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Protein

6,7-dimethyl-8-ribityllumazine synthase

Gene

RIB4

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's 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.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.1 Publication

Kineticsi

  1. KM=4.0 µM for 5-amino-6-(D-ribitylamino)uracil1 Publication
  2. KM=90 µM for 3,4-dihydroxy-2-butanone 4-phosphate1 Publication
  1. Vmax=15400 nmol/h/mg enzyme1 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.2 Publications
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 sitei98Proton donorSequence analysis1
Binding sitei1235-amino-6-(D-ribitylamino)uracil; via amide nitrogen and carbonyl oxygen1
Binding sitei1371-deoxy-L-glycero-tetrulose 4-phosphate1

GO - Molecular functioni

  • 6,7-dimethyl-8-ribityllumazine synthase activity Source: SGD
  • transferase activity Source: UniProtKB-KW

GO - Biological processi

  • riboflavin biosynthetic process Source: SGD
Complete GO annotation...

Keywords - Molecular functioni

Transferase

Keywords - Biological processi

Riboflavin biosynthesis

Enzyme and pathway databases

BioCyciMetaCyc:YOL143C-MONOMER.
YEAST:YOL143C-MONOMER.
BRENDAi2.5.1.78. 984.
SABIO-RKP50861.
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:RIB4
Ordered Locus Names:YOL143C
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome XV

Organism-specific databases

EuPathDBiFungiDB:YOL143C.
SGDiS000005503. RIB4.

Subcellular locationi

GO - Cellular componenti

  • mitochondrial intermembrane space Source: SGD
  • riboflavin synthase complex Source: InterPro
Complete GO annotation...

Keywords - Cellular componenti

Mitochondrion

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001348571 – 1696,7-dimethyl-8-ribityllumazine synthaseAdd BLAST169

Proteomic databases

MaxQBiP50861.
PRIDEiP50861.
TopDownProteomicsiP50861.

Expressioni

Inductioni

Is constitutively expressed at moderate levels.1 Publication

Interactioni

Subunit structurei

Homopentamer.3 Publications

Protein-protein interaction databases

BioGridi34274. 25 interactors.
DIPiDIP-1931N.
IntActiP50861. 9 interactors.
MINTiMINT-397811.

Structurei

Secondary structure

1169
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi20 – 24Combined sources5
Helixi29 – 45Combined sources17
Helixi50 – 52Combined sources3
Beta strandi53 – 57Combined sources5
Helixi61 – 63Combined sources3
Helixi64 – 77Combined sources14
Beta strandi83 – 92Combined sources10
Beta strandi95 – 97Combined sources3
Helixi98 – 117Combined sources20
Beta strandi124 – 130Combined sources7
Helixi131 – 137Combined sources7
Helixi149 – 164Combined sources16

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1EJBX-ray1.85A/B/C/D/E2-169[»]
ProteinModelPortaliP50861.
SMRiP50861.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP50861.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni61 – 635-amino-6-(D-ribitylamino)uracil binding3
Regioni90 – 925-amino-6-(D-ribitylamino)uracil binding3
Regioni95 – 961-deoxy-L-glycero-tetrulose 4-phosphate binding2

Sequence similaritiesi

Belongs to the DMRL synthase family.Curated

Phylogenomic databases

HOGENOMiHOG000229253.
InParanoidiP50861.
KOiK00794.
OMAiCDTVDQA.
OrthoDBiEOG092C573E.

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.

P50861-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAVKGLGKPD QVYDGSKIRV GIIHARWNRV IIDALVKGAI ERMASLGVEE
60 70 80 90 100
NNIIIETVPG SYELPWGTKR FVDRQAKLGK PLDVVIPIGV LIKGSTMHFE
110 120 130 140 150
YISDSTTHAL MNLQEKVDMP VIFGLLTCMT EEQALARAGI DEAHSMHNHG
160
EDWGAAAVEM AVKFGKNAF
Length:169
Mass (Da):18,556
Last modified:May 30, 2000 - v2
Checksum:i574E847FA6F2860E
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti44A → V in CAA79744 (PubMed:7559556).Curated1
Sequence conflicti51N → K in CAA79744 (PubMed:7559556).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z21620 Genomic DNA. Translation: CAA79744.1.
Z74885 Genomic DNA. Translation: CAA99164.1.
AY558430 Genomic DNA. Translation: AAS56756.1.
BK006948 Genomic DNA. Translation: DAA10642.1.
PIRiS61871.
RefSeqiNP_014498.1. NM_001183397.1.

Genome annotation databases

EnsemblFungiiYOL143C; YOL143C; YOL143C.
GeneIDi854022.
KEGGisce:YOL143C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z21620 Genomic DNA. Translation: CAA79744.1.
Z74885 Genomic DNA. Translation: CAA99164.1.
AY558430 Genomic DNA. Translation: AAS56756.1.
BK006948 Genomic DNA. Translation: DAA10642.1.
PIRiS61871.
RefSeqiNP_014498.1. NM_001183397.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1EJBX-ray1.85A/B/C/D/E2-169[»]
ProteinModelPortaliP50861.
SMRiP50861.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi34274. 25 interactors.
DIPiDIP-1931N.
IntActiP50861. 9 interactors.
MINTiMINT-397811.

Proteomic databases

MaxQBiP50861.
PRIDEiP50861.
TopDownProteomicsiP50861.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYOL143C; YOL143C; YOL143C.
GeneIDi854022.
KEGGisce:YOL143C.

Organism-specific databases

EuPathDBiFungiDB:YOL143C.
SGDiS000005503. RIB4.

Phylogenomic databases

HOGENOMiHOG000229253.
InParanoidiP50861.
KOiK00794.
OMAiCDTVDQA.
OrthoDBiEOG092C573E.

Enzyme and pathway databases

UniPathwayiUPA00275; UER00404.
BioCyciMetaCyc:YOL143C-MONOMER.
YEAST:YOL143C-MONOMER.
BRENDAi2.5.1.78. 984.
SABIO-RKP50861.

Miscellaneous databases

EvolutionaryTraceiP50861.
PROiP50861.

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_YEAST
AccessioniPrimary (citable) accession number: P50861
Secondary accession number(s): D6W1S6, Q08286
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: May 30, 2000
Last modified: November 2, 2016
This is version 144 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 3260 molecules/cell in log phase SD medium.1 Publication

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
  4. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  5. Yeast chromosome XV
    Yeast (Saccharomyces cerevisiae) chromosome XV: entries and gene names

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.