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Protein

3,4-dihydroxy-2-butanone 4-phosphate synthase

Gene

ribB

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the conversion of D-ribulose 5-phosphate to formate and 3,4-dihydroxy-2-butanone 4-phosphate.

Catalytic activityi

D-ribulose 5-phosphate = formate + L-3,4-dihydroxybutan-2-one 4-phosphate.

Cofactori

Mg2+1 Publication, Mn2+1 PublicationNote: Binds 2 divalent metal cations per subunit. Magnesium or manganese.1 Publication

Pathwayi: riboflavin biosynthesis

This protein is involved in step 1 of the subpathway that synthesizes 2-hydroxy-3-oxobutyl phosphate from D-ribulose 5-phosphate.
Proteins known to be involved in this subpathway in this organism are:
  1. 3,4-dihydroxy-2-butanone 4-phosphate synthase (ribB)
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 2-hydroxy-3-oxobutyl phosphate from D-ribulose 5-phosphate, the pathway riboflavin biosynthesis and in Cofactor biosynthesis.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi38 – 381Magnesium or manganese 1By similarity
Metal bindingi38 – 381Magnesium or manganese 2By similarity
Binding sitei42 – 421SubstrateBy similarity
Sitei136 – 1361Essential for catalytic activity
Metal bindingi153 – 1531Magnesium or manganese 2By similarity
Binding sitei174 – 1741SubstrateBy similarity
Sitei174 – 1741Essential for catalytic activity

GO - Molecular functioni

  • 3,4-dihydroxy-2-butanone-4-phosphate synthase activity Source: EcoCyc
  • identical protein binding Source: IntAct
  • magnesium ion binding Source: EcoCyc
  • manganese ion binding Source: UniProtKB-HAMAP

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Lyase

Keywords - Biological processi

Riboflavin biosynthesis, Stress response

Keywords - Ligandi

Magnesium, Manganese, Metal-binding

Enzyme and pathway databases

BioCyciEcoCyc:DIOHBUTANONEPSYN-MONOMER.
ECOL316407:JW3009-MONOMER.
MetaCyc:DIOHBUTANONEPSYN-MONOMER.
BRENDAi4.1.99.12. 2026.
UniPathwayiUPA00275; UER00399.

Names & Taxonomyi

Protein namesi
Recommended name:
3,4-dihydroxy-2-butanone 4-phosphate synthase (EC:4.1.99.12)
Short name:
DHBP synthase
Gene namesi
Name:ribB
Synonyms:htrP
Ordered Locus Names:b3041, JW3009
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10465. ribB.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: UniProtKB
  • plasma membrane Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Cell membrane, Membrane

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi33 – 331D → S: Loss of activity. 1 Publication
Mutagenesisi35 – 351E → S: Reduces activity by 85%. 1 Publication
Mutagenesisi37 – 371R → E: Loss of activity. 1 Publication
Mutagenesisi38 – 381E → S: Loss of activity. 1 Publication
Mutagenesisi40 – 401E → S: Loss of activity. 1 Publication
Mutagenesisi42 – 421D → S: Loss of activity. 1 Publication
Mutagenesisi67 – 671C → S: Reduces activity by 80%. 1 Publication
Mutagenesisi107 – 1071T → S: Loss of activity. 1 Publication
Mutagenesisi110 – 1101S → A: Reduces activity by 85%. 1 Publication
Mutagenesisi113 – 1131D → S: Reduces activity by 88%. 1 Publication
Mutagenesisi117 – 1171T → A: Reduces activity by 75%. 1 Publication
Mutagenesisi136 – 1361H → S: Loss of activity. 1 Publication
Mutagenesisi150 – 1501R → S: Loss of activity. 1 Publication
Mutagenesisi153 – 1531H → S: Loss of activity. 1 Publication
Mutagenesisi155 – 1551E → S: Reduces activity by 83%. 1 Publication
Mutagenesisi174 – 1741E → S: Loss of activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 2172173,4-dihydroxy-2-butanone 4-phosphate synthasePRO_0000151797Add
BLAST

Proteomic databases

PaxDbiP0A7J0.
PRIDEiP0A7J0.

Expressioni

Inductioni

Is expressed at all temperatures, but accumulation of transcripts decline with raising temperature. Thus, its expression is repressed by heat shock.

Interactioni

Subunit structurei

Homodimer.2 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
itself4EBI-553653,EBI-553653

GO - Molecular functioni

  • identical protein binding Source: IntAct

Protein-protein interaction databases

BioGridi4260672. 13 interactions.
DIPiDIP-35934N.
IntActiP0A7J0. 26 interactions.
MINTiMINT-1239671.
STRINGi511145.b3041.

Structurei

Secondary structure

1
217
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi6 – 94Combined sources
Helixi12 – 2413Combined sources
Beta strandi29 – 335Combined sources
Beta strandi34 – 363Combined sources
Beta strandi40 – 467Combined sources
Turni47 – 493Combined sources
Helixi52 – 6110Combined sources
Beta strandi67 – 704Combined sources
Helixi72 – 776Combined sources
Beta strandi90 – 923Combined sources
Beta strandi95 – 973Combined sources
Beta strandi99 – 1046Combined sources
Beta strandi106 – 1083Combined sources
Helixi111 – 12212Combined sources
Helixi128 – 1303Combined sources
Beta strandi131 – 14111Combined sources
Helixi146 – 1483Combined sources
Helixi153 – 16311Combined sources
Beta strandi170 – 1767Combined sources
Beta strandi180 – 1823Combined sources
Helixi185 – 19410Combined sources
Beta strandi198 – 2014Combined sources
Helixi202 – 21211Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1G57X-ray1.40A/B3-217[»]
1G58X-ray1.55A/B3-217[»]
1IEZNMR-A1-217[»]
ProteinModelPortaliP0A7J0.
SMRiP0A7J0. Positions 1-217.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0A7J0.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni37 – 382Substrate bindingBy similarity
Regioni150 – 1545Substrate bindingBy similarity

Sequence similaritiesi

Belongs to the DHBP synthase family.Curated

Phylogenomic databases

eggNOGiENOG4105C66. Bacteria.
COG0108. LUCA.
HOGENOMiHOG000115444.
InParanoidiP0A7J0.
KOiK02858.
OMAiQMAKLIR.
PhylomeDBiP0A7J0.

