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Protein

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

Gene

ribB

Organism
Ralstonia pickettii (strain 12D)
Status
Unreviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

Functioni

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

Catalytic activityi

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

Cofactori

Protein has several cofactor binding sites:
  • Mg2+UniRule annotation, Mn2+UniRule annotationNote: Binds 2 divalent metal cations per subunit. Magnesium or manganese.UniRule annotation
  • Mn2+SAAS 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 annotationSAAS annotation
Proteins known to be involved in this subpathway in this organism are:
  1. 3,4-dihydroxy-2-butanone 4-phosphate synthase (ribB), 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 bindingi28Magnesium or manganese 1UniRule annotation1
Metal bindingi28Magnesium or manganese 2UniRule annotation1
Binding sitei32SubstrateUniRule annotation1
Sitei126Essential for catalytic activityUniRule annotation1
Metal bindingi143Magnesium or manganese 2UniRule annotation1
Binding sitei164SubstrateUniRule annotation1
Sitei164Essential for catalytic activityUniRule annotation1

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionLyaseUniRule annotation
Biological processRiboflavin biosynthesisUniRule annotationSAAS annotation
LigandMagnesiumUniRule annotationSAAS annotation, ManganeseUniRule annotation, Metal-bindingUniRule annotationSAAS annotation

Enzyme and pathway databases

BioCyciRPIC428406:GH9Y-699-MONOMER.
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:Rpic12D_0706Imported
OrganismiRalstonia pickettii (strain 12D)Imported
Taxonomic identifieri428406 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaBetaproteobacteriaBurkholderialesBurkholderiaceaeRalstonia
Proteomesi
  • UP000008208 Componenti: Chromosome 1

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Structurei

3D structure databases

ProteinModelPortaliC6BE47.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini208 – 361GTP_cyclohydro2InterPro annotationAdd BLAST154

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni27 – 28Substrate bindingUniRule annotation2
Regioni140 – 144Substrate bindingUniRule annotation5

Sequence similaritiesi

Belongs to the DHBP synthase family.UniRule annotation
In the N-terminal section; belongs to the DHBP synthase family.SAAS annotation

Phylogenomic databases

HOGENOMiHOG000115440.
KOiK14652.
OMAiECKLPTE.
OrthoDBiPOG091H008U.

Family and domain databases

Gene3Di3.90.870.10. 1 hit.
HAMAPiMF_00180. RibB. 1 hit.
InterProiView protein in InterPro
IPR017945. DHBP_synth_RibB-like_a/b_dom.
IPR000422. DHBP_synthase_RibB.
IPR032677. GTP_cyclohydro_II.
PfamiView protein in Pfam
PF00926. DHBP_synthase. 1 hit.
PF00925. GTP_cyclohydro2. 1 hit.
SUPFAMiSSF142695. SSF142695. 1 hit.
SSF55821. SSF55821. 1 hit.
TIGRFAMsiTIGR00506. ribB. 1 hit.

Sequencei

Sequence statusi: Complete.

C6BE47-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSIATVEEII AEIRAGRMVI LVDEEDRENE GDLILASDFV TPEAINFMVT
60 70 80 90 100
HARGLVCLTL TEEHCDQLDL PMMASRNGTQ FGTNFTVSIE AAEGVTTGIS
110 120 130 140 150
AADRARTIQV AAAKNAKPSD LVNPGHIFPL RAQKGGVLMR AGHTEAGCDL
160 170 180 190 200
TAMAGLTPAA VICEILKDDG TMARLPDLVE FAEKHGLKIG TIADMIQYRS
210 220 230 240 250
RTESIVERVG ERTMETQFGT FHAVAFRDRA AGRAHLALVK GTPTPDTETL
260 270 280 290 300
VRVHEPLSVL DLLECQRTTH SWSVPAALRA IQAAPTGVVV LLNCGDSADR
310 320 330 340 350
LFTQFSALDA PHERPRTKPD PRIYGIGAQI LKDVGVGKMR VLASPLKLPS
360 370
MVGYDLEVTA YQSMADAPDV TSSASTATH
Length:379
Mass (Da):40,737
Last modified:September 1, 2009 - v1
Checksum:iACA6D44F5D9643BC
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001644 Genomic DNA. Translation: ACS62007.1.
RefSeqiWP_012761450.1. NC_012856.1.

Genome annotation databases

EnsemblBacteriaiACS62007; ACS62007; Rpic12D_0706.
KEGGirpf:Rpic12D_0706.
PATRICi20240400. VBIRalPic57998_1317.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001644 Genomic DNA. Translation: ACS62007.1.
RefSeqiWP_012761450.1. NC_012856.1.

3D structure databases

ProteinModelPortaliC6BE47.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiACS62007; ACS62007; Rpic12D_0706.
KEGGirpf:Rpic12D_0706.
PATRICi20240400. VBIRalPic57998_1317.

Phylogenomic databases

HOGENOMiHOG000115440.
KOiK14652.
OMAiECKLPTE.
OrthoDBiPOG091H008U.

Enzyme and pathway databases

UniPathwayiUPA00275; UER00399.
BioCyciRPIC428406:GH9Y-699-MONOMER.

Family and domain databases

Gene3Di3.90.870.10. 1 hit.
HAMAPiMF_00180. RibB. 1 hit.
InterProiView protein in InterPro
IPR017945. DHBP_synth_RibB-like_a/b_dom.
IPR000422. DHBP_synthase_RibB.
IPR032677. GTP_cyclohydro_II.
PfamiView protein in Pfam
PF00926. DHBP_synthase. 1 hit.
PF00925. GTP_cyclohydro2. 1 hit.
SUPFAMiSSF142695. SSF142695. 1 hit.
SSF55821. SSF55821. 1 hit.
TIGRFAMsiTIGR00506. ribB. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiC6BE47_RALP1
AccessioniPrimary (citable) accession number: C6BE47
Entry historyiIntegrated into UniProtKB/TrEMBL: September 1, 2009
Last sequence update: September 1, 2009
Last modified: February 15, 2017
This is version 58 of the entry and version 1 of the sequence. See complete history.
Entry statusiUnreviewed (UniProtKB/TrEMBL)

Miscellaneousi

Keywords - Technical termi

Complete proteomeImported

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.