ID C1DLH7_AZOVD Unreviewed; 359 AA.
AC C1DLH7;
DT 26-MAY-2009, integrated into UniProtKB/TrEMBL.
DT 26-MAY-2009, sequence version 1.
DT 27-MAR-2024, entry version 89.
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 ECO:0000313|EMBL:ACO76925.1};
GN OrderedLocusNames=Avin_06740 {ECO:0000313|EMBL:ACO76925.1};
OS Azotobacter vinelandii (strain DJ / ATCC BAA-1303).
OC Bacteria; Pseudomonadota; Gammaproteobacteria; Pseudomonadales;
OC Pseudomonadaceae; Azotobacter.
OX NCBI_TaxID=322710 {ECO:0000313|EMBL:ACO76925.1, ECO:0000313|Proteomes:UP000002424};
RN [1] {ECO:0000313|EMBL:ACO76925.1, ECO:0000313|Proteomes:UP000002424}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DJ / ATCC BAA-1303 {ECO:0000313|Proteomes:UP000002424};
RX PubMed=19429624; DOI=10.1128/JB.00504-09;
RA Setubal J.C., dos Santos P., Goldman B.S., Ertesvag H., Espin G.,
RA Rubio L.M., Valla S., Almeida N.F., Balasubramanian D., Cromes L.,
RA Curatti L., Du Z., Godsy E., Goodner B., Hellner-Burris K., Hernandez J.A.,
RA Houmiel K., Imperial J., Kennedy C., Larson T.J., Latreille P., Ligon L.S.,
RA Lu J., Maerk M., Miller N.M., Norton S., O'Carroll I.P., Paulsen I.,
RA Raulfs E.C., Roemer R., Rosser J., Segura D., Slater S., Stricklin S.L.,
RA Studholme D.J., Sun J., Viana C.J., Wallin E., Wang B., Wheeler C., Zhu H.,
RA Dean D.R., Dixon R., Wood D.;
RT "Genome sequence of Azotobacter vinelandii, an obligate aerobe specialized
RT to support diverse anaerobic metabolic processes.";
RL J. Bacteriol. 191:4534-4545(2009).
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}.
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DR EMBL; CP001157; ACO76925.1; -; Genomic_DNA.
DR RefSeq; WP_012699350.1; NC_012560.1.
DR AlphaFoldDB; C1DLH7; -.
DR STRING; 322710.Avin_06740; -.
DR EnsemblBacteria; ACO76925; ACO76925; Avin_06740.
DR KEGG; avn:Avin_06740; -.
DR eggNOG; COG0108; Bacteria.
DR eggNOG; COG0807; Bacteria.
DR HOGENOM; CLU_020273_1_2_6; -.
DR OrthoDB; 9793111at2; -.
DR UniPathway; UPA00275; UER00399.
DR Proteomes; UP000002424; Chromosome.
DR GO; GO:0008686; F:3,4-dihydroxy-2-butanone-4-phosphate synthase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0016787; F:hydrolase activity; IEA:UniProtKB-KW.
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 Hydrolase {ECO:0000313|EMBL:ACO76925.1};
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 208..357
FT /note="GTP cyclohydrolase II"
FT /evidence="ECO:0000259|Pfam:PF00925"
FT BINDING 27..28
FT /ligand="D-ribulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:58121"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00180"
FT BINDING 28
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00180"
FT BINDING 28
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00180"
FT BINDING 32
FT /ligand="D-ribulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:58121"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00180"
FT BINDING 140..144
FT /ligand="D-ribulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:58121"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00180"
FT BINDING 143
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00180"
FT SITE 126
FT /note="Essential for catalytic activity"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00180"
FT SITE 164
FT /note="Essential for catalytic activity"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00180"
SQ SEQUENCE 359 AA; 39204 MW; 24B3BB0C15AEE27C CRC64;
MALNSIDELI EDIRQGKMVI LMDDEDRENE GDLIMAAECV QAEHINFMAK YARGLICMPM
TRERCETLKL PLMAPRNGSG FGTKFTVSIE AAEGVTTGIS AADRARTVQV AAAKGAKADD
IVSPGHIFPL MAQSGGVLAR AGHTEAACDL ARMAGFEPSG VICEIMNDDG SMARRPELEL
FAEQHGIKIG TIADLIHYRL IHERTIQRIA EQELDSELGR FHLVTYRDAV EGDVHMALIM
GEIQADEPTL VRVHNMDPLR DLLMVRQPGR WSLRAAMAEV ARAGSGVVLL LGHPLDANEV
LTLLREGTPK SPSTYSTVGA GSQILRDLGV RKMRLMSAPM KFNAISGFDL EVVEYLPAE
//
