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Protein

Riboflavin biosynthesis protein RibBA

Gene

ribBA

Organism
Desulfovibrio desulfuricans (strain ATCC 27774 / DSM 6949)
Status
Unreviewed-Annotation score: Annotation score: 4 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
Catalyzes the conversion of GTP to 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate (DARP), formate and pyrophosphate.UniRule annotationSAAS annotation

Catalytic activityi

D-ribulose 5-phosphate = formate + L-3,4-dihydroxybutan-2-one 4-phosphate.UniRule annotation
GTP + 3 H2O = formate + 2,5-diamino-6-hydroxy-4-(5-phospho-D-ribosylamino)pyrimidine + diphosphate.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
  • Zn2+UniRule annotationSAAS annotationNote: Binds 1 zinc ion per subunit.UniRule annotationSAAS annotation

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi28 – 281Magnesium or manganese 1UniRule annotation
Metal bindingi28 – 281Magnesium or manganese 2UniRule annotation
Binding sitei32 – 321D-ribulose 5-phosphateUniRule annotation
Sitei126 – 1261Essential for DHBP synthase activityUniRule annotation
Binding sitei164 – 1641D-ribulose 5-phosphateUniRule annotation
Sitei164 – 1641Essential for DHBP synthase activityUniRule annotation
Metal bindingi258 – 2581Zinc; catalyticUniRule annotation
Metal bindingi269 – 2691Zinc; catalyticUniRule annotation
Metal bindingi271 – 2711Zinc; catalyticUniRule annotation
Binding sitei274 – 2741GTPUniRule annotation
Binding sitei318 – 3181GTPUniRule annotation
Active sitei330 – 3301Proton acceptor; for GTP cyclohydrolase activityUniRule annotation
Active sitei332 – 3321Nucleophile; for GTP cyclohydrolase activityUniRule annotation
Binding sitei353 – 3531GTPUniRule annotation
Binding sitei358 – 3581GTPUniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi253 – 2575GTPUniRule annotation
Nucleotide bindingi296 – 2983GTPUniRule annotation

GO - Molecular functioni

  1. 3,4-dihydroxy-2-butanone-4-phosphate synthase activity Source: UniProtKB-HAMAP
  2. GTP binding Source: UniProtKB-KW
  3. GTP cyclohydrolase II activity Source: UniProtKB-HAMAP
  4. magnesium ion binding Source: UniProtKB-HAMAP
  5. manganese ion binding Source: UniProtKB-HAMAP
  6. zinc ion binding Source: UniProtKB-HAMAP

GO - Biological processi

  1. riboflavin biosynthetic process Source: UniProtKB-HAMAP
Complete GO annotation...

Keywords - Molecular functioni

HydrolaseUniRule annotationImported, LyaseUniRule annotationSAAS annotation

Keywords - Biological processi

Riboflavin biosynthesisUniRule annotationSAAS annotation

Keywords - Ligandi

GTP-bindingUniRule annotationSAAS annotation, MagnesiumUniRule annotation, ManganeseUniRule annotation, Metal-bindingUniRule annotationSAAS annotation, Nucleotide-binding, ZincUniRule annotationSAAS annotation

Enzyme and pathway databases

BioCyciDDES525146:GIWF-2202-MONOMER.
UniPathwayiUPA00275; UER00399.
UPA00275; UER00400.

Names & Taxonomyi

Protein namesi
Recommended name:
Riboflavin biosynthesis protein RibBAUniRule annotationSAAS annotation
Gene namesi
Name:ribBAUniRule annotation
Ordered Locus Names:Ddes_2136Imported
OrganismiDesulfovibrio desulfuricans (strain ATCC 27774 / DSM 6949)Imported
Taxonomic identifieri525146 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaDeltaproteobacteriaDesulfovibrionalesDesulfovibrionaceaeDesulfovibrio
ProteomesiUP000002598 Componenti: Chromosome

Interactioni

Protein-protein interaction databases

STRINGi525146.Ddes_2136.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni1 – 201201DHBP synthaseUniRule annotationAdd
BLAST
Regioni27 – 282D-ribulose 5-phosphate bindingUniRule annotation
Regioni202 – 404203GTP cyclohydrolase IIUniRule annotationAdd
BLAST

Sequence similaritiesi

In the C-terminal section; belongs to the GTP cyclohydrolase II family.UniRule annotation
In the N-terminal section; belongs to the DHBP synthase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0108.
HOGENOMiHOG000115440.
KOiK14652.
OMAiYESETEQ.
OrthoDBiEOG679TK8.

