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P66038

- RISB_SALTY

UniProt

P66038 - RISB_SALTY

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Protein
6,7-dimethyl-8-ribityllumazine synthase
Gene
ribH, STM0417
Organism
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Status
Reviewed - 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.UniRule annotation

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.UniRule annotation

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei22 – 2215-amino-6-(D-ribitylamino)uracil By similarity
Active sitei89 – 891Proton donor Reviewed prediction
Binding sitei114 – 11415-amino-6-(D-ribitylamino)uracil; via amide nitrogen and carbonyl oxygen By similarity
Binding sitei128 – 12811-deoxy-L-glycero-tetrulose 4-phosphate Inferred

GO - Molecular functioni

  1. 6,7-dimethyl-8-ribityllumazine synthase activity Source: UniProtKB-HAMAP
  2. transferase activity Source: UniProtKB-KW

GO - Biological processi

  1. riboflavin biosynthetic process Source: UniProtKB-HAMAP
Complete GO annotation...

Keywords - Molecular functioni

Transferase

Keywords - Biological processi

Riboflavin biosynthesis

Enzyme and pathway databases

BioCyciSENT99287:GCTI-418-MONOMER.
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: Chromosome

Subcellular locationi

GO - Cellular componenti

  1. riboflavin synthase complex Source: InterPro
Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 1561566,7-dimethyl-8-ribityllumazine synthaseUniRule annotation
PRO_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

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

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
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.

Family & Domainsi

Region

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

Sequence similaritiesi

Belongs to the DMRL synthase family.

Phylogenomic databases

HOGENOMiHOG000229253.
KOiK00794.
OMAiISRFNDF.
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

MNIIKANVAA PDARVAITIA RFNQFINDSL LDGAVDALTR IGQVKDDNIT    50
VVWVPGAYEL PLATEALAKS GKYDAVVALG TVIRGGTAHF EYVAGGASNG 100
LASVAQDSGV PVAFGVLTTE SIEQAIERAG TKAGNKGAEA ALTALEMINV 150
LKAIKA 156
Length:156
Mass (Da):16,008
Last modified:October 11, 2004 - v1
Checksum:iA19018478C53A294
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AE006468 Genomic DNA. Translation: AAL19371.1.
RefSeqiNP_459412.1. NC_003197.1.

Genome annotation databases

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

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AE006468 Genomic DNA. Translation: AAL19371.1 .
RefSeqi NP_459412.1. NC_003197.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
3MK3 X-ray 3.57 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 [» ]
3NQ4 X-ray 3.50 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 [» ]
ProteinModelPortali P66038.
SMRi P66038. Positions 1-155.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 99287.STM0417.

Proteomic databases

PRIDEi P66038.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAL19371 ; AAL19371 ; STM0417 .
GeneIDi 1251936.
KEGGi stm:STM0417.
PATRICi 32379169. VBISalEnt20916_0446.

Phylogenomic databases

HOGENOMi HOG000229253.
KOi K00794.
OMAi ISRFNDF.
OrthoDBi EOG6RC3WC.
PhylomeDBi P66038.

Enzyme and pathway databases

UniPathwayi UPA00275 ; UER00404 .
BioCyci SENT99287:GCTI-418-MONOMER.

Family and domain databases

Gene3Di 3.40.50.960. 1 hit.
HAMAPi MF_00178. Lumazine_synth.
InterProi IPR002180. DMRL_synthase.
[Graphical view ]
PANTHERi PTHR21058. PTHR21058. 1 hit.
Pfami PF00885. DMRL_synthase. 1 hit.
[Graphical view ]
SUPFAMi SSF52121. SSF52121. 1 hit.
TIGRFAMsi TIGR00114. lumazine-synth. 1 hit.
ProtoNeti Search...

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: July 9, 2014
This is version 63 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

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