ID M7P1Z9_9GAMM Unreviewed; 392 AA.
AC M7P1Z9;
DT 29-MAY-2013, integrated into UniProtKB/TrEMBL.
DT 29-MAY-2013, sequence version 1.
DT 27-MAR-2024, entry version 53.
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=MPL1_04617 {ECO:0000313|EMBL:EMR13497.1};
OS Methylophaga lonarensis MPL.
OC Bacteria; Pseudomonadota; Gammaproteobacteria; Thiotrichales;
OC Piscirickettsiaceae; Methylophaga.
OX NCBI_TaxID=1286106 {ECO:0000313|EMBL:EMR13497.1, ECO:0000313|Proteomes:UP000012019};
RN [1] {ECO:0000313|EMBL:EMR13497.1, ECO:0000313|Proteomes:UP000012019}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=MPL {ECO:0000313|EMBL:EMR13497.1,
RC ECO:0000313|Proteomes:UP000012019};
RX PubMed=23661481;
RA Shetty S.A., Marathe N.P., Munot H., Antony C.P., Dhotre D.P.,
RA Murrell J.C., Shouche Y.S.;
RT "Draft Genome Sequence of Methylophaga lonarensis MPLT, a Haloalkaliphilic
RT (Non-Methane-Utilizing) Methylotroph.";
RL Genome Announc. 1:E00202-13(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:EMR13497.1}.
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DR EMBL; APHR01000021; EMR13497.1; -; Genomic_DNA.
DR RefSeq; WP_009725941.1; NZ_APHR01000021.1.
DR AlphaFoldDB; M7P1Z9; -.
DR STRING; 1286106.MPL1_04617; -.
DR PATRIC; fig|1286106.3.peg.927; -.
DR eggNOG; COG0108; Bacteria.
DR OrthoDB; 9793111at2; -.
DR UniPathway; UPA00275; UER00399.
DR Proteomes; UP000012019; 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}; Reference proteome {ECO:0000313|Proteomes:UP000012019};
KW Riboflavin biosynthesis {ECO:0000256|ARBA:ARBA00022619, ECO:0000256|HAMAP-
KW Rule:MF_00180}.
FT DOMAIN 225..373
FT /note="GTP cyclohydrolase II"
FT /evidence="ECO:0000259|Pfam:PF00925"
FT BINDING 42..43
FT /ligand="D-ribulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:58121"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00180"
FT BINDING 43
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00180"
FT BINDING 43
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00180"
FT BINDING 47
FT /ligand="D-ribulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:58121"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00180"
FT BINDING 155..159
FT /ligand="D-ribulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:58121"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00180"
FT BINDING 158
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00180"
FT SITE 141
FT /note="Essential for catalytic activity"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00180"
FT SITE 179
FT /note="Essential for catalytic activity"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00180"
SQ SEQUENCE 392 AA; 42744 MW; 0427FBEADB90989C CRC64;
MNSPNHSLHL PHSSHPDIAP VTEILAAIAA GEMVILIDDE DRENEGDIVI AADAVTAEHI
NFMARYARGL ICLTLTEQRC KQLDLPLMVK HNRAQLTTNF TVSIEAAKGV TTGISTADRA
HTVRVAVADN ARATDIVRPG HIFPLMAQPG GVLARAGHTE AGCDVSRMAG RAPAAVICEI
MNDDGSMARL PDLVDFARQH GLKIGTIADL IQYRHQTETL IVRESSRPIA TAFGTFELTG
FRDITTDKIH LALSYGDPAQ QSSCLVRVHE PISLIELLDT EAHSHSWSVH DALQTIANEG
AGVMILLRRD EAEADILRQL SQPDALLTAS YELKDYGIGA QILRELGVKR MRLMTHPRKI
PSMTGFGLSV DSYLLPQVHQ SEEQHNLAAL LV
//
