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Protein

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

Gene

ribB

Organism
Methylobacterium extorquens (strain PA1)
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)
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 bindingi49Magnesium or manganese 1UniRule annotation1
Metal bindingi49Magnesium or manganese 2UniRule annotation1
Binding sitei53SubstrateUniRule annotation1
Sitei147Essential for catalytic activityUniRule annotation1
Metal bindingi164Magnesium or manganese 2UniRule annotation1
Binding sitei185SubstrateUniRule annotation1
Sitei185Essential 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

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:Mext_2991Imported
OrganismiMethylobacterium extorquens (strain PA1)Imported
Taxonomic identifieri419610 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhizobialesMethylobacteriaceaeMethylobacterium
Proteomesi
  • UP000008546 Componenti: Chromosome

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi419610.Mext_2991.

Structurei

3D structure databases

ProteinModelPortaliA9W6U8.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini232 – 374GTP_cyclohydro2InterPro annotationAdd BLAST143

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni48 – 49Substrate bindingUniRule annotation2
Regioni161 – 165Substrate 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

eggNOGiENOG4105C66. Bacteria.
COG0108. LUCA.
COG0807. LUCA.
HOGENOMiHOG000115440.
KOiK14652.
OMAiVAIYMRG.
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.

A9W6U8-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MDGGSSIGVT TLFEPLNETK PVPHCSVTEA IEAFARGEIV VVTDDDDREN
60 70 80 90 100
EGDLVVAASL CTPEKMAFII RNTCGIVCAP ITLDEARRLH LDPMVASNDA
110 120 130 140 150
PLGTAFTVTV DVRHGLTTGI SAEQRCNTVR ALANGNMGAG DFVRPGHVFP
160 170 180 190 200
LIARDGGVLM RSGHTEAAVD LCKLAGLPPV GVICELANDD GTVMKGPQID
210 220 230 240 250
AFSEQHNLKR VSVADLIAYR QARDRLVERV GTFPVKTEFG AMTGYAYVTP
260 270 280 290 300
FEPIQQFAFV HGAIGDGRNM PVRLHRSNVV ADVIEGGGQI ESVMRRFAKE
310 320 330 340 350
GRGILVYLRD GTAGVPLNRY AEEEGAEAQR VRQWREVGLG AQILRDLGVV
360 370 380
SIRNLSSSSR SYVGLSGFGI ELVSDEPLEG
Length:380
Mass (Da):40,799
Last modified:February 5, 2008 - v1
Checksum:iBAD96E7E572BA0F6
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000908 Genomic DNA. Translation: ABY31380.1.

Genome annotation databases

EnsemblBacteriaiABY31380; ABY31380; Mext_2991.
KEGGimex:Mext_2991.
PATRICi22536554. VBIMetExt98426_3026.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000908 Genomic DNA. Translation: ABY31380.1.

3D structure databases

ProteinModelPortaliA9W6U8.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi419610.Mext_2991.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABY31380; ABY31380; Mext_2991.
KEGGimex:Mext_2991.
PATRICi22536554. VBIMetExt98426_3026.

Phylogenomic databases

eggNOGiENOG4105C66. Bacteria.
COG0108. LUCA.
COG0807. LUCA.
HOGENOMiHOG000115440.
KOiK14652.
OMAiVAIYMRG.
OrthoDBiPOG091H008U.

Enzyme and pathway databases

UniPathwayiUPA00275; UER00399.

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 nameiA9W6U8_METEP
AccessioniPrimary (citable) accession number: A9W6U8
Entry historyiIntegrated into UniProtKB/TrEMBL: February 5, 2008
Last sequence update: February 5, 2008
Last modified: February 15, 2017
This is version 73 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.