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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: riboflavin biosynthesis

This protein is involved in step 1 of the subpathway that synthesizes riboflavin from 2-hydroxy-3-oxobutyl phosphate and 5-amino-6-(D-ribitylamino)uracil.1 Publication
Proteins known to be involved in the 2 steps of the subpathway in this organism are:
  1. 6,7-dimethyl-8-ribityllumazine synthase (ribH)
  2. no protein annotated in this organism
This subpathway is part of the pathway riboflavin biosynthesis, which is itself part of Cofactor biosynthesis.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes riboflavin from 2-hydroxy-3-oxobutyl phosphate and 5-amino-6-(D-ribitylamino)uracil, the pathway riboflavin biosynthesis and in Cofactor biosynthesis.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei225-amino-6-(D-ribitylamino)uracilBy similarity1
Active sitei89Proton donorSequence analysis1
Binding sitei1145-amino-6-(D-ribitylamino)uracil; via amide nitrogen and carbonyl oxygenBy similarity1
Binding sitei1281-deoxy-L-glycero-tetrulose 4-phosphateCurated1

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Transferase

Keywords - Biological processi

Riboflavin biosynthesis

Enzyme and pathway databases

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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeSalmonella
Proteomesi
  • UP000001014 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001348001 – 1566,7-dimethyl-8-ribityllumazine synthaseAdd BLAST156

Proteomic databases

PaxDbiP66038.
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

1156
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi2 – 5Combined sources4
Beta strandi15 – 21Combined sources7
Helixi24 – 40Combined sources17
Beta strandi48 – 56Combined sources9
Turni57 – 59Combined sources3
Helixi60 – 70Combined sources11
Beta strandi74 – 83Combined sources10
Beta strandi86 – 88Combined sources3
Helixi89 – 108Combined sources20
Beta strandi112 – 120Combined sources9
Helixi122 – 128Combined sources7
Helixi136 – 152Combined sources17

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni57 – 595-amino-6-(D-ribitylamino)uracil bindingBy similarity3
Regioni81 – 835-amino-6-(D-ribitylamino)uracil bindingBy similarity3
Regioni86 – 871-deoxy-L-glycero-tetrulose 4-phosphate bindingCurated2

Sequence similaritiesi

Belongs to the DMRL synthase family.Curated

Phylogenomic databases

eggNOGiENOG4108UTT. Bacteria.
COG0054. LUCA.
HOGENOMiHOG000229253.
KOiK00794.
OMAiSHVAMNS.
PhylomeDBiP66038.

Family and domain databases

Gene3Di3.40.50.960. 1 hit.
HAMAPiMF_00178. Lumazine_synth. 1 hit.
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
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi99287.STM0417.

Proteomic databases

PaxDbiP66038.
PRIDEiP66038.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Phylogenomic databases

eggNOGiENOG4108UTT. Bacteria.
COG0054. LUCA.
HOGENOMiHOG000229253.
KOiK00794.
OMAiSHVAMNS.
PhylomeDBiP66038.

Enzyme and pathway databases

UniPathwayiUPA00275; UER00404.
BRENDAi2.5.1.78. 5542.

Family and domain databases

Gene3Di3.40.50.960. 1 hit.
HAMAPiMF_00178. Lumazine_synth. 1 hit.
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...

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: November 2, 2016
This is version 75 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

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 one 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.