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Protein

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

Gene

ribB

Organism
Methylobacterium extorquens (strain PA1)
Status
Unreviewed-Annotation score: -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 annotationSAAS 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

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
OMAiGCTTGIS
OrthoDBiPOG091H008U

Family and domain databases

Gene3Di3.40.50.10990, 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
IPR036144 RibA-like_sf
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

Similar proteinsi

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: April 25, 2018
This is version 80 of the entry and version 1 of the sequence. See complete history.
Entry statusiUnreviewed (UniProtKB/TrEMBL)

Miscellaneousi

Keywords - Technical termi

Complete proteomeImported

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