RISB_BACSU
ID RISB_BACSU Reviewed; 154 AA.
AC P11998; P17621;
DT 01-OCT-1989, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1994, sequence version 2.
DT 03-AUG-2022, entry version 157.
DE RecName: Full=6,7-dimethyl-8-ribityllumazine synthase;
DE Short=DMRL synthase;
DE Short=LS;
DE Short=Lumazine synthase;
DE EC=2.5.1.78;
DE AltName: Full=Heavy riboflavin synthase beta subunit;
DE Short=HRS beta subunit;
GN Name=ribH; OrderedLocusNames=BSU23250;
OS Bacillus subtilis (strain 168).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus.
OX NCBI_TaxID=224308;
RN [1]
RP PROTEIN SEQUENCE.
RX PubMed=3100522; DOI=10.1016/s0021-9258(19)75742-1;
RA Ludwig H.C., Lottspeich F., Henschen A., Ladenstein R., Bacher A.;
RT "Heavy riboflavin synthase of Bacillus subtilis. Primary structure of the
RT beta subunit.";
RL J. Biol. Chem. 262:1016-1021(1987).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=168 / Marburg / ATCC 6051 / DSM 10 / JCM 1465 / NBRC 13719 / NCIMB
RC 3610 / NRRL NRS-744 / VKM B-501;
RX PubMed=7934829; DOI=10.1111/j.1365-2958.1993.tb02670.x;
RA Sorokin A.V., Zumstein E., Azevedo V., Ehrlich S.D., Serror P.;
RT "The organization of the Bacillus subtilis 168 chromosome region between
RT the spoVA and serA genetic loci, based on sequence data.";
RL Mol. Microbiol. 10:385-395(1993).
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=168 / SHGW;
RA Mironov V.N.;
RL Thesis (1989), USSR Academy of Sciences, Russia.
RN [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, CATALYTIC ACTIVITY, KINETIC
RP PARAMETERS, MUTAGENESIS OF HIS-88 AND ARG-127, AND MUTAGENESIS OF OTHER
RP RESIDUES.
RX PubMed=12581640; DOI=10.1016/s0022-2836(02)01473-0;
RA Fischer M., Haase I., Kis K., Meining W., Ladenstein R., Cushman M.,
RA Schramek N., Huber R., Bacher A.;
RT "Enzyme catalysis via control of activation entropy: site-directed
RT mutagenesis of 6,7-dimethyl-8-ribityllumazine synthase.";
RL J. Mol. Biol. 326:783-793(2003).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=168;
RX PubMed=9384377; DOI=10.1038/36786;
RA Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V.,
RA Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R.,
RA Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S.,
RA Bruschi C.V., Caldwell B., Capuano V., Carter N.M., Choi S.-K.,
RA Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F.,
RA Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D.,
RA Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M.,
RA Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P.,
RA Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K.,
RA Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S.,
RA Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y.,
RA Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G.,
RA Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J.,
RA Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C.,
RA Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S.,
RA Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B.,
RA Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S.,
RA Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M.,
RA Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y.,
RA Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J.,
RA Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A.,
RA Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M.,
RA Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S.,
RA Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E.,
RA Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K.,
RA Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E.,
RA Yoshikawa H., Danchin A.;
RT "The complete genome sequence of the Gram-positive bacterium Bacillus
RT subtilis.";
RL Nature 390:249-256(1997).
RN [6]
RP PROTEIN SEQUENCE OF 1-20.
RC STRAIN=168 / JH642;
RX PubMed=8755892; DOI=10.1128/jb.178.15.4611-4619.1996;
RA Graumann P., Schroeder K., Schmid R., Marahiel M.A.;
RT "Cold shock stress-induced proteins in Bacillus subtilis.";
RL J. Bacteriol. 178:4611-4619(1996).
RN [7]
RP SUBUNIT.
RX PubMed=3083108; DOI=10.1016/0022-2836(86)90407-9;
RA Bacher A., Ludwig H.C., Schnepple H., Ben-Shaul Y.;
RT "Heavy riboflavin synthase from Bacillus subtilis. Quaternary structure and
RT reaggregation.";
RL J. Mol. Biol. 187:75-86(1986).
