BLUB_RHIME
ID BLUB_RHIME Reviewed; 227 AA.
AC Q92PC8;
DT 16-OCT-2013, integrated into UniProtKB/Swiss-Prot.
DT 01-DEC-2001, sequence version 1.
DT 03-AUG-2022, entry version 104.
DE RecName: Full=5,6-dimethylbenzimidazole synthase;
DE Short=DMB synthase;
DE EC=1.13.11.79;
GN Name=bluB; OrderedLocusNames=R01841; ORFNames=SMc00166;
OS Rhizobium meliloti (strain 1021) (Ensifer meliloti) (Sinorhizobium
OS meliloti).
OC Bacteria; Proteobacteria; Alphaproteobacteria; Hyphomicrobiales;
OC Rhizobiaceae; Sinorhizobium/Ensifer group; Sinorhizobium.
OX NCBI_TaxID=266834;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=1021;
RX PubMed=11481430; DOI=10.1073/pnas.161294398;
RA Capela D., Barloy-Hubler F., Gouzy J., Bothe G., Ampe F., Batut J.,
RA Boistard P., Becker A., Boutry M., Cadieu E., Dreano S., Gloux S.,
RA Godrie T., Goffeau A., Kahn D., Kiss E., Lelaure V., Masuy D., Pohl T.,
RA Portetelle D., Puehler A., Purnelle B., Ramsperger U., Renard C.,
RA Thebault P., Vandenbol M., Weidner S., Galibert F.;
RT "Analysis of the chromosome sequence of the legume symbiont Sinorhizobium
RT meliloti strain 1021.";
RL Proc. Natl. Acad. Sci. U.S.A. 98:9877-9882(2001).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=1021;
RX PubMed=11474104; DOI=10.1126/science.1060966;
RA Galibert F., Finan T.M., Long S.R., Puehler A., Abola P., Ampe F.,
RA Barloy-Hubler F., Barnett M.J., Becker A., Boistard P., Bothe G.,
RA Boutry M., Bowser L., Buhrmester J., Cadieu E., Capela D., Chain P.,
RA Cowie A., Davis R.W., Dreano S., Federspiel N.A., Fisher R.F., Gloux S.,
RA Godrie T., Goffeau A., Golding B., Gouzy J., Gurjal M., Hernandez-Lucas I.,
RA Hong A., Huizar L., Hyman R.W., Jones T., Kahn D., Kahn M.L., Kalman S.,
RA Keating D.H., Kiss E., Komp C., Lelaure V., Masuy D., Palm C., Peck M.C.,
RA Pohl T.M., Portetelle D., Purnelle B., Ramsperger U., Surzycki R.,
RA Thebault P., Vandenbol M., Vorhoelter F.J., Weidner S., Wells D.H.,
RA Wong K., Yeh K.-C., Batut J.;
RT "The composite genome of the legume symbiont Sinorhizobium meliloti.";
RL Science 293:668-672(2001).
RN [3]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=16537439; DOI=10.1073/pnas.0509384103;
RA Campbell G.R., Taga M.E., Mistry K., Lloret J., Anderson P.J., Roth J.R.,
RA Walker G.C.;
RT "Sinorhizobium meliloti bluB is necessary for production of 5,6-
RT dimethylbenzimidazole, the lower ligand of B12.";
RL Proc. Natl. Acad. Sci. U.S.A. 103:4634-4639(2006).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (2.10 ANGSTROMS) IN COMPLEX WITH FMNH(2) AND
RP DIOXYGEN, FUNCTION, CATALYTIC ACTIVITY, MUTAGENESIS OF ASP-32 AND SER-167,
RP BIOPHYSICOCHEMICAL PROPERTIES, ACTIVITY REGULATION, REACTION MECHANISM, AND
RP SUBUNIT.
