrated into UniProtKB/TrEMBL.
DT 22-AUG-2006, sequence version 1.
DT 27-MAR-2024, entry version 116.
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, ECO:0000256|RuleBase:RU003843};
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=Bxe_A0635 {ECO:0000313|EMBL:ABE32299.1};
OS Paraburkholderia xenovorans (strain LB400).
OC Bacteria; Pseudomonadota; Betaproteobacteria; Burkholderiales;
OC Burkholderiaceae; Paraburkholderia.
OX NCBI_TaxID=266265 {ECO:0000313|EMBL:ABE32299.1, ECO:0000313|Proteomes:UP000001817};
RN [1] {ECO:0000313|EMBL:ABE32299.1, ECO:0000313|Proteomes:UP000001817}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=LB400 {ECO:0000313|EMBL:ABE32299.1,
RC ECO:0000313|Proteomes:UP000001817};
RX PubMed=17030797; DOI=10.1073/pnas.0606924103;
RA Chain P.S., Denef V.J., Konstantinidis K.T., Vergez L.M., Agullo L.,
RA Reyes V.L., Hauser L., Cordova M., Gomez L., Gonzalez M., Land M., Lao V.,
RA Larimer F., LiPuma J.J., Mahenthiralingam E., Malfatti S.A., Marx C.J.,
RA Parnell J.J., Ramette A., Richardson P., Seeger M., Smith D., Spilker T.,
RA Sul W.J., Tsoi T.V., Ulrich L.E., Zhulin I.B., Tiedje J.M.;
RT "Burkholderia xenovorans LB400 harbors a multi-replicon, 9.73-Mbp genome
RT shaped for versatility.";
RL Proc. Natl. Acad. Sci. U.S.A. 103:15280-15287(2006).
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 ECO:0000256|RuleBase:RU003843}.
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_00180,
CC ECO:0000256|RuleBase:RU003843};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000256|HAMAP-Rule:MF_00180,
CC ECO:0000256|RuleBase:RU003843};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000256|HAMAP-Rule:MF_00180,
CC ECO:0000256|RuleBase:RU003843};
CC Note=Binds 2 divalent metal cations per subunit. Magnesium or
CC manganese. {ECO:0000256|HAMAP-Rule:MF_00180,
CC ECO:0000256|RuleBase:RU003843};
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 ECO:0000256|RuleBase:RU003843}.
CC -!- SUBUNIT: Homodimer. {ECO:0000256|HAMAP-Rule:MF_00180,
CC ECO:0000256|RuleBase:RU003843}.
CC -!- SIMILARITY: Belongs to the DHBP synthase family. {ECO:0000256|HAMAP-
CC Rule:MF_00180, ECO:0000256|RuleBase:RU003843}.
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DR EMBL; CP000270; ABE32299.1; -; Genomic_DNA.
DR AlphaFoldDB; Q13UE0; -.
DR STRING; 266265.Bxe_A0635; -.
DR KEGG; bxe:Bxe_A0635; -.
DR eggNOG; COG0108; Bacteria.
DR UniPathway; UPA00275; UER00399.
DR Proteomes; UP000001817; Chromosome 1.
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 HAMAP; MF_00180; RibB; 1.
DR InterPro; IPR017945; DHBP_synth_RibB-like_a/b_dom.
DR InterPro; IPR000422; DHBP_synthase_RibB.
DR NCBIfam; TIGR00506; ribB; 1.
DR PANTHER; PTHR21327:SF38; 3,4-DIHYDROXY-2-BUTANONE 4-PHOSPHATE SYNTHASE; 1.
DR PANTHER; PTHR21327; GTP CYCLOHYDROLASE II-RELATED; 1.
DR Pfam; PF00926; DHBP_synthase; 1.
DR SUPFAM; SSF55821; YrdC/RibB; 1.
PE 3: Inferred from homology;
KW Lyase {ECO:0000256|ARBA:ARBA00023239, ECO:0000256|HAMAP-Rule:MF_00180};
KW Magnesium {ECO:0000256|HAMAP-Rule:MF_00180, ECO:0000256|RuleBase:RU003843};
KW Manganese {ECO:0000256|ARBA:ARBA00023211, 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 BINDING 58..59
FT /ligand="D-ribulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:58121"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00180"
FT BINDING 59
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00180"
FT BINDING 59
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00180"
FT BINDING 63
FT /ligand="D-ribulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:58121"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00180"
FT BINDING 171..175
FT /ligand="D-ribulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:58121"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00180"
FT BINDING 174
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00180"
FT SITE 157
FT /note="Essential for catalytic activity"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00180"
FT SITE 195
FT /note="Essential for catalytic activity"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00180"
SQ SEQUENCE 244 AA; 25971 MW; 137329B6A78E9389 CRC64;
MSVSTMSFAT FPAPSTIADS AFLDLPLLDA DAVPPRIAAA LQAMREGRAV VLQDDHDREN
EADLIVSAER LSVETMALLI RECSGIVCLC LPDEKIRALE LPPMAVNNES RHGTAFTVSI
EAREGVTTGV SALDRVTTIR AAIADTAKPA DIVRPGHVFP LRAQPGGVLA RRGHTEGTVD
LAILAGLKPA GVLCELMNPD GTMTRGADVE RFAAQHNLPM LTIAELVEFR QALAQARECV
ADEA
//