Family and domain databases

Gene3Di3.90.870.10. 1 hit.
HAMAPiMF_00180. RibB. 1 hit.
InterProiIPR017945. DHBP_synth_RibB-like_a/b_dom.
IPR000422. DHBP_synthase_RibB.
[Graphical view]
PfamiPF00926. DHBP_synthase. 1 hit.
[Graphical view]
SUPFAMiSSF55821. SSF55821. 1 hit.
TIGRFAMsiTIGR00506. ribB. 1 hit.

Sequencei

Sequence statusi: Complete.

P0A7J0-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNQTLLSSFG TPFERVENAL AALREGRGVM VLDDEDRENE GDMIFPAETM
60 70 80 90 100
TVEQMALTIR HGSGIVCLCI TEDRRKQLDL PMMVENNTSA YGTGFTVTIE
110 120 130 140 150
AAEGVTTGVS AADRITTVRA AIADGAKPSD LNRPGHVFPL RAQAGGVLTR
160 170 180 190 200
GGHTEATIDL MTLAGFKPAG VLCELTNDDG TMARAPECIE FANKHNMALV
210
TIEDLVAYRQ AHERKAS
Length:217
Mass (Da):23,353
Last modified:June 7, 2005 - v1
Checksum:i6833C120A1442608
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti120 – 1234AAIA → SDS in AAA23996 (PubMed:1917833).Curated
Sequence conflicti211 – 2177AHERKAS → HMSVKPAENRCLIYCLNQET EVVAGFGFYFSLLCKMLIPL LFL in AAA23996 (PubMed:1917833).Curated

Mass spectrometryi

Molecular mass is 23352±2 Da from positions 1 - 217. Determined by ESI. 1 Publication

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M64472 Genomic DNA. Translation: AAA23996.1.
M77129 Genomic DNA. Translation: AAA71879.1.
X66720 Genomic DNA. Translation: CAA47252.1.
U28377 Genomic DNA. Translation: AAA69209.1.
U00096 Genomic DNA. Translation: AAC76077.1.
AP009048 Genomic DNA. Translation: BAE77097.1.
PIRiA38159.
RefSeqiNP_417513.1. NC_000913.3.
WP_001076997.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC76077; AAC76077; b3041.
BAE77097; BAE77097; BAE77097.
GeneIDi947526.
KEGGiecj:JW3009.
eco:b3041.
PATRICi32121494. VBIEscCol129921_3134.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M64472 Genomic DNA. Translation: AAA23996.1.
M77129 Genomic DNA. Translation: AAA71879.1.
X66720 Genomic DNA. Translation: CAA47252.1.
U28377 Genomic DNA. Translation: AAA69209.1.
U00096 Genomic DNA. Translation: AAC76077.1.
AP009048 Genomic DNA. Translation: BAE77097.1.
PIRiA38159.
RefSeqiNP_417513.1. NC_000913.3.
WP_001076997.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1G57X-ray1.40A/B3-217[»]
1G58X-ray1.55A/B3-217[»]
1IEZNMR-A1-217[»]
ProteinModelPortaliP0A7J0.
SMRiP0A7J0. Positions 1-217.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4260672. 13 interactions.
DIPiDIP-35934N.
IntActiP0A7J0. 26 interactions.
MINTiMINT-1239671.
STRINGi511145.b3041.

Proteomic databases

PaxDbiP0A7J0.
PRIDEiP0A7J0.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC76077; AAC76077; b3041.
BAE77097; BAE77097; BAE77097.
GeneIDi947526.
KEGGiecj:JW3009.
eco:b3041.
PATRICi32121494. VBIEscCol129921_3134.

Organism-specific databases

EchoBASEiEB0460.
EcoGeneiEG10465. ribB.

Phylogenomic databases

eggNOGiENOG4105C66. Bacteria.
COG0108. LUCA.
HOGENOMiHOG000115444.
InParanoidiP0A7J0.
KOiK02858.
OMAiQMAKLIR.
PhylomeDBiP0A7J0.

Enzyme and pathway databases

UniPathwayiUPA00275; UER00399.
BioCyciEcoCyc:DIOHBUTANONEPSYN-MONOMER.
ECOL316407:JW3009-MONOMER.
MetaCyc:DIOHBUTANONEPSYN-MONOMER.
BRENDAi4.1.99.12. 2026.

Miscellaneous databases

EvolutionaryTraceiP0A7J0.
PROiP0A7J0.

Family and domain databases

Gene3Di3.90.870.10. 1 hit.
HAMAPiMF_00180. RibB. 1 hit.
InterProiIPR017945. DHBP_synth_RibB-like_a/b_dom.
IPR000422. DHBP_synthase_RibB.
[Graphical view]
PfamiPF00926. DHBP_synthase. 1 hit.
[Graphical view]
SUPFAMiSSF55821. SSF55821. 1 hit.
TIGRFAMsiTIGR00506. ribB. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiRIBB_ECOLI
AccessioniPrimary (citable) accession number: P0A7J0
Secondary accession number(s): P24199, Q2M9F9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 7, 2005
Last sequence update: June 7, 2005
Last modified: September 7, 2016
This is version 97 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, Direct protein sequencing, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  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.