RN [8]
RP FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, BIOPHYSICOCHEMICAL
RP PROPERTIES, STEREOSPECIFICITY, REACTION MECHANISM, AND PATHWAY.
RX PubMed=7893702; DOI=10.1021/bi00009a019;
RA Kis K., Volk R., Bacher A.;
RT "Biosynthesis of riboflavin. Studies on the reaction mechanism of 6,7-
RT dimethyl-8-ribityllumazine synthase.";
RL Biochemistry 34:2883-2892(1995).
RN [9]
RP X-RAY CRYSTALLOGRAPHY (3.3 ANGSTROMS), AND SUBUNIT.
RX PubMed=3145341; DOI=10.1016/0022-2836(88)90128-3;
RA Ladenstein R., Schneider M., Huber R., Bartunik H.-D., Wilson K.,
RA Schott K., Bacher A.;
RT "Heavy riboflavin synthase from Bacillus subtilis. Crystal structure
RT analysis of the icosahedral beta 60 capsid at 3.3-A resolution.";
RL J. Mol. Biol. 203:1045-1070(1988).
RN [10]
RP X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOG
RP INHIBITOR AND PHOSPHATE, SUBUNIT, ACTIVE SITE, AND REACTION MECHANISM.
RX PubMed=7473709; DOI=10.1006/jmbi.1995.0542;
RA Ritseert K., Huber R., Turk D., Ladenstein R., Schmidt-Baese K., Bacher A.;
RT "Studies on the lumazine synthase/riboflavin synthase complex of Bacillus
RT subtilis: crystal structure analysis of reconstituted, icosahedral beta-
RT subunit capsids with bound substrate analogue inhibitor at 2.4-A
RT resolution.";
RL J. Mol. Biol. 253:151-167(1995).
RN [11]
RP X-RAY CRYSTALLOGRAPHY (2.90 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOG
RP INHIBITOR AND PHOSPHATE.
RA Lopez-Jaramillo F.J.;
RT "Crystal structure of recombinant lumazine synthase (hexagonal form).";
RL Submitted (FEB-2009) to the PDB data bank.
CC -!- FUNCTION: Catalyzes the formation of 6,7-dimethyl-8-ribityllumazine by
CC condensation of 5-amino-6-(D-ribitylamino)uracil with 3,4-dihydroxy-2-
CC butanone 4-phosphate. This is the penultimate step in the biosynthesis
CC of riboflavin. Is able to use the non-natural R enantiomer of 3,4-
CC dihydroxy-2-butanone 4-phosphate as a substrate, but with less
CC efficiency than the natural S enantiomer. Cannot use unphosphorylated
CC 3,4-dihydroxy-2-butanone, 3,4-dihydroxy-2-butanone 3-phosphate or
CC diacetyl as substrates. {ECO:0000269|PubMed:12581640,
CC ECO:0000269|PubMed:7893702}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(2S)-2-hydroxy-3-oxobutyl phosphate + 5-amino-6-(D-
CC ribitylamino)uracil = 6,7-dimethyl-8-(1-D-ribityl)lumazine + H(+) + 2
CC H2O + phosphate; Xref=Rhea:RHEA:26152, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:15934, ChEBI:CHEBI:43474,
CC ChEBI:CHEBI:58201, ChEBI:CHEBI:58830; EC=2.5.1.78;
CC Evidence={ECO:0000269|PubMed:12581640, ECO:0000269|PubMed:7893702};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=5 uM for 5-amino-6-(D-ribitylamino)uracil
CC {ECO:0000269|PubMed:12581640, ECO:0000269|PubMed:7893702};
CC KM=9 uM for 5-amino-6-(D-ribitylamino)uracil
CC {ECO:0000269|PubMed:12581640, ECO:0000269|PubMed:7893702};
CC KM=130 uM for (3S)-3,4-dihydroxy-2-butanone 4-phosphate
CC {ECO:0000269|PubMed:12581640, ECO:0000269|PubMed:7893702};
CC KM=55 uM for (3S)-3,4-dihydroxy-2-butanone 4-phosphate
CC {ECO:0000269|PubMed:12581640, ECO:0000269|PubMed:7893702};
CC Vmax=12000 nmol/h/mg enzyme {ECO:0000269|PubMed:12581640,
CC ECO:0000269|PubMed:7893702};
CC Note=kcat is 0.056 sec(-1). {ECO:0000269|PubMed:12581640};
CC pH dependence:
CC Optimum pH is 6.5-8.0. {ECO:0000269|PubMed:7893702};
CC -!- PATHWAY: Cofactor biosynthesis; riboflavin biosynthesis; riboflavin
CC from 2-hydroxy-3-oxobutyl phosphate and 5-amino-6-(D-
CC ribitylamino)uracil: step 1/2. {ECO:0000269|PubMed:7893702}.
