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 27-MAR-2024, entry version 165. 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; Bacillota; 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 / RC NCIMB 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}. CC --------------------------------------------------------------------------- CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms CC Distributed under the Creative Commons Attribution (CC BY 4.0) License CC --------------------------------------------------------------------------- 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; 224308-BSU23250; -. DR EnsemblBacteria; CAB14257; CAB14257; BSU_23250. DR GeneID; 83886195; -. DR GeneID; 938949; -. DR KEGG; bsu:BSU23250; -. DR PATRIC; fig|224308.179.peg.2532; -. DR eggNOG; COG0054; Bacteria. DR InParanoid; P11998; -. DR OrthoDB; 9809709at2; -. DR PhylomeDB; P11998; -. DR BioCyc; BSUB:BSU23250-MONOMER; -. DR BioCyc; MetaCyc:MONOMER-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; Lumazine/riboflavin synthase; 1. DR HAMAP; MF_00178; Lumazine_synth; 1. DR InterPro; IPR034964; LS. DR InterPro; IPR002180; LS/RS. DR InterPro; IPR036467; LS/RS_sf. DR NCBIfam; TIGR00114; lumazine-synth; 1. DR PANTHER; PTHR21058:SF0; 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE; 1. DR PANTHER; PTHR21058; 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE DMRL SYNTHASE LUMAZINE SYNTHASE; 1. DR Pfam; PF00885; DMRL_synthase; 1. DR SUPFAM; SSF52121; Lumazine synthase; 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 //