RX PubMed=17377583; DOI=10.1038/nature05611;
RA Taga M.E., Larsen N.A., Howard-Jones A.R., Walsh C.T., Walker G.C.;
RT "BluB cannibalizes flavin to form the lower ligand of vitamin B12.";
RL Nature 446:449-453(2007).
CC -!- FUNCTION: Involved in the biosynthesis of cobalamin (vitamin B12).
CC Catalyzes the oxidative fragmentation and contraction of the
CC isoalloxazine heterocycle and the cleavage of the ribityl tail of
CC FMN(2) to form 5,6-dimethylbenzimidazole (DMB) and D-erythrose 4-
CC phosphate (E4P). NAD(P)H is only required initially to reduce FMN and
CC oxygen drives the oxidative fragmentation.
CC {ECO:0000269|PubMed:16537439, ECO:0000269|PubMed:17377583}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=FMNH2 + O2 = 5,6-dimethylbenzimidazole + D-erythrose 4-
CC phosphate + dialurate + H(+); Xref=Rhea:RHEA:27345,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:15379, ChEBI:CHEBI:15890,
CC ChEBI:CHEBI:16897, ChEBI:CHEBI:57618, ChEBI:CHEBI:140629;
CC EC=1.13.11.79; Evidence={ECO:0000269|PubMed:17377583};
CC -!- ACTIVITY REGULATION: Inhibited by high concentrations of FMN.
CC {ECO:0000269|PubMed:17377583}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=64 uM for FMN {ECO:0000269|PubMed:17377583};
CC KM=4.4 mM for NADP {ECO:0000269|PubMed:17377583};
CC KM=5.1 mM for NAD {ECO:0000269|PubMed:17377583};
CC Note=kcat is 15 h(-1), 7.2 h(-1) and 7.6 h(-1) for FMN, NAD and NADP,
CC respectively.;
CC -!- SUBUNIT: Homooctamer. {ECO:0000269|PubMed:17377583}.
CC -!- DISRUPTION PHENOTYPE: Cells lacking this gene are unable to grow in
CC minimal media and fails to establish a symbiosis with alfalfa, and
CC these defects can be rescued by the addition of vitamin B12
CC (cyanocobalamin) or the lower ligand of cobalamin, 5,6-
CC dimethylbenzimidazole (DMB). {ECO:0000269|PubMed:16537439}.
CC -!- SIMILARITY: Belongs to the BluB family. {ECO:0000305}.
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DR EMBL; AL591688; CAC46420.1; -; Genomic_DNA.
DR RefSeq; NP_385947.1; NC_003047.1.
DR RefSeq; WP_010969508.1; NC_003047.1.
DR PDB; 2ISJ; X-ray; 2.30 A; A/B/C/D/E/F/G/H=1-227.
DR PDB; 2ISK; X-ray; 2.10 A; A/B/C/D/E/F/G/H=1-227.
DR PDB; 2ISL; X-ray; 2.90 A; A/B/C/D/E/F/G/H=1-227.
DR PDBsum; 2ISJ; -.
DR PDBsum; 2ISK; -.
DR PDBsum; 2ISL; -.
DR AlphaFoldDB; Q92PC8; -.
DR SMR; Q92PC8; -.
DR DIP; DIP-60275N; -.
DR STRING; 266834.SMc00166; -.
DR EnsemblBacteria; CAC46420; CAC46420; SMc00166.
DR GeneID; 61603312; -.
DR KEGG; sme:SMc00166; -.
DR PATRIC; fig|266834.11.peg.3284; -.
DR eggNOG; COG0778; Bacteria.
DR HOGENOM; CLU_070764_3_1_5; -.
DR OMA; FMQPWDF; -.
DR BioCyc; MetaCyc:MON-13177; -.
DR BRENDA; 1.14.99.40; 5347.
DR EvolutionaryTrace; Q92PC8; -.
DR Proteomes; UP000001976; Chromosome.