CC -!- SUBUNIT: Forms an icosahedral capsid composed of 60 subunits, arranged
CC as a dodecamer of pentamers. Can interact with riboflavin synthase,
CC forming a lumazine synthase/riboflavin synthase complex, also
CC designated as 'heavy riboflavin synthase complex', which consists of a
CC trimer of riboflavin synthase enclosed within the icosahedral structure
CC composed of 60 subunits of 6,7-dimethyl-8-ribityllumazine synthase.
CC {ECO:0000269|PubMed:3083108, ECO:0000269|PubMed:3145341,
CC ECO:0000269|PubMed:7473709, ECO:0000269|Ref.11}.
CC -!- SIMILARITY: Belongs to the DMRL synthase family. {ECO:0000305}.
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DR EMBL; L09228; AAA67484.1; -; Genomic_DNA.
DR EMBL; X51510; CAA35881.1; -; Genomic_DNA.
DR EMBL; AF516949; AAN01132.1; -; Genomic_DNA.
DR EMBL; AL009126; CAB14257.1; -; Genomic_DNA.
DR PIR; S45546; A26708.
DR RefSeq; NP_390206.1; NC_000964.3.
DR RefSeq; WP_003223915.1; NZ_JNCM01000036.1.
DR PDB; 1RVV; X-ray; 2.40 A; 1/2/3/4/A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P/Q/R/S/T/U/V/W/X/Y/Z=1-154.
DR PDB; 1ZIS; X-ray; 2.90 A; A/B/C/D/E/F/G/H/I/J=1-154.
DR PDBsum; 1RVV; -.
DR PDBsum; 1ZIS; -.
DR AlphaFoldDB; P11998; -.
DR SMR; P11998; -.
DR STRING; 224308.BSU23250; -.
DR DrugBank; DB04162; 5-Nitro-6-ribityl-amino-2,4(1H,3H)-pyrimidinedione.
DR jPOST; P11998; -.
DR PaxDb; P11998; -.
DR PRIDE; P11998; -.
DR EnsemblBacteria; CAB14257; CAB14257; BSU_23250.
DR GeneID; 64304106; -.
DR GeneID; 938949; -.
DR KEGG; bsu:BSU23250; -.
DR PATRIC; fig|224308.179.peg.2532; -.
DR eggNOG; COG0054; Bacteria.
DR InParanoid; P11998; -.
DR OMA; CQGVTQG; -.
DR PhylomeDB; P11998; -.
DR BioCyc; BSUB:BSU23250-MON; -.
DR BioCyc; MetaCyc:MON-14609; -.
DR BRENDA; 2.5.1.78; 658.
DR SABIO-RK; P11998; -.
DR UniPathway; UPA00275; UER00404.
DR EvolutionaryTrace; P11998; -.
DR PRO; PR:P11998; -.
DR Proteomes; UP000001570; Chromosome.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0009349; C:riboflavin synthase complex; IEA:InterPro.
DR GO; GO:0000906; F:6,7-dimethyl-8-ribityllumazine synthase activity; IBA:GO_Central.
DR GO; GO:0009231; P:riboflavin biosynthetic process; IBA:GO_Central.
DR CDD; cd09209; Lumazine_synthase-I; 1.
DR Gene3D; 3.40.50.960; -; 1.
DR HAMAP; MF_00178; Lumazine_synth; 1.
DR InterPro; IPR034964; LS.
