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Protein

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

Gene

RIB3

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 4 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.By similarity

Catalytic activityi

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

Cofactori

Mg2+By similarity, Mn2+By similarityNote: Binds 2 divalent metal cations per subunit. Magnesium or manganese.By similarity

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 (RIB3)
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 bindingi27Magnesium or manganese 1By similarity1
Metal bindingi27Magnesium or manganese 2By similarity1
Binding sitei31SubstrateBy similarity1
Sitei131Essential for catalytic activityBy similarity1
Metal bindingi148Magnesium or manganese 2By similarity1
Binding sitei169SubstrateBy similarity1
Sitei169Essential for catalytic activityBy similarity1

GO - Molecular functioni

  • 3,4-dihydroxy-2-butanone-4-phosphate synthase activity Source: SGD
  • metal ion binding Source: UniProtKB-KW

GO - Biological processi

  • aerobic respiration Source: SGD
  • riboflavin biosynthetic process Source: SGD
Complete GO annotation...

Keywords - Molecular functioni

Lyase

Keywords - Biological processi

Riboflavin biosynthesis

Keywords - Ligandi

Magnesium, Manganese, Metal-binding

Enzyme and pathway databases

BioCyciYEAST:MONOMER3O-89.
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:RIB3
Ordered Locus Names:YDR487C
ORF Names:D8035.30
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome IV

Organism-specific databases

EuPathDBiFungiDB:YDR487C.
SGDiS000002895. RIB3.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: SGD
  • mitochondrial intermembrane space Source: SGD
Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001518291 – 2083,4-dihydroxy-2-butanone 4-phosphate synthaseAdd BLAST208

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei3PhosphothreonineCombined sources1

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiQ99258.
PRIDEiQ99258.

PTM databases

iPTMnetiQ99258.

Interactioni

Subunit structurei

Homodimer.By similarity

Protein-protein interaction databases

BioGridi32539. 13 interactors.
DIPiDIP-4316N.
IntActiQ99258. 2 interactors.
MINTiMINT-477205.

Structurei

3D structure databases

ProteinModelPortaliQ99258.
SMRiQ99258.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni26 – 27Substrate bindingBy similarity2
Regioni145 – 149Substrate bindingBy similarity5

Sequence similaritiesi

Belongs to the DHBP synthase family.Curated

Phylogenomic databases

HOGENOMiHOG000115444.
InParanoidiQ99258.
KOiK02858.
OMAiQMAKLIR.
OrthoDBiEOG092C42BA.

Family and domain databases

Gene3Di3.90.870.10. 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.

Q99258-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MFTPIDQAIE HFKQNKFVIV MDDAGRENEG DLICAAENVS TEQMAFLVRH
60 70 80 90 100
SSGYVCAPMT NAIADKLDLP LLRTGMKFES NDDDRHGTAY TITVDVAQGT
110 120 130 140 150
TTGISAHDRS MTCRALADSS STPKSFLKPG HICPLRAADG GVLQRRGHTE
160 170 180 190 200
AGVDLCKLSG LSPVAVIGEL VNDDEQGTMM RLNDCQAFGK KHGIPLISIE

ELAQYLKK
Length:208
Mass (Da):22,568
Last modified:November 1, 1996 - v1
Checksum:iECA30183FAFCBA9E
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z21619 Genomic DNA. Translation: CAA79743.1.
U33050 Genomic DNA. Translation: AAB64927.1.
AY557810 Genomic DNA. Translation: AAS56136.1.
BK006938 Genomic DNA. Translation: DAA12320.1.
PIRiS50973.
RefSeqiNP_010775.1. NM_001180795.1.

Genome annotation databases

EnsemblFungiiYDR487C; YDR487C; YDR487C.
GeneIDi852098.
KEGGisce:YDR487C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z21619 Genomic DNA. Translation: CAA79743.1.
U33050 Genomic DNA. Translation: AAB64927.1.
AY557810 Genomic DNA. Translation: AAS56136.1.
BK006938 Genomic DNA. Translation: DAA12320.1.
PIRiS50973.
RefSeqiNP_010775.1. NM_001180795.1.

3D structure databases

ProteinModelPortaliQ99258.
SMRiQ99258.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi32539. 13 interactors.
DIPiDIP-4316N.
IntActiQ99258. 2 interactors.
MINTiMINT-477205.

PTM databases

iPTMnetiQ99258.

Proteomic databases

MaxQBiQ99258.
PRIDEiQ99258.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYDR487C; YDR487C; YDR487C.
GeneIDi852098.
KEGGisce:YDR487C.

Organism-specific databases

EuPathDBiFungiDB:YDR487C.
SGDiS000002895. RIB3.

Phylogenomic databases

HOGENOMiHOG000115444.
InParanoidiQ99258.
KOiK02858.
OMAiQMAKLIR.
OrthoDBiEOG092C42BA.

Enzyme and pathway databases

UniPathwayiUPA00275; UER00399.
BioCyciYEAST:MONOMER3O-89.

Miscellaneous databases

PROiQ99258.

Family and domain databases

Gene3Di3.90.870.10. 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 nameiRIB3_YEAST
AccessioniPrimary (citable) accession number: Q99258
Secondary accession number(s): D6VTB0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 1, 2000
Last sequence update: November 1, 1996
Last modified: November 2, 2016
This is version 136 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 5460 molecules/cell in log phase SD medium.1 Publication

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. SIMILARITY comments
    Index of protein domains and families
  3. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  4. Yeast chromosome IV
    Yeast (Saccharomyces cerevisiae) chromosome IV: entries and gene names

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.