DR GO; GO:0102919; F:5,6-dimethylbenzimidazole synthase activity; IEA:UniProtKB-EC.
DR GO; GO:0000166; F:nucleotide binding; IEA:UniProtKB-KW.
DR GO; GO:0016705; F:oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen; IDA:UniProtKB.
DR GO; GO:0009236; P:cobalamin biosynthetic process; IDA:UniProtKB.
DR CDD; cd02145; BluB; 1.
DR Gene3D; 3.40.109.10; -; 1.
DR InterPro; IPR012825; BluB.
DR InterPro; IPR029479; Nitroreductase.
DR InterPro; IPR000415; Nitroreductase-like.
DR Pfam; PF00881; Nitroreductase; 1.
DR SUPFAM; SSF55469; SSF55469; 1.
DR TIGRFAMs; TIGR02476; BluB; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cobalamin biosynthesis; Flavoprotein; FMN; NAD; NADP;
KW Nucleotide-binding; Oxidoreductase; Reference proteome.
FT CHAIN 1..227
FT /note="5,6-dimethylbenzimidazole synthase"
FT /id="PRO_0000424085"
FT BINDING 30..34
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT BINDING 59
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT BINDING 108
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT BINDING 167
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT MUTAGEN 32
FT /note="D->A,N,S: Abrogates DMB formation but retains flavin
FT binding."
FT /evidence="ECO:0000269|PubMed:17377583"
FT MUTAGEN 167
FT /note="S->C: Completely abolishes DMB formation."
FT /evidence="ECO:0000269|PubMed:17377583"
FT MUTAGEN 167
FT /note="S->G: Reduces DMB formation by 30-fold."
FT /evidence="ECO:0000269|PubMed:17377583"
FT HELIX 17..29
FT /evidence="ECO:0007829|PDB:2ISK"
FT HELIX 44..55
FT /evidence="ECO:0007829|PDB:2ISK"
FT HELIX 60..62
FT /evidence="ECO:0007829|PDB:2ISK"
FT STRAND 66..71
FT /evidence="ECO:0007829|PDB:2ISK"
FT HELIX 74..93
FT /evidence="ECO:0007829|PDB:2ISK"
FT HELIX 97..105
FT /evidence="ECO:0007829|PDB:2ISK"
FT TURN 111..113
FT /evidence="ECO:0007829|PDB:2ISK"
FT STRAND 114..123
FT /evidence="ECO:0007829|PDB:2ISK"
FT TURN 124..127
FT /evidence="ECO:0007829|PDB:2ISK"
FT HELIX 140..159
FT /evidence="ECO:0007829|PDB:2ISK"
FT STRAND 161..165
FT /evidence="ECO:0007829|PDB:2ISK"
FT HELIX 171..178
FT /evidence="ECO:0007829|PDB:2ISK"
FT STRAND 184..194
FT /evidence="ECO:0007829|PDB:2ISK"
FT STRAND 196..198
FT /evidence="ECO:0007829|PDB:2ISK"
FT HELIX 203..206
FT /evidence="ECO:0007829|PDB:2ISK"
FT HELIX 215..218
FT /evidence="ECO:0007829|PDB:2ISK"
FT STRAND 219..223
FT /evidence="ECO:0007829|PDB:2ISK"
SQ SEQUENCE 227 AA; 25508 MW; 68BE6DA9CC4E595F CRC64;
MLPDPNGCLT AAGAFSSDER AAVYRAIETR RDVRDEFLPE PLSEELIARL LGAAHQAPSV
GFMQPWNFVL VRQDETREKV WQAFQRANDE AAEMFSGERQ AKYRSLKLEG IRKAPLSICV
TCDRTRGGAV VLGRTHNPQM DLYSTVCAVQ NLWLAARAEG VGVGWVSIFH ESEIKAILGI
PDHVEIVAWL CLGFVDRLYQ EPELAAKGWR QRLPLEDLVF EEGWGVR
