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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)DescriptionActionsGraphical viewLength
Metal bindingi38Magnesium or manganese 1By similarity1
Metal bindingi38Magnesium or manganese 2By similarity1
Binding sitei42SubstrateBy similarity1
Sitei136Essential for catalytic activity1
Metal bindingi153Magnesium or manganese 2By similarity1
Binding sitei174SubstrateBy similarity1
Sitei174Essential for catalytic activity1

GO - Molecular functioni

  • 3,4-dihydroxy-2-butanone-4-phosphate synthase activity Source: EcoCyc
  • 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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
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)DescriptionActionsGraphical viewLength
Mutagenesisi33D → S: Loss of activity. 1 Publication1
Mutagenesisi35E → S: Reduces activity by 85%. 1 Publication1
Mutagenesisi37R → E: Loss of activity. 1 Publication1
Mutagenesisi38E → S: Loss of activity. 1 Publication1
Mutagenesisi40E → S: Loss of activity. 1 Publication1
Mutagenesisi42D → S: Loss of activity. 1 Publication1
Mutagenesisi67C → S: Reduces activity by 80%. 1 Publication1
Mutagenesisi107T → S: Loss of activity. 1 Publication1
Mutagenesisi110S → A: Reduces activity by 85%. 1 Publication1
Mutagenesisi113D → S: Reduces activity by 88%. 1 Publication1
Mutagenesisi117T → A: Reduces activity by 75%. 1 Publication1
Mutagenesisi136H → S: Loss of activity. 1 Publication1
Mutagenesisi150R → S: Loss of activity. 1 Publication1
Mutagenesisi153H → S: Loss of activity. 1 Publication1
Mutagenesisi155E → S: Reduces activity by 83%. 1 Publication1
Mutagenesisi174E → S: Loss of activity. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001517971 – 2173,4-dihydroxy-2-butanone 4-phosphate synthaseAdd BLAST217

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

Protein-protein interaction databases

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

Structurei

Secondary structure

1217
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi6 – 9Combined sources4
Helixi12 – 24Combined sources13
Beta strandi29 – 33Combined sources5
Beta strandi34 – 36Combined sources3
Beta strandi40 – 46Combined sources7
Turni47 – 49Combined sources3
Helixi52 – 61Combined sources10
Beta strandi67 – 70Combined sources4
Helixi72 – 77Combined sources6
Beta strandi90 – 92Combined sources3
Beta strandi95 – 97Combined sources3
Beta strandi99 – 104Combined sources6
Beta strandi106 – 108Combined sources3
Helixi111 – 122Combined sources12
Helixi128 – 130Combined sources3
Beta strandi131 – 141Combined sources11
Helixi146 – 148Combined sources3
Helixi153 – 163Combined sources11
Beta strandi170 – 176Combined sources7
Beta strandi180 – 182Combined sources3
Helixi185 – 194Combined sources10
Beta strandi198 – 201Combined sources4
Helixi202 – 212Combined sources11

3D structure databases

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

Miscellaneous databases

EvolutionaryTraceiP0A7J0.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni37 – 38Substrate bindingBy similarity2
Regioni150 – 154Substrate bindingBy similarity5

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)DescriptionActionsGraphical viewLength
Sequence conflicti120 – 123AAIA → SDS in AAA23996 (PubMed:1917833).Curated4
Sequence conflicti211 – 217AHERKAS → HMSVKPAENRCLIYCLNQET EVVAGFGFYFSLLCKMLIPL LFL in AAA23996 (PubMed:1917833).Curated7

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
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1G57X-ray1.40A/B3-217[»]
1G58X-ray1.55A/B3-217[»]
1IEZNMR-A1-217[»]
ProteinModelPortaliP0A7J0.
SMRiP0A7J0.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4260672. 13 interactors.
DIPiDIP-35934N.
IntActiP0A7J0. 26 interactors.
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: November 2, 2016
This is version 98 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.