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Entry version 170 (17 Jun 2020)
Sequence version 2 (30 May 2000)
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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

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the 'correct annotation' for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the 'protein existence' evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>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

Miscellaneous

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

<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes the catalytic activity of an enzyme, i.e. a chemical reaction that the enzyme catalyzes.<p><a href='/help/catalytic_activity' target='_top'>More...</a></p>Catalytic activityi

<p>This subsection of the 'Function' section describes biophysical and chemical properties, such as maximal absorption, kinetic parameters, pH dependence, redox potentials and temperature dependence.<p><a href='/help/biophysicochemical_properties' target='_top'>More...</a></p>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

<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">'Function'</a> section describes the metabolic pathway(s) associated with a protein.<p><a href='/help/pathway' target='_top'>More...</a></p>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
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes the interaction between a single amino acid and another chemical entity. Priority is given to the annotation of physiological ligands.<p><a href='/help/binding' target='_top'>More...</a></p>Binding sitei275-amino-6-(D-ribitylamino)uracil1
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section is used for enzymes and indicates the residues directly involved in catalysis.<p><a href='/help/act_site' target='_top'>More...</a></p>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

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

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

GO - Biological processi

  • riboflavin biosynthetic process Source: SGD

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

Molecular functionTransferase
Biological processRiboflavin biosynthesis

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...
BioCyci
MetaCyc:YOL143C-MONOMER
YEAST:YOL143C-MONOMER

BRENDA Comprehensive Enzyme Information System

More...
BRENDAi
2.5.1.78 984

SABIO-RK: Biochemical Reaction Kinetics Database

More...
SABIO-RKi
P50861

UniPathway: a resource for the exploration and annotation of metabolic pathways

More...
UniPathwayi
UPA00275;UER00404

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>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
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: 'Name', 'Synonyms', 'Ordered locus names' and 'ORF names'.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:RIB4
Ordered Locus Names:YOL143C
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the 'taxonomic identifier' or 'taxid'.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri559292 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
  • UP000002311 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes%5Fmanual">proteome</a> can consist of several components.<br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome XV

Organism-specific databases

Eukaryotic Pathogen Database Resources

More...
EuPathDBi
FungiDB:YOL143C

Saccharomyces Genome Database

More...
SGDi
S000005503 RIB4

<p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cell wall Cytoskeleton Vacuole Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte & Seán O’Donoghue; Source: COMPARTMENTS

Keywords - Cellular componenti

Mitochondrion

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'PTM / Processing' section describes the extent of a polypeptide chain in the mature protein following processing or proteolytic cleavage.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00001348571 – 1696,7-dimethyl-8-ribityllumazine synthaseAdd BLAST169

Proteomic databases

MaxQB - The MaxQuant DataBase

More...
MaxQBi
P50861

PaxDb, a database of protein abundance averages across all three domains of life

More...
PaxDbi
P50861

PRoteomics IDEntifications database

More...
PRIDEi
P50861

Consortium for Top Down Proteomics

More...
TopDownProteomicsi
P50861

<p>This section provides information on the expression of a gene at the mRNA or protein level in cells or in tissues of multicellular organisms.<p><a href='/help/expression_section' target='_top'>More...</a></p>Expressioni

<p>This subsection of the 'Expression' section reports the experimentally proven effects of inducers and repressors (usually chemical compounds or environmental factors) on the level of protein (or mRNA) expression (up-regulation, down-regulation, constitutive expression).<p><a href='/help/induction' target='_top'>More...</a></p>Inductioni

Is constitutively expressed at moderate levels.1 Publication

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

<p>This subsection of the <a href="http://www.uniprot.org/help/interaction%5Fsection">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function%5Fsection">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Homopentamer.

3 Publications

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGRID)

More...
BioGRIDi
34274, 30 interactors

Database of interacting proteins

More...
DIPi
DIP-1931N

Protein interaction database and analysis system

More...
IntActi
P50861, 9 interactors

Molecular INTeraction database

More...
MINTi
P50861

STRING: functional protein association networks

More...
STRINGi
4932.YOL143C

Miscellaneous databases

RNAct, Protein-RNA interaction predictions for model organisms.

More...
RNActi
P50861 protein

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

Secondary structure

1169
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

SWISS-MODEL Repository - a database of annotated 3D protein structure models

More...
SMRi
P50861

Database of comparative protein structure models

More...
ModBasei
Search...

Protein Data Bank in Europe - Knowledge Base

More...
PDBe-KBi
Search...