DR InterPro; IPR002180; LS/RS.
DR InterPro; IPR036467; LS/RS_sf.
DR PANTHER; PTHR21058; PTHR21058; 1.
DR Pfam; PF00885; DMRL_synthase; 1.
DR SUPFAM; SSF52121; SSF52121; 1.
DR TIGRFAMs; TIGR00114; lumazine-synth; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Direct protein sequencing; Reference proteome;
KW Riboflavin biosynthesis; Transferase.
FT CHAIN 1..154
FT /note="6,7-dimethyl-8-ribityllumazine synthase"
FT /id="PRO_0000134715"
FT ACT_SITE 88
FT /note="Proton donor"
FT /evidence="ECO:0000255"
FT BINDING 22..23
FT /ligand="5-amino-6-(D-ribitylamino)uracil"
FT /ligand_id="ChEBI:CHEBI:15934"
FT BINDING 56..58
FT /ligand="5-amino-6-(D-ribitylamino)uracil"
FT /ligand_id="ChEBI:CHEBI:15934"
FT BINDING 80..82
FT /ligand="5-amino-6-(D-ribitylamino)uracil"
FT /ligand_id="ChEBI:CHEBI:15934"
FT BINDING 85..86
FT /ligand="(2S)-2-hydroxy-3-oxobutyl phosphate"
FT /ligand_id="ChEBI:CHEBI:58830"
FT /evidence="ECO:0000305"
FT BINDING 113
FT /ligand="5-amino-6-(D-ribitylamino)uracil"
FT /ligand_id="ChEBI:CHEBI:15934"
FT BINDING 127
FT /ligand="(2S)-2-hydroxy-3-oxobutyl phosphate"
FT /ligand_id="ChEBI:CHEBI:58830"
FT /evidence="ECO:0000305"
FT MUTAGEN 88
FT /note="H->A: 10% of wild-type activity. 17-fold decrease in
FT the affinity for the pyrimidine substrate, but no effect on
FT that for 1-deoxy-L-glycero-tetrulose 4-phosphate."
FT /evidence="ECO:0000269|PubMed:12581640"
FT MUTAGEN 127
FT /note="R->T: About 1% of wild-type activity."
FT /evidence="ECO:0000269|PubMed:12581640"
FT CONFLICT 65
FT /note="K -> G (in Ref. 1; AA sequence)"
FT /evidence="ECO:0000305"
FT STRAND 2..4
FT /evidence="ECO:0007829|PDB:1RVV"
FT STRAND 15..21
FT /evidence="ECO:0007829|PDB:1RVV"
FT HELIX 24..40
FT /evidence="ECO:0007829|PDB:1RVV"
FT HELIX 45..47
FT /evidence="ECO:0007829|PDB:1RVV"
FT STRAND 48..55
FT /evidence="ECO:0007829|PDB:1RVV"
FT HELIX 56..58
FT /evidence="ECO:0007829|PDB:1RVV"
FT HELIX 59..68
FT /evidence="ECO:0007829|PDB:1RVV"
FT STRAND 73..82
FT /evidence="ECO:0007829|PDB:1RVV"
FT STRAND 85..87
FT /evidence="ECO:0007829|PDB:1RVV"
FT HELIX 88..107
FT /evidence="ECO:0007829|PDB:1RVV"
FT STRAND 111..120
FT /evidence="ECO:0007829|PDB:1RVV"
FT HELIX 121..126
FT /evidence="ECO:0007829|PDB:1RVV"
FT STRAND 128..130
FT /evidence="ECO:0007829|PDB:1RVV"
FT HELIX 135..152
FT /evidence="ECO:0007829|PDB:1RVV"
SQ SEQUENCE 154 AA; 16287 MW; 76CB336DF6A4BFEB CRC64;
MNIIQGNLVG TGLKIGIVVG RFNDFITSKL LSGAEDALLR HGVDTNDIDV AWVPGAFEIP
FAAKKMAETK KYDAIITLGT VIRGATTHYD YVCNEAAKGI AQAANTTGVP VIFGIVTTEN
IEQAIERAGT KAGNKGVDCA VSAIEMANLN RSFE
