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Protein

6,7-dimethyl-8-ribityllumazine synthase

Gene

rib4

Organism
Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast)
Status
Reviewed-Annotation score: Annotation score: 5 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. Also binds riboflavin with an unexpected high affinity.1 Publication

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.1 Publication

Enzyme regulationi

Competitively inhibited by riboflavin (Ki of 17 µM).1 Publication

Kineticsi

  1. KM=5 µM for 5-amino-6-(D-ribitylamino)uracil (at 37 degrees Celsius and pH 7.0)1 Publication
  2. KM=67 µM for 3,4-dihydroxy-2-butanone 4-phosphate (at 37 degrees Celsius and pH 7.0)1 Publication
  1. Vmax=13000 nmol/h/mg enzyme (at 37 degrees Celsius and pH 7.0)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 (rib4)
  2. Riboflavin synthase (rib5)
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 sitei275-amino-6-(D-ribitylamino)uracil1
Active sitei94Proton donorSequence analysis1
Binding sitei1195-amino-6-(D-ribitylamino)uracil; via amide nitrogen and carbonyl oxygen1
Binding sitei1331-deoxy-L-glycero-tetrulose 4-phosphateCurated1

GO - Molecular functioni

  • 6,7-dimethyl-8-ribityllumazine synthase activity Source: PomBase
  • riboflavin binding Source: PomBase
  • transferase activity Source: UniProtKB-KW

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Transferase

Keywords - Biological processi

Riboflavin biosynthesis

Enzyme and pathway databases

BRENDAi2.5.1.78. 5613.
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
Alternative name(s):
Riboflavin synthase beta chain
Gene namesi
Name:rib4
ORF Names:SPBC409.13
OrganismiSchizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast)
Taxonomic identifieri284812 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaTaphrinomycotinaSchizosaccharomycetesSchizosaccharomycetalesSchizosaccharomycetaceaeSchizosaccharomyces
Proteomesi
  • UP000002485 Componenti: Chromosome II

Organism-specific databases

EuPathDBiFungiDB:SPBC409.13.
PomBaseiSPBC409.13. rib4.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: PomBase
  • mitochondrial intermembrane space Source: GO_Central
  • nucleus Source: PomBase
  • riboflavin synthase complex Source: InterPro
Complete GO annotation...

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi27W → F or Y: Minor effects on the kinetic properties. 1 Publication1
Mutagenesisi27W → G, H, I or S: Reduced affinity for riboflavin and for the substrate 5-amino-6-(D-ribitylamino)uracil. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001348561 – 1596,7-dimethyl-8-ribityllumazine synthaseAdd BLAST159

Proteomic databases

MaxQBiQ9UUB1.
PRIDEiQ9UUB1.

Interactioni

Subunit structurei

Homopentamer.3 Publications

Protein-protein interaction databases

BioGridi277640. 4 interactors.
MINTiMINT-4711607.

Structurei

Secondary structure

1159
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi20 – 24Combined sources5
Helixi29 – 47Combined sources19
Helixi51 – 53Combined sources3
Beta strandi54 – 58Combined sources5
Helixi62 – 64Combined sources3
Helixi65 – 75Combined sources11
Beta strandi79 – 88Combined sources10
Beta strandi91 – 93Combined sources3
Helixi94 – 113Combined sources20
Beta strandi117 – 126Combined sources10
Helixi127 – 133Combined sources7
Helixi142 – 156Combined sources15

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1KYVX-ray2.40A/B/C/D/E1-159[»]
1KYXX-ray2.60A/B/C/D/E1-159[»]
1KYYX-ray2.40A/B/C/D/E1-159[»]
1KZ1X-ray2.00A/B/C/D/E1-159[»]
1KZ4X-ray3.10A/B/C/D/E1-159[»]
1KZ6X-ray2.70A/B/C/D/E1-159[»]
1KZ9X-ray3.10A/B/C/D/E1-159[»]
2A57X-ray2.75A/B/C/D/E1-159[»]
2A58X-ray2.80A/B/C/D/E1-159[»]
2A59X-ray2.70A/B/C/D/E1-159[»]
ProteinModelPortaliQ9UUB1.
SMRiQ9UUB1.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9UUB1.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni62 – 645-amino-6-(D-ribitylamino)uracil binding3
Regioni86 – 885-amino-6-(D-ribitylamino)uracil binding3
Regioni91 – 921-deoxy-L-glycero-tetrulose 4-phosphate bindingCurated2

