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UniProtKB - P61714 (RISB_ECOLI)

Entry version 135 (17 Jun 2020)
Sequence version 1 (07 Jun 2004)
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Protein

6,7-dimethyl-8-ribityllumazine synthase

Gene

ribE

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score:

Annotation score:4 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.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=4.2 µM for 5-amino-6-(D-ribitylamino)uracil1 Publication
  2. KM=62 µM for 3,4-dihydroxy-2-butanone 4-phosphate1 Publication
  1. Vmax=11800 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.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 (ribE)
  2. Riboflavin synthase (ribC)
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 sitei225-amino-6-(D-ribitylamino)uracilBy similarity1
<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 sitei89Proton donorSequence analysis1
Binding sitei1145-amino-6-(D-ribitylamino)uracil; via amide nitrogen and carbonyl oxygenBy similarity1
Binding sitei1281-deoxy-L-glycero-tetrulose 4-phosphateBy similarity1

<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

Complete GO annotation on QuickGO ...

GO - Biological processi

Complete GO annotation on QuickGO ...

<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		EcoCyc:LUMAZINESYN-MONOMER
ECOL316407:JW0405-MONOMER
MetaCyc:LUMAZINESYN-MONOMER

SABIO-RK: Biochemical Reaction Kinetics Database

More...SABIO-RKi		P61714

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:ribE
Synonyms:ribH, ybaF
Ordered Locus Names:b0415, JW0405
<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>OrganismiEscherichia coli (strain K12)
<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 identifieri83333 [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 lineageiBacteria › Proteobacteria › Gammaproteobacteria › Enterobacterales › Enterobacteriaceae › Escherichia ›
<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
  • UP000000318 <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
  • UP000000625 Componenti: Chromosome

<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

GO - Cellular componenti

Complete GO annotation on QuickGO ...

<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_00001347541 – 1566,7-dimethyl-8-ribityllumazine synthaseAdd BLAST156

Proteomic databases

jPOST - Japan Proteome Standard Repository/Database

More...jPOSTi		P61714

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

More...PaxDbi		P61714

PRoteomics IDEntifications database

More...PRIDEi		P61714

2D gel databases

Two-dimensional polyacrylamide gel electrophoresis database from the Geneva University Hospital

More...SWISS-2DPAGEi		P61714

<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

Forms a hollow icosahedral capsid composed of 60 subunits, probably arranged as a dodecamer of pentamers. Unlike in B.subtilis, does not interact with riboflavin synthase, and the core of the icosahedral capsid is empty.

1 Publication

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGRID)

More...BioGRIDi		4259505, 92 interactors

Database of interacting proteins

More...DIPi		DIP-10711N

Protein interaction database and analysis system

More...IntActi		P61714, 16 interactors

STRING: functional protein association networks

More...STRINGi		511145.b0415

<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

3D structure databases

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

More...SMRi		P61714

Database of comparative protein structure models

More...ModBasei		Search...

<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>Regioni57 – 595-amino-6-(D-ribitylamino)uracil bindingBy similarity3
Regioni81 – 835-amino-6-(D-ribitylamino)uracil bindingBy similarity3
Regioni86 – 871-deoxy-L-glycero-tetrulose 4-phosphate bindingBy similarity2

<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

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...eggNOGi		ENOG4108UTT Bacteria
COG0054 LUCA

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...HOGENOMi		CLU_089358_1_1_6

InParanoid: Eukaryotic Ortholog Groups

More...InParanoidi		P61714

KEGG Orthology (KO)

More...KOi		K00794

Database for complete collections of gene phylogenies

More...PhylomeDBi		P61714

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.

P61714-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MNIIEANVAT PDARVAITIA RFNNFINDSL LEGAIDALKR IGQVKDENIT 
        60         70         80         90        100
VVWVPGAYEL PLAAGALAKT GKYDAVIALG TVIRGGTAHF EYVAGGASNG 
       110        120        130        140        150
LAHVAQDSEI PVAFGVLTTE SIEQAIERAG TKAGNKGAEA ALTALEMINV 

LKAIKA
Length:156
Mass (Da):16,157
Last modified:June 7, 2004 - v1
<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:i1F8504B2892195C7
GO

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
X64395 Genomic DNA Translation: CAA45736.1
U82664 Genomic DNA Translation: AAB40171.1
U00096 Genomic DNA Translation: AAC73518.1
AP009048 Genomic DNA Translation: BAE76195.1

Protein sequence database of the Protein Information Resource

More...PIRi		S26202

NCBI Reference Sequences

More...RefSeqi		NP_414949.1, NC_000913.3
WP_001021161.1, NZ_STEB01000007.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...EnsemblBacteriai		AAC73518; AAC73518; b0415
BAE76195; BAE76195; BAE76195

Database of genes from NCBI RefSeq genomes

More...GeneIDi		42820627
946453

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...KEGGi		ecj:JW0405
eco:b0415

Pathosystems Resource Integration Center (PATRIC)

More...PATRICi		fig|1411691.4.peg.1862

<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
X64395 Genomic DNA Translation: CAA45736.1
U82664 Genomic DNA Translation: AAB40171.1
U00096 Genomic DNA Translation: AAC73518.1
AP009048 Genomic DNA Translation: BAE76195.1
PIRiS26202
RefSeqiNP_414949.1, NC_000913.3
WP_001021161.1, NZ_STEB01000007.1

3D structure databases

SMRiP61714
ModBaseiSearch...

Protein-protein interaction databases

BioGRIDi4259505, 92 interactors
DIPiDIP-10711N
IntActiP61714, 16 interactors
STRINGi511145.b0415

2D gel databases

SWISS-2DPAGEiP61714

Proteomic databases

jPOSTiP61714
PaxDbiP61714
PRIDEiP61714

Genome annotation databases

EnsemblBacteriaiAAC73518; AAC73518; b0415
BAE76195; BAE76195; BAE76195
GeneIDi42820627
946453
KEGGiecj:JW0405
eco:b0415
PATRICifig|1411691.4.peg.1862

Organism-specific databases

EchoBASE - an integrated post-genomic database for E. coli

More...EchoBASEi		EB1298

Phylogenomic databases

eggNOGiENOG4108UTT Bacteria
COG0054 LUCA
HOGENOMiCLU_089358_1_1_6
InParanoidiP61714
KOiK00794
PhylomeDBiP61714

Enzyme and pathway databases

UniPathwayiUPA00275;UER00404
BioCyciEcoCyc:LUMAZINESYN-MONOMER
ECOL316407:JW0405-MONOMER
MetaCyc:LUMAZINESYN-MONOMER
SABIO-RKiP61714

Miscellaneous databases

Protein Ontology

More...PROi		PR:P61714

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 nameiRISB_ECOLI
<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: P61714
Secondary accession number(s): P25540, P77114, Q2MC11
<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: June 7, 2004
Last sequence update: June 7, 2004
Last modified: June 17, 2020
This is version 135 of the entry and version 1 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 programProkaryotic 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

Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. SIMILARITY comments
    Index of protein domains and families
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