RISB_SALTY
ID RISB_SALTY Reviewed; 156 AA.
AC P66038; Q8XFI9;
DT 11-OCT-2004, integrated into UniProtKB/Swiss-Prot.
DT 11-OCT-2004, sequence version 1.
DT 03-AUG-2022, entry version 98.
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;
GN Name=ribH; OrderedLocusNames=STM0417;
OS Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Salmonella.
OX NCBI_TaxID=99287;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=LT2 / SGSC1412 / ATCC 700720;
RX PubMed=11677609; DOI=10.1038/35101614;
RA McClelland M., Sanderson K.E., Spieth J., Clifton S.W., Latreille P.,
RA Courtney L., Porwollik S., Ali J., Dante M., Du F., Hou S., Layman D.,
RA Leonard S., Nguyen C., Scott K., Holmes A., Grewal N., Mulvaney E.,
RA Ryan E., Sun H., Florea L., Miller W., Stoneking T., Nhan M., Waterston R.,
RA Wilson R.K.;
RT "Complete genome sequence of Salmonella enterica serovar Typhimurium LT2.";
RL Nature 413:852-856(2001).
RN [2]
RP X-RAY CRYSTALLOGRAPHY (3.50 ANGSTROMS) IN COMPLEX WITH SULFATE, SUBUNIT,
RP AND PATHWAY.
RX PubMed=21245535; DOI=10.1107/s0907444910053370;
RA Kumar P., Singh M., Karthikeyan S.;
RT "Crystal structure analysis of icosahedral lumazine synthase from
RT Salmonella typhimurium, an antibacterial drug target.";
RL Acta Crystallogr. D 67:131-139(2011).
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 (By similarity). {ECO:0000250}.
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 -!- 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:21245535}.
CC -!- SUBUNIT: Forms an icosahedral capsid composed of 60 subunits, arranged
CC as a dodecamer of pentamers. {ECO:0000269|PubMed:21245535}.
CC -!- SIMILARITY: Belongs to the DMRL synthase family. {ECO:0000305}.
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DR EMBL; AE006468; AAL19371.1; -; Genomic_DNA.
DR RefSeq; NP_459412.1; NC_003197.2.
DR RefSeq; WP_001021372.1; NC_003197.2.
DR PDB; 3MK3; X-ray; 3.57 A; 1/2/3/4/5/6/7/8/9/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/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=1-156.
DR PDB; 3NQ4; X-ray; 3.50 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=1-156.
DR PDBsum; 3MK3; -.
DR PDBsum; 3NQ4; -.
DR AlphaFoldDB; P66038; -.
DR SMR; P66038; -.
DR STRING; 99287.STM0417; -.
DR PaxDb; P66038; -.
DR EnsemblBacteria; AAL19371; AAL19371; STM0417.
DR GeneID; 1251936; -.
DR KEGG; stm:STM0417; -.
DR PATRIC; fig|99287.12.peg.446; -.
DR HOGENOM; CLU_089358_1_1_6; -.
DR OMA; CQGVTQG; -.
DR PhylomeDB; P66038; -.
DR BioCyc; SENT99287:STM0417-MON; -.
DR BRENDA; 2.5.1.78; 5542.
DR UniPathway; UPA00275; UER00404.
DR Proteomes; UP000001014; 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; Reference proteome; Riboflavin biosynthesis; Transferase.
FT CHAIN 1..156
FT /note="6,7-dimethyl-8-ribityllumazine synthase"
FT /id="PRO_0000134800"
FT ACT_SITE 89
FT /note="Proton donor"
FT /evidence="ECO:0000255"
FT BINDING 22
FT /ligand="5-amino-6-(D-ribitylamino)uracil"
FT /ligand_id="ChEBI:CHEBI:15934"
FT /evidence="ECO:0000250"
FT BINDING 57..59
FT /ligand="5-amino-6-(D-ribitylamino)uracil"
FT /ligand_id="ChEBI:CHEBI:15934"
FT /evidence="ECO:0000250"
FT BINDING 81..83
FT /ligand="5-amino-6-(D-ribitylamino)uracil"
FT /ligand_id="ChEBI:CHEBI:15934"
FT /evidence="ECO:0000250"
FT BINDING 86..87
FT /ligand="(2S)-2-hydroxy-3-oxobutyl phosphate"
FT /ligand_id="ChEBI:CHEBI:58830"
FT /evidence="ECO:0000305"
FT BINDING 114
FT /ligand="5-amino-6-(D-ribitylamino)uracil"
FT /ligand_id="ChEBI:CHEBI:15934"
FT /evidence="ECO:0000250"
FT BINDING 128
FT /ligand="(2S)-2-hydroxy-3-oxobutyl phosphate"
FT /ligand_id="ChEBI:CHEBI:58830"
FT /evidence="ECO:0000305"
FT STRAND 2..5
FT /evidence="ECO:0007829|PDB:3NQ4"
FT STRAND 15..21
FT /evidence="ECO:0007829|PDB:3NQ4"
FT HELIX 24..40
FT /evidence="ECO:0007829|PDB:3NQ4"
FT STRAND 48..56
FT /evidence="ECO:0007829|PDB:3NQ4"
FT TURN 57..59
FT /evidence="ECO:0007829|PDB:3NQ4"
FT HELIX 60..70
FT /evidence="ECO:0007829|PDB:3NQ4"
FT STRAND 74..83
FT /evidence="ECO:0007829|PDB:3NQ4"
FT STRAND 86..88
FT /evidence="ECO:0007829|PDB:3NQ4"
FT HELIX 89..108
FT /evidence="ECO:0007829|PDB:3NQ4"
FT STRAND 112..120
FT /evidence="ECO:0007829|PDB:3NQ4"
FT HELIX 122..128
FT /evidence="ECO:0007829|PDB:3NQ4"
FT HELIX 136..152
FT /evidence="ECO:0007829|PDB:3NQ4"
SQ SEQUENCE 156 AA; 16008 MW; A19018478C53A294 CRC64;
MNIIKANVAA PDARVAITIA RFNQFINDSL LDGAVDALTR IGQVKDDNIT VVWVPGAYEL
PLATEALAKS GKYDAVVALG TVIRGGTAHF EYVAGGASNG LASVAQDSGV PVAFGVLTTE
SIEQAIERAG TKAGNKGAEA ALTALEMINV LKAIKA
