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Protein

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

Gene

ribB

Organism
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Status
Reviewed-Annotation score: Annotation score: 3 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.UniRule annotation

Catalytic activityi

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

Cofactori

Mg2+UniRule annotation, Mn2+UniRule annotationNote: Binds 2 divalent metal cations per subunit. Magnesium or manganese.UniRule annotation

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.UniRule annotation
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 1UniRule annotation
Metal bindingi38 – 381Magnesium or manganese 2UniRule annotation
Binding sitei42 – 421SubstrateUniRule annotation
Sitei136 – 1361Essential for catalytic activityUniRule annotation
Metal bindingi153 – 1531Magnesium or manganese 2UniRule annotation
Binding sitei174 – 1741SubstrateUniRule annotation
Sitei174 – 1741Essential for catalytic activityUniRule annotation

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Lyase

Keywords - Biological processi

Riboflavin biosynthesis

Keywords - Ligandi

Magnesium, Manganese, Metal-binding

Enzyme and pathway databases

BioCyciSENT99287:GCTI-3215-MONOMER.
BRENDAi4.1.99.12. 5542.
UniPathwayiUPA00275; UER00399.

Names & Taxonomyi

Protein namesi
Recommended name:
3,4-dihydroxy-2-butanone 4-phosphate synthaseUniRule annotation (EC:4.1.99.12UniRule annotation)
Short name:
DHBP synthaseUniRule annotation
Gene namesi
Name:ribBUniRule annotation
Ordered Locus Names:STM3195
OrganismiSalmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Taxonomic identifieri99287 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeSalmonella
Proteomesi
  • UP000001014 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 2172173,4-dihydroxy-2-butanone 4-phosphate synthasePRO_0000151810Add
BLAST

Proteomic databases

PaxDbiP66032.
PRIDEiP66032.

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi99287.STM3195.

Structurei

Secondary structure

1
217
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi12 – 2413Combined sources
Beta strandi29 – 324Combined sources
Turni35 – 384Combined sources
Beta strandi41 – 466Combined sources
Turni47 – 493Combined sources
Helixi52 – 6110Combined sources
Beta strandi67 – 704Combined sources
Helixi72 – 776Combined sources
Beta strandi99 – 1046Combined sources
Beta strandi106 – 1083Combined sources
Helixi111 – 12212Combined sources
Helixi128 – 1303Combined sources
Beta strandi131 – 14111Combined sources
Helixi146 – 1483Combined sources
Helixi153 – 16412Combined sources
Beta strandi170 – 1767Combined sources
Beta strandi180 – 1823Combined sources
Helixi185 – 19410Combined sources
Beta strandi198 – 2014Combined sources
Helixi202 – 2109Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3LQUX-ray2.52A/B1-217[»]
3LRJX-ray2.80A/B/C/D1-217[»]
3LS6X-ray1.86A/B1-217[»]
ProteinModelPortaliP66032.
SMRiP66032. Positions 1-217.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP66032.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni37 – 382Substrate bindingUniRule annotation
Regioni150 – 1545Substrate bindingUniRule annotation

Sequence similaritiesi

Belongs to the DHBP synthase family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105C66. Bacteria.
COG0108. LUCA.
HOGENOMiHOG000115444.
KOiK02858.
OMAiQMAKLIR.
OrthoDBiEOG679TK8.
PhylomeDBiP66032.

Family and domain databases

Gene3Di3.90.870.10. 1 hit.
HAMAPiMF_00180. RibB.
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.

P66032-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNQTLLSSFG TPFERVELAL DALREGRGVM VLDDEDRENE GDMIFPAETM
60 70 80 90 100
TVEQMALTIR HGSGIVCLCI TEDRRKQLDL PMMVENNTSA YGTGFTVTIE
110 120 130 140 150
AAEGVTTGVS AADRVTTVRA AIKDGAKPSD LNRPGHVFPL RAQAGGVLTR
160 170 180 190 200
GGHTEATIDL MTLAGFKPAG VLCELTNDDG TMARAPECIA FAGQHNMAVV
210
TIEDLVAYRQ AHERKAS
Length:217
Mass (Da):23,310
Last modified:October 11, 2004 - v1
Checksum:iEE07D4C93C3F4EB7
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE006468 Genomic DNA. Translation: AAL22069.1.
RefSeqiNP_462110.1. NC_003197.1.
WP_001076978.1. NC_003197.1.

Genome annotation databases

EnsemblBacteriaiAAL22069; AAL22069; STM3195.
GeneIDi1254718.
KEGGistm:STM3195.
PATRICi32385164. VBISalEnt20916_3389.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE006468 Genomic DNA. Translation: AAL22069.1.
RefSeqiNP_462110.1. NC_003197.1.
WP_001076978.1. NC_003197.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3LQUX-ray2.52A/B1-217[»]
3LRJX-ray2.80A/B/C/D1-217[»]
3LS6X-ray1.86A/B1-217[»]
ProteinModelPortaliP66032.
SMRiP66032. Positions 1-217.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi99287.STM3195.

Proteomic databases

PaxDbiP66032.
PRIDEiP66032.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAL22069; AAL22069; STM3195.
GeneIDi1254718.
KEGGistm:STM3195.
PATRICi32385164. VBISalEnt20916_3389.

Phylogenomic databases

eggNOGiENOG4105C66. Bacteria.
COG0108. LUCA.
HOGENOMiHOG000115444.
KOiK02858.
OMAiQMAKLIR.
OrthoDBiEOG679TK8.
PhylomeDBiP66032.

Enzyme and pathway databases

UniPathwayiUPA00275; UER00399.
BioCyciSENT99287:GCTI-3215-MONOMER.
BRENDAi4.1.99.12. 5542.

Miscellaneous databases

EvolutionaryTraceiP66032.

Family and domain databases

Gene3Di3.90.870.10. 1 hit.
HAMAPiMF_00180. RibB.
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...

Publicationsi

  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: LT2 / SGSC1412 / ATCC 700720.

Entry informationi

Entry nameiRIBB_SALTY
AccessioniPrimary (citable) accession number: P66032
Secondary accession number(s): Q8XES0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 11, 2004
Last sequence update: October 11, 2004
Last modified: November 11, 2015
This is version 71 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, 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

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.