Family and domain databases

Gene3Di3.90.870.10. 1 hit.
HAMAPiMF_00179. RibA.
MF_00180. RibB.
MF_01283. RibBA.
InterProiIPR017945. DHBP_synth_RibB-like_a/b_dom.
IPR000422. DHBP_synthase_RibB.
IPR000926. GTP_CycHdrlaseII_RibA.
IPR016299. Riboflavin_synth_RibBA.
[Graphical view]
PfamiPF00926. DHBP_synthase. 1 hit.
PF00925. GTP_cyclohydro2. 1 hit.
[Graphical view]
PIRSFiPIRSF001259. RibA. 1 hit.
SUPFAMiSSF55821. SSF55821. 1 hit.
TIGRFAMsiTIGR00505. ribA. 1 hit.
TIGR00506. ribB. 1 hit.

Sequencei

Sequence statusi: Complete.

B8J3Y7-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MPLCSIEEAV ADIKQGKMVI LVDDEGRENE GDLTMAAEFV TPEAINFMAK
60 70 80 90 100
YGRGLICLPM SPEMIDRLDL PLMTQRNGSR FGTNFTISIE AREGVTTGIS
110 120 130 140 150
AADRATTILA AVGDDVRPDD LVTPGHVFPL RAKAGGVLSR AGQTEGGVDL
160 170 180 190 200
SKLAGLKPAS VICEIMRDDG TMARMPDLET FAEEHGLKIV AVKDIIRHRL
210 220 230 240 250
NRGQVSVRNV AKAHLPTRFG DFTVYAYESE TEQGTHLALV KGDLSGPEPV
260 270 280 290 300
LARVHSECLT GDALGSLRCD CGGQLGAALR QIEKEGRGAL LYMRQEGRGI
310 320 330 340 350
GLANKIRAYA LQDEGYDTVE ANRKLGFPPD LRDYGTGAQM LVDLGIHKVR
360 370 380 390 400
LLTNNPKKIV GLSGYGIEIV ERVPIEMDAC PENEHYLRTK KEKMQHMLHC

SCCR
Length:404
Mass (Da):44,044
Last modified:March 3, 2009 - v1
Checksum:iD4526371C276D7E5
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001358 Genomic DNA. Translation: ACL50032.1.
RefSeqiWP_015939141.1. NC_011883.1.
YP_002480710.1. NC_011883.1.

Genome annotation databases

EnsemblBacteriaiACL50032; ACL50032; Ddes_2136.
KEGGidds:Ddes_2136.
PATRICi21738316. VBIDesDes50650_2490.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001358 Genomic DNA. Translation: ACL50032.1.
RefSeqiWP_015939141.1. NC_011883.1.
YP_002480710.1. NC_011883.1.

3D structure databases

ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi525146.Ddes_2136.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiACL50032; ACL50032; Ddes_2136.
KEGGidds:Ddes_2136.
PATRICi21738316. VBIDesDes50650_2490.

Phylogenomic databases

eggNOGiCOG0108.
HOGENOMiHOG000115440.
KOiK14652.
OMAiYESETEQ.
OrthoDBiEOG679TK8.

Enzyme and pathway databases

UniPathwayiUPA00275; UER00399.
UPA00275; UER00400.
BioCyciDDES525146:GIWF-2202-MONOMER.

Family and domain databases

Gene3Di3.90.870.10. 1 hit.
HAMAPiMF_00179. RibA.
MF_00180. RibB.
MF_01283. RibBA.
InterProiIPR017945. DHBP_synth_RibB-like_a/b_dom.
IPR000422. DHBP_synthase_RibB.
IPR000926. GTP_CycHdrlaseII_RibA.
IPR016299. Riboflavin_synth_RibBA.
[Graphical view]
PfamiPF00926. DHBP_synthase. 1 hit.
PF00925. GTP_cyclohydro2. 1 hit.
[Graphical view]
PIRSFiPIRSF001259. RibA. 1 hit.
SUPFAMiSSF55821. SSF55821. 1 hit.
TIGRFAMsiTIGR00505. ribA. 1 hit.
TIGR00506. ribB. 1 hit.
ProtoNetiSearch...

Publicationsi

  1. "Complete sequence of Desulfovibrio desulfuricans subsp. desulfuricans str. ATCC 27774."
    US DOE Joint Genome Institute
    Lucas S., Copeland A., Lapidus A., Glavina del Rio T., Tice H., Bruce D., Goodwin L., Pitluck S., Sims D., Lu M., Kiss H., Meineke L., Brettin T., Detter J.C., Han C., Larimer F., Land M., Hauser L.
    , Kyrpides N., Ovchinnikova G., Hazen T.C.
    Submitted (JAN-2009) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 27774 / DSM 6949Imported.

Entry informationi

Entry nameiB8J3Y7_DESDA
AccessioniPrimary (citable) accession number: B8J3Y7
Entry historyi
Integrated into UniProtKB/TrEMBL: March 3, 2009
Last sequence update: March 3, 2009
Last modified: April 29, 2015
This is version 46 of the entry and version 1 of the sequence. [Complete history]
Entry statusiUnreviewed (UniProtKB/TrEMBL)

Miscellaneousi

Keywords - Technical termi

Complete proteome, Multifunctional enzymeUniRule annotation, Reference proteomeImported

External Data

Dasty 3

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 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.