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O66529 (RISB_AQUAE) Reviewed, UniProtKB/Swiss-Prot

Last modified February 19, 2014. Version 91. 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:aq_132
OrganismAquifex aeolicus (strain VF5) [Reference proteome] [HAMAP]
Taxonomic identifier224324 [NCBI]
Taxonomic lineageBacteriaAquificaeAquificalesAquificaceaeAquifex

Protein attributes

Sequence length154 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. Ref.2 Ref.3

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. Ref.2 Ref.3

Pathway

Cofactor biosynthesis; riboflavin biosynthesis; riboflavin from 2-hydroxy-3-oxobutyl phosphate and 5-amino-6-(D-ribitylamino)uracil: step 1/2. Ref.4

Subunit structure

Forms an icosahedral capsid composed of 60 subunits, arranged as a dodecamer of pentamers. Ref.3

Sequence similarities

Belongs to the DMRL synthase family.

Biophysicochemical properties

Kinetic parameters:

KM=10.0 µM for 5-amino-6-(D-ribitylamino)uracil (at 37 degrees Celsius and pH 7.0) Ref.2

KM=26 µM for 3,4-dihydroxy-2-butanone 4-phosphate (at 37 degrees Celsius and pH 7.0)

Vmax=31 nmol/min/mg enzyme (at 37 degrees Celsius and pH 7.0)

Vmax=425 nmol/min/mg enzyme (at 70 degrees Celsius and pH 7.0)

Temperature dependence:

Extremely thermostable. Has a melting temperature of 119.9 degrees Celsius.

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 – 1541546,7-dimethyl-8-ribityllumazine synthase HAMAP-Rule MF_00178
PRO_0000134708

Regions

Region22 – 2325-amino-6-(D-ribitylamino)uracil binding HAMAP-Rule MF_00178
Region56 – 5835-amino-6-(D-ribitylamino)uracil binding HAMAP-Rule MF_00178
Region80 – 8235-amino-6-(D-ribitylamino)uracil binding HAMAP-Rule MF_00178
Region85 – 8621-deoxy-L-glycero-tetrulose 4-phosphate binding Probable

Sites

Active site881Proton donor Potential
Binding site11315-amino-6-(D-ribitylamino)uracil; via amide nitrogen and carbonyl oxygen
Binding site12711-deoxy-L-glycero-tetrulose 4-phosphate Probable
Binding site13515-amino-6-(D-ribitylamino)uracil

Secondary structure

...................... 154
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
O66529 [UniParc].

Last modified August 1, 1998. Version 1.
Checksum: A189410A16454AB7

FASTA15416,705
        10         20         30         40         50         60 
MQIYEGKLTA EGLRFGIVAS RFNHALVDRL VEGAIDCIVR HGGREEDITL VRVPGSWEIP 

        70         80         90        100        110        120 
VAAGELARKE DIDAVIAIGV LIRGATPHFD YIASEVSKGL ANLSLELRKP ITFGVITADT 

       130        140        150 
LEQAIERAGT KHGNKGWEAA LSAIEMANLF KSLR 

« Hide

References

« Hide 'large scale' references
[1]"The complete genome of the hyperthermophilic bacterium Aquifex aeolicus."
Deckert G., Warren P.V., Gaasterland T., Young W.G., Lenox A.L., Graham D.E., Overbeek R., Snead M.A., Keller M., Aujay M., Huber R., Feldman R.A., Short J.M., Olsen G.J., Swanson R.V.
Nature 392:353-358(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: VF5.
[2]"Biosynthesis of riboflavin in archaea. 6,7-dimethyl-8-ribityllumazine synthase of Methanococcus jannaschii."
Haase I., Mortl S., Kohler P., Bacher A., Fischer M.
Eur. J. Biochem. 270:1025-1032(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, CATALYTIC ACTIVITY, KINETIC PARAMETERS.
Strain: VF5.
[3]"X-ray structure analysis and crystallographic refinement of lumazine synthase from the hyperthermophile Aquifex aeolicus at 1.6 A resolution: determinants of thermostability revealed from structural comparisons."
Zhang X., Meining W., Fischer M., Bacher A., Ladenstein R.
J. Mol. Biol. 306:1099-1114(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS) OF APOENZYME, FUNCTION, CATALYTIC ACTIVITY, TEMPERATURE DEPENDENCE, SUBUNIT.
Strain: VF5.
[4]"A structure-based model of the reaction catalyzed by lumazine synthase from Aquifex aeolicus."
Zhang X., Meining W., Cushman M., Haase I., Fischer M., Bacher A., Ladenstein R.
J. Mol. Biol. 328:167-182(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.75 ANGSTROMS) IN COMPLEXES WITH SUBSTRATE ANALOG OR REACTION INTERMEDIATE ANALOG INHIBITORS AND PHOSPHATE, PATHWAY, ACTIVE SITE, REACTION MECHANISM.
Strain: VF5.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AE000657 Genomic DNA. Translation: AAC06489.1.
PIRF70312.
RefSeqNP_213089.1. NC_000918.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1HQKX-ray1.60A/B/C/D/E1-154[»]
1NQUX-ray1.75A/B/C/D/E1-154[»]
1NQVX-ray2.05A/B/C/D/E1-154[»]
1NQWX-ray2.20A/B/C/D/E1-154[»]
1NQXX-ray1.82A/B/C/D/E1-154[»]
ProteinModelPortalO66529.
SMRO66529. Positions 1-154.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING224324.aq_132.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAC06489; AAC06489; aq_132.
GeneID1192672.
KEGGaae:aq_132.
PATRIC20957942. VBIAquAeo85532_0111.

Phylogenomic databases

eggNOGCOG0054.
HOGENOMHOG000229253.
KOK00794.
OMAGRFNSFI.
OrthoDBEOG6RC3WC.
ProtClustDBPRK00061.

Enzyme and pathway databases

BioCycAAEO224324:GJBH-104-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...

Other

EvolutionaryTraceO66529.

Entry information

Entry nameRISB_AQUAE
AccessionPrimary (citable) accession number: O66529
Entry history
Integrated into UniProtKB/Swiss-Prot: December 1, 2000
Last sequence update: August 1, 1998
Last modified: February 19, 2014
This is version 91 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