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Protein

6,7-dimethyl-8-ribityllumazine synthase

Gene

ribH

Organism
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

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).By similarity

Catalytic activityi

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

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei22 – 2215-amino-6-(D-ribitylamino)uracilBy similarity
Active sitei89 – 891Proton donorSequence Analysis
Binding sitei114 – 11415-amino-6-(D-ribitylamino)uracil; via amide nitrogen and carbonyl oxygenBy similarity
Binding sitei128 – 12811-deoxy-L-glycero-tetrulose 4-phosphateCurated

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Transferase

Keywords - Biological processi

Riboflavin biosynthesis

Enzyme and pathway databases

BioCyciSENT99287:GCTI-418-MONOMER.
BRENDAi2.5.1.78. 5542.
UniPathwayiUPA00275; UER00404.

Names & Taxonomyi

Protein namesi
Recommended name:
6,7-dimethyl-8-ribityllumazine synthase (EC:2.5.1.78)
Short name:
DMRL synthase
Short name:
LS
Short name:
Lumazine synthase
Gene namesi
Name:ribH
Ordered Locus Names:STM0417
OrganismiSalmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Taxonomic identifieri99287 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeSalmonella
ProteomesiUP000001014 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 1561566,7-dimethyl-8-ribityllumazine synthasePRO_0000134800Add
BLAST

Proteomic databases

PRIDEiP66038.

Interactioni

Subunit structurei

Forms an icosahedral capsid composed of 60 subunits, arranged as a dodecamer of pentamers.1 Publication

Protein-protein interaction databases

STRINGi99287.STM0417.

Structurei

Secondary structure

1
156
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi2 – 54Combined sources
Beta strandi15 – 217Combined sources
Helixi24 – 4017Combined sources
Beta strandi48 – 569Combined sources
Turni57 – 593Combined sources
Helixi60 – 7011Combined sources
Beta strandi74 – 8310Combined sources
Beta strandi86 – 883Combined sources
Helixi89 – 10820Combined sources
Beta strandi112 – 1209Combined sources
Helixi122 – 1287Combined sources
Helixi136 – 15217Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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[»]
ProteinModelPortaliP66038.
SMRiP66038. Positions 1-155.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni57 – 5935-amino-6-(D-ribitylamino)uracil bindingBy similarity
Regioni81 – 8335-amino-6-(D-ribitylamino)uracil bindingBy similarity
Regioni86 – 8721-deoxy-L-glycero-tetrulose 4-phosphate bindingCurated

Sequence similaritiesi

Belongs to the DMRL synthase family.Curated

Phylogenomic databases

HOGENOMiHOG000229253.
KOiK00794.
OMAiSHVAMNS.
OrthoDBiEOG6RC3WC.
PhylomeDBiP66038.

Family and domain databases

Gene3Di3.40.50.960. 1 hit.
HAMAPiMF_00178. Lumazine_synth.
InterProiIPR002180. DMRL_synthase.
[Graphical view]
PANTHERiPTHR21058. PTHR21058. 1 hit.
PfamiPF00885. DMRL_synthase. 1 hit.
[Graphical view]
SUPFAMiSSF52121. SSF52121. 1 hit.
TIGRFAMsiTIGR00114. lumazine-synth. 1 hit.

Sequencei

Sequence statusi: Complete.

P66038-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNIIKANVAA PDARVAITIA RFNQFINDSL LDGAVDALTR IGQVKDDNIT
60 70 80 90 100
VVWVPGAYEL PLATEALAKS GKYDAVVALG TVIRGGTAHF EYVAGGASNG
110 120 130 140 150
LASVAQDSGV PVAFGVLTTE SIEQAIERAG TKAGNKGAEA ALTALEMINV

LKAIKA
Length:156
Mass (Da):16,008
Last modified:October 11, 2004 - v1
Checksum:iA19018478C53A294
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE006468 Genomic DNA. Translation: AAL19371.1.
RefSeqiNP_459412.1. NC_003197.1.
WP_001021372.1. NC_003197.1.

Genome annotation databases

EnsemblBacteriaiAAL19371; AAL19371; STM0417.
GeneIDi1251936.
KEGGistm:STM0417.
PATRICi32379169. VBISalEnt20916_0446.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE006468 Genomic DNA. Translation: AAL19371.1.
RefSeqiNP_459412.1. NC_003197.1.
WP_001021372.1. NC_003197.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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[»]
ProteinModelPortaliP66038.
SMRiP66038. Positions 1-155.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi99287.STM0417.

Proteomic databases

PRIDEiP66038.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAL19371; AAL19371; STM0417.
GeneIDi1251936.
KEGGistm:STM0417.
PATRICi32379169. VBISalEnt20916_0446.

Phylogenomic databases

HOGENOMiHOG000229253.
KOiK00794.
OMAiSHVAMNS.
OrthoDBiEOG6RC3WC.
PhylomeDBiP66038.

Enzyme and pathway databases

UniPathwayiUPA00275; UER00404.
BioCyciSENT99287:GCTI-418-MONOMER.
BRENDAi2.5.1.78. 5542.

Family and domain databases

Gene3Di3.40.50.960. 1 hit.
HAMAPiMF_00178. Lumazine_synth.
InterProiIPR002180. DMRL_synthase.
[Graphical view]
PANTHERiPTHR21058. PTHR21058. 1 hit.
PfamiPF00885. DMRL_synthase. 1 hit.
[Graphical view]
SUPFAMiSSF52121. SSF52121. 1 hit.
TIGRFAMsiTIGR00114. lumazine-synth. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. 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.

Entry informationi

Entry nameiRISB_SALTY
AccessioniPrimary (citable) accession number: P66038
Secondary accession number(s): Q8XFI9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 11, 2004
Last sequence update: October 11, 2004
Last modified: May 27, 2015
This is version 68 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.