Miscellaneous databases

Relative evolutionary importance of amino acids within a protein sequence

More...
EvolutionaryTracei
P50861

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'Family and Domains' section describes a region of interest that cannot be described in other subsections.<p><a href='/help/region' target='_top'>More...</a></p>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

<p>This subsection of the 'Family and domains' section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Belongs to the DMRL synthase family.Curated

Phylogenomic databases

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
CLU_089358_2_2_1

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
P50861

KEGG Orthology (KO)

More...
KOi
K00794

Identification of Orthologs from Complete Genome Data

More...
OMAi
CQGVTQG

Family and domain databases

Conserved Domains Database

More...
CDDi
cd09209 Lumazine_synthase-I, 1 hit

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
3.40.50.960, 1 hit

HAMAP database of protein families

More...
HAMAPi
MF_00178 Lumazine_synth, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR034964 LS
IPR002180 LS/RS
IPR036467 LS/RS_sf

The PANTHER Classification System

More...
PANTHERi
PTHR21058 PTHR21058, 1 hit

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF00885 DMRL_synthase, 1 hit

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF52121 SSF52121, 1 hit

TIGRFAMs; a protein family database

More...
TIGRFAMsi
TIGR00114 lumazine-synth, 1 hit

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence%5Flength">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>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
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:i574E847FA6F2860E
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'Sequence' section reports difference(s) between the canonical sequence (displayed by default in the entry) and the different sequence submissions merged in the entry. These various submissions may originate from different sequencing projects, different types of experiments, or different biological samples. Sequence conflicts are usually of unknown origin.<p><a href='/help/conflict' target='_top'>More...</a></p>Sequence conflicti44A → V in CAA79744 (PubMed:7559556).Curated1
Sequence conflicti51N → K in CAA79744 (PubMed:7559556).Curated1

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...
EMBLi

GenBank nucleotide sequence database

More...
GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
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

Protein sequence database of the Protein Information Resource

More...
PIRi
S61871

NCBI Reference Sequences

More...
RefSeqi
NP_014498.1, NM_001183397.1

Genome annotation databases

Ensembl fungal genome annotation project

More...
EnsemblFungii
YOL143C_mRNA; YOL143C; YOL143C

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
854022

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
sce:YOL143C

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>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:

Protein Data Bank Europe

More...
PDBei

Protein Data Bank RCSB

More...
RCSB PDBi

Protein Data Bank Japan

More...
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1EJBX-ray1.85A/B/C/D/E2-169[»]
SMRiP50861
ModBaseiSearch...
PDBe-KBiSearch...

Protein-protein interaction databases

BioGRIDi34274, 30 interactors
DIPiDIP-1931N
IntActiP50861, 9 interactors
MINTiP50861
STRINGi4932.YOL143C

Proteomic databases

MaxQBiP50861
PaxDbiP50861
PRIDEiP50861
TopDownProteomicsiP50861

Genome annotation databases

EnsemblFungiiYOL143C_mRNA; YOL143C; YOL143C
GeneIDi854022
KEGGisce:YOL143C

Organism-specific databases

EuPathDBiFungiDB:YOL143C
SGDiS000005503 RIB4

Phylogenomic databases

HOGENOMiCLU_089358_2_2_1
InParanoidiP50861
KOiK00794
OMAiCQGVTQG

Enzyme and pathway databases

UniPathwayiUPA00275;UER00404
BioCyciMetaCyc:YOL143C-MONOMER
YEAST:YOL143C-MONOMER
BRENDAi2.5.1.78 984
SABIO-RKiP50861

Miscellaneous databases

EvolutionaryTraceiP50861

Protein Ontology

More...
PROi
PR:P50861
RNActiP50861 protein

Family and domain databases

CDDicd09209 Lumazine_synthase-I, 1 hit
Gene3Di3.40.50.960, 1 hit
HAMAPiMF_00178 Lumazine_synth, 1 hit
InterProiView protein in InterPro
IPR034964 LS
IPR002180 LS/RS
IPR036467 LS/RS_sf
PANTHERiPTHR21058 PTHR21058, 1 hit
PfamiView protein in Pfam
PF00885 DMRL_synthase, 1 hit
SUPFAMiSSF52121 SSF52121, 1 hit
TIGRFAMsiTIGR00114 lumazine-synth, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

More...
ProtoNeti
Search...

MobiDB: a database of protein disorder and mobility annotations

More...
MobiDBi
Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the 'Entry information' section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiRIB4_YEAST
<p>This subsection of the 'Entry information' section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called 'Primary (citable) accession number'.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: P50861
Secondary accession number(s): D6W1S6, Q08286
<p>This subsection of the 'Entry information' section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification ('Last modified'). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: May 30, 2000
Last modified: June 17, 2020
This is version 170 of the entry and version 2 of the sequence. See complete history.
<p>This subsection of the 'Entry information' section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

<p>This section contains any relevant information that doesn't fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

3D-structure, 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
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