Sequence similaritiesi

Belongs to the DMRL synthase family.Curated

Phylogenomic databases

HOGENOMiHOG000229253.
InParanoidiQ9UUB1.
KOiK00794.
OMAiMFGADKG.
OrthoDBiEOG092C573E.
PhylomeDBiQ9UUB1.

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.

Q9UUB1-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MFSGIKGPNP SDLKGPELRI LIVHARWNLQ AIEPLVKGAV ETMIEKHDVK
60 70 80 90 100
LENIDIESVP GSWELPQGIR ASIARNTYDA VIGIGVLIKG STMHFEYISE
110 120 130 140 150
AVVHGLMRVG LDSGVPVILG LLTVLNEEQA LYRAGLNGGH NHGNDWGSAA

VEMGLKALY
Length:159
Mass (Da):17,188
Last modified:May 1, 2000 - v1
Checksum:iADB5F20D5BA74601
GO

Mass spectrometryi

Molecular mass is 17189 Da from positions 1 - 159. Determined by ESI. 1 Publication

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CU329671 Genomic DNA. Translation: CAB52615.1.
PIRiT40440.
RefSeqiNP_595463.1. NM_001021373.2.

Genome annotation databases

EnsemblFungiiSPBC409.13.1; SPBC409.13.1:pep; SPBC409.13.
GeneIDi2541125.
KEGGispo:SPBC409.13.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CU329671 Genomic DNA. Translation: CAB52615.1.
PIRiT40440.
RefSeqiNP_595463.1. NM_001021373.2.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1KYVX-ray2.40A/B/C/D/E1-159[»]
1KYXX-ray2.60A/B/C/D/E1-159[»]
1KYYX-ray2.40A/B/C/D/E1-159[»]
1KZ1X-ray2.00A/B/C/D/E1-159[»]
1KZ4X-ray3.10A/B/C/D/E1-159[»]
1KZ6X-ray2.70A/B/C/D/E1-159[»]
1KZ9X-ray3.10A/B/C/D/E1-159[»]
2A57X-ray2.75A/B/C/D/E1-159[»]
2A58X-ray2.80A/B/C/D/E1-159[»]
2A59X-ray2.70A/B/C/D/E1-159[»]
ProteinModelPortaliQ9UUB1.
SMRiQ9UUB1.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi277640. 4 interactors.
MINTiMINT-4711607.

Proteomic databases

MaxQBiQ9UUB1.
PRIDEiQ9UUB1.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiSPBC409.13.1; SPBC409.13.1:pep; SPBC409.13.
GeneIDi2541125.
KEGGispo:SPBC409.13.

Organism-specific databases

EuPathDBiFungiDB:SPBC409.13.
PomBaseiSPBC409.13. rib4.

Phylogenomic databases

HOGENOMiHOG000229253.
InParanoidiQ9UUB1.
KOiK00794.
OMAiMFGADKG.
OrthoDBiEOG092C573E.
PhylomeDBiQ9UUB1.

Enzyme and pathway databases

UniPathwayiUPA00275; UER00404.
BRENDAi2.5.1.78. 5613.

Miscellaneous databases

EvolutionaryTraceiQ9UUB1.
PROiQ9UUB1.

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 nameiRIB4_SCHPO
AccessioniPrimary (citable) accession number: Q9UUB1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 16, 2003
Last sequence update: May 1, 2000
Last modified: November 2, 2016
This is version 112 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, 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. Schizosaccharomyces pombe
    Schizosaccharomyces pombe: entries and gene names
  4. 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.