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P66038 (RISB_SALTY) Reviewed, UniProtKB/Swiss-Prot

Last modified February 19, 2014. Version 61. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
6,7-dimethyl-8-ribityllumazine synthase

Short name=DMRL synthase
Short name=LS
Short name=Lumazine synthase
EC=2.5.1.78
Gene names
Name:ribH
Ordered Locus Names:STM0417
OrganismSalmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) [Reference proteome] [HAMAP]
Taxonomic identifier99287 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeSalmonella

Protein attributes

Sequence length156 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Catalyzes the formation of 6,7-dimethyl-8-ribityllumazine by condensation of 5-amino-6-(D-ribitylamino)uracil with 3,4-dihydroxy-2-butanone 4-phosphate. This is the penultimate step in the biosynthesis of riboflavin By similarity. HAMAP-Rule MF_00178

Catalytic activity

1-deoxy-L-glycero-tetrulose 4-phosphate + 5-amino-6-(D-ribitylamino)uracil = 6,7-dimethyl-8-(D-ribityl)lumazine + 2 H2O + phosphate. HAMAP-Rule MF_00178

Pathway

Cofactor biosynthesis; riboflavin biosynthesis; riboflavin from 2-hydroxy-3-oxobutyl phosphate and 5-amino-6-(D-ribitylamino)uracil: step 1/2. Ref.2

Subunit structure

Forms an icosahedral capsid composed of 60 subunits, arranged as a dodecamer of pentamers. Ref.2

Sequence similarities

Belongs to the DMRL synthase family.

Ontologies

Keywords
   Biological processRiboflavin biosynthesis
   Molecular functionTransferase
   Technical term3D-structure
Complete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processriboflavin biosynthetic process

Inferred from electronic annotation. Source: UniProtKB-HAMAP

   Cellular_componentriboflavin synthase complex

Inferred from electronic annotation. Source: InterPro

   Molecular_function6,7-dimethyl-8-ribityllumazine synthase activity

Inferred from electronic annotation. Source: UniProtKB-HAMAP

transferase activity

Inferred from electronic annotation. Source: UniProtKB-KW

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 1561566,7-dimethyl-8-ribityllumazine synthase HAMAP-Rule MF_00178
PRO_0000134800

Regions

Region57 – 5935-amino-6-(D-ribitylamino)uracil binding By similarity
Region81 – 8335-amino-6-(D-ribitylamino)uracil binding By similarity
Region86 – 8721-deoxy-L-glycero-tetrulose 4-phosphate binding Probable

Sites

Active site891Proton donor Potential
Binding site2215-amino-6-(D-ribitylamino)uracil By similarity
Binding site11415-amino-6-(D-ribitylamino)uracil; via amide nitrogen and carbonyl oxygen By similarity
Binding site12811-deoxy-L-glycero-tetrulose 4-phosphate Probable

Secondary structure

...................... 156
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P66038 [UniParc].

Last modified October 11, 2004. Version 1.
Checksum: A19018478C53A294

FASTA15616,008
        10         20         30         40         50         60 
MNIIKANVAA PDARVAITIA RFNQFINDSL LDGAVDALTR IGQVKDDNIT VVWVPGAYEL 

        70         80         90        100        110        120 
PLATEALAKS GKYDAVVALG TVIRGGTAHF EYVAGGASNG LASVAQDSGV PVAFGVLTTE 

       130        140        150 
SIEQAIERAG TKAGNKGAEA ALTALEMINV LKAIKA 

« Hide

References

« Hide 'large scale' references
[1]"Complete genome sequence of Salmonella enterica serovar Typhimurium LT2."
McClelland M., Sanderson K.E., Spieth J., Clifton S.W., Latreille P., Courtney L., Porwollik S., Ali J., Dante M., Du F., Hou S., Layman D., Leonard S., Nguyen C., Scott K., Holmes A., Grewal N., Mulvaney E. expand/collapse author list , Ryan E., Sun H., Florea L., Miller W., Stoneking T., Nhan M., Waterston R., Wilson R.K.
Nature 413:852-856(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: LT2 / SGSC1412 / ATCC 700720.
[2]"Crystal structure analysis of icosahedral lumazine synthase from Salmonella typhimurium, an antibacterial drug target."
Kumar P., Singh M., Karthikeyan S.
Acta Crystallogr. D 67:131-139(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (3.50 ANGSTROMS) IN COMPLEX WITH SULFATE, SUBUNIT, PATHWAY.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AE006468 Genomic DNA. Translation: AAL19371.1.
RefSeqNP_459412.1. NC_003197.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
3MK3X-ray3.571/2/3/4/5/6/7/8/9/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/y1-156[»]
3NQ4X-ray3.501/2/3/4/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/Z1-156[»]
ProteinModelPortalP66038.
SMRP66038. Positions 1-155.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING99287.STM0417.

Proteomic databases

PRIDEP66038.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAL19371; AAL19371; STM0417.
GeneID1251936.
KEGGstm:STM0417.
PATRIC32379169. VBISalEnt20916_0446.

Phylogenomic databases

HOGENOMHOG000229253.
KOK00794.
OMATALEMVS.
OrthoDBEOG6RC3WC.
ProtClustDBPRK00061.

Enzyme and pathway databases

BioCycSENT99287:GCTI-418-MONOMER.
UniPathwayUPA00275; UER00404.

Family and domain databases

Gene3D3.40.50.960. 1 hit.
HAMAPMF_00178. Lumazine_synth.
InterProIPR002180. DMRL_synthase.
[Graphical view]
PANTHERPTHR21058. PTHR21058. 1 hit.
PfamPF00885. DMRL_synthase. 1 hit.
[Graphical view]
SUPFAMSSF52121. SSF52121. 1 hit.
TIGRFAMsTIGR00114. lumazine-synth. 1 hit.
ProtoNetSearch...

Entry information

Entry nameRISB_SALTY
AccessionPrimary (citable) accession number: P66038
Secondary accession number(s): Q8XFI9
Entry history
Integrated into UniProtKB/Swiss-Prot: October 11, 2004
Last sequence update: October 11, 2004
Last modified: February 19, 2014
This is version 61 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

PATHWAY comments

Index of metabolic and biosynthesis pathways