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Protein

6,7-dimethyl-8-ribityllumazine synthase

Gene

ribH

Organism
Aquifex aeolicus (strain VF5)
Status
Reviewed-Annotation score: Annotation score: 4 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.2 Publications

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.2 Publications

Kineticsi

  1. KM=10.0 µM for 5-amino-6-(D-ribitylamino)uracil (at 37 degrees Celsius and pH 7.0)1 Publication
  2. KM=26 µM for 3,4-dihydroxy-2-butanone 4-phosphate (at 37 degrees Celsius and pH 7.0)1 Publication
  1. Vmax=31 nmol/min/mg enzyme (at 37 degrees Celsius and pH 7.0)1 Publication
  2. Vmax=425 nmol/min/mg enzyme (at 70 degrees Celsius and pH 7.0)1 Publication

Temperature dependencei

Extremely thermostable. Has a melting temperature of 119.9 degrees Celsius.1 Publication

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. Riboflavin synthase (ribE)
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)LengthDescriptionGraphical viewFeature identifierActions
Active sitei88 – 881Proton donorSequence analysis
Binding sitei113 – 11315-amino-6-(D-ribitylamino)uracil; via amide nitrogen and carbonyl oxygen
Binding sitei127 – 12711-deoxy-L-glycero-tetrulose 4-phosphateCurated
Binding sitei135 – 13515-amino-6-(D-ribitylamino)uracil

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Transferase

Keywords - Biological processi

Riboflavin biosynthesis

Enzyme and pathway databases

BioCyciAAEO224324:GJBH-104-MONOMER.
BRENDAi2.5.1.78. 396.
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:aq_132
OrganismiAquifex aeolicus (strain VF5)
Taxonomic identifieri224324 [NCBI]
Taxonomic lineageiBacteriaAquificaeAquificalesAquificaceaeAquifex
Proteomesi
  • UP000000798 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 1541546,7-dimethyl-8-ribityllumazine synthasePRO_0000134708Add
BLAST

Interactioni

Subunit structurei

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

Protein-protein interaction databases

STRINGi224324.aq_132.

Structurei

Secondary structure

1
154
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi2 – 43Combined sources
Beta strandi15 – 206Combined sources
Helixi24 – 4017Combined sources
Helixi45 – 473Combined sources
Beta strandi48 – 558Combined sources
Helixi56 – 583Combined sources
Helixi59 – 679Combined sources
Beta strandi74 – 829Combined sources
Helixi88 – 10720Combined sources
Beta strandi111 – 12010Combined sources
Helixi121 – 1277Combined sources
Beta strandi128 – 1303Combined sources
Helixi135 – 15319Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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[»]
ProteinModelPortaliO66529.
SMRiO66529. Positions 1-154.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO66529.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni22 – 2325-amino-6-(D-ribitylamino)uracil binding
Regioni56 – 5835-amino-6-(D-ribitylamino)uracil binding
Regioni80 – 8235-amino-6-(D-ribitylamino)uracil binding
Regioni85 – 8621-deoxy-L-glycero-tetrulose 4-phosphate bindingCurated

Sequence similaritiesi

Belongs to the DMRL synthase family.Curated

Phylogenomic databases

eggNOGiENOG4108UTT. Bacteria.
COG0054. LUCA.
HOGENOMiHOG000229253.
InParanoidiO66529.
KOiK00794.
OMAiWNYALQA.
OrthoDBiEOG6RC3WC.

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.

O66529-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MQIYEGKLTA EGLRFGIVAS RFNHALVDRL VEGAIDCIVR HGGREEDITL
60 70 80 90 100
VRVPGSWEIP VAAGELARKE DIDAVIAIGV LIRGATPHFD YIASEVSKGL
110 120 130 140 150
ANLSLELRKP ITFGVITADT LEQAIERAGT KHGNKGWEAA LSAIEMANLF

KSLR
Length:154
Mass (Da):16,705
Last modified:August 1, 1998 - v1
Checksum:iA189410A16454AB7
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000657 Genomic DNA. Translation: AAC06489.1.
PIRiF70312.
RefSeqiNP_213089.1. NC_000918.1.
WP_010880027.1. NC_000918.1.

Genome annotation databases

EnsemblBacteriaiAAC06489; AAC06489; aq_132.
GeneIDi1192672.
KEGGiaae:aq_132.
PATRICi20957942. VBIAquAeo85532_0111.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000657 Genomic DNA. Translation: AAC06489.1.
PIRiF70312.
RefSeqiNP_213089.1. NC_000918.1.
WP_010880027.1. NC_000918.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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[»]
ProteinModelPortaliO66529.
SMRiO66529. Positions 1-154.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi224324.aq_132.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC06489; AAC06489; aq_132.
GeneIDi1192672.
KEGGiaae:aq_132.
PATRICi20957942. VBIAquAeo85532_0111.

Phylogenomic databases

eggNOGiENOG4108UTT. Bacteria.
COG0054. LUCA.
HOGENOMiHOG000229253.
InParanoidiO66529.
KOiK00794.
OMAiWNYALQA.
OrthoDBiEOG6RC3WC.

Enzyme and pathway databases

UniPathwayiUPA00275; UER00404.
BioCyciAAEO224324:GJBH-104-MONOMER.
BRENDAi2.5.1.78. 396.

Miscellaneous databases

EvolutionaryTraceiO66529.

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: 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.

Entry informationi

Entry nameiRISB_AQUAE
AccessioniPrimary (citable) accession number: O66529
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 1, 2000
Last sequence update: August 1, 1998
Last modified: February 17, 2016
This is version 105 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.