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Protein

Riboflavin biosynthesis protein RibBA

Gene

ribBA

Organism
Desulfomicrobium baculatum (strain DSM 4028 / VKM B-1378) (Desulfovibrio baculatus)
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 annotationNote: Binds 1 zinc ion per subunit.UniRule annotation

Pathway:iriboflavin biosynthesis

This protein is involved in step 1 of the subpathway that synthesizes 2-hydroxy-3-oxobutyl phosphate from D-ribulose 5-phosphate.UniRule annotation
Proteins known to be involved in this subpathway in this organism are:
  1. 3,4-dihydroxy-2-butanone 4-phosphate synthase (ribB), Riboflavin biosynthesis protein RibBA (ribBA)
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.

Pathway:iriboflavin biosynthesis

This protein is involved in step 1 of the subpathway that synthesizes 5-amino-6-(D-ribitylamino)uracil from GTP.UniRule annotationSAAS annotation
Proteins known to be involved in the 4 steps of the subpathway in this organism are:
  1. Riboflavin biosynthesis protein RibBA (ribBA)
  2. Riboflavin biosynthesis protein RibD (Dbac_0062)
  3. Riboflavin biosynthesis protein RibD (Dbac_0062)
  4. no protein annotated in this organism
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 5-amino-6-(D-ribitylamino)uracil from GTP, the pathway riboflavin biosynthesis and in Cofactor biosynthesis.

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 bindingi257 – 2571Zinc; catalyticUniRule annotation
Metal bindingi268 – 2681Zinc; catalyticUniRule annotation
Metal bindingi270 – 2701Zinc; catalyticUniRule annotation
Binding sitei273 – 2731GTPUniRule annotation
Binding sitei317 – 3171GTPUniRule annotation
Active sitei329 – 3291Proton acceptor; for GTP cyclohydrolase activityUniRule annotation
Active sitei331 – 3311Nucleophile; for GTP cyclohydrolase activityUniRule annotation
Binding sitei352 – 3521GTPUniRule annotation
Binding sitei357 – 3571GTPUniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi252 – 2565GTPUniRule annotation
Nucleotide bindingi295 – 2973GTPUniRule annotation

GO - Molecular functioni

GO - Biological processi

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

BioCyciDBAC525897:GI50-62-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:Dbac_0060Imported
OrganismiDesulfomicrobium baculatum (strain DSM 4028 / VKM B-1378) (Desulfovibrio baculatus)Imported
Taxonomic identifieri525897 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaDeltaproteobacteriaDesulfovibrionalesDesulfomicrobiaceaeDesulfomicrobium
ProteomesiUP000002216 Componenti: Chromosome

Interactioni

Protein-protein interaction databases

STRINGi525897.Dbac_0060.

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.
OMAiLMVDRNT.
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.

C7LSH6-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MHKCSAEEAI KEIKAGKMII LVDDEDRENE GDLTIAAEMV TPEAINFMAK
60 70 80 90 100
YGRGLICLAL EPALVDKLEL PLMARRNTSK FGTNFTVSIE AKQGVTTGIS
110 120 130 140 150
AHDRALTIQT AVADQTTPED LATPGHIFPL RAKPGGVLVR AGQTEGSVDL
160 170 180 190 200
ARLAGLKGAA VICEIMNDDG SMSRMPDLRK FAEEHDMKIA TIADLIAYRS
210 220 230 240 250
RKDSLVRRVA EARMPTCYGE FTIVAYENDI DSHTHIALVK GEINEETPVL
260 270 280 290 300
VRVHSECLTG DVFGSMRCDC GSQLQRAMQM VNDEGAGVIL YMRQEGRGIG
310 320 330 340 350
LGNKIKAYHL QDEGRDTVEA NLELGFAPDL RDYGLGAQIL VDLGVKRMRL
360 370 380 390 400
LTNNPKKIIG LEGYGLKVEE RISIEIPACD DNKCYLHTKH SKLGHLLQFE

AENK
Length:404
Mass (Da):44,379
Last modified:October 13, 2009 - v1
Checksum:iD4CB39048F1F5266
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001629 Genomic DNA. Translation: ACU88190.1.
RefSeqiWP_012805275.1. NC_013173.1.

Genome annotation databases

EnsemblBacteriaiACU88190; ACU88190; Dbac_0060.
KEGGidba:Dbac_0060.
PATRICi21702370. VBIDesBac69216_0058.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001629 Genomic DNA. Translation: ACU88190.1.
RefSeqiWP_012805275.1. NC_013173.1.

3D structure databases

ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi525897.Dbac_0060.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiACU88190; ACU88190; Dbac_0060.
KEGGidba:Dbac_0060.
PATRICi21702370. VBIDesBac69216_0058.

Phylogenomic databases

eggNOGiCOG0108.
HOGENOMiHOG000115440.
KOiK14652.
OMAiLMVDRNT.
OrthoDBiEOG679TK8.

Enzyme and pathway databases

UniPathwayiUPA00275; UER00399.
UPA00275; UER00400.
BioCyciDBAC525897:GI50-62-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. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: DSM 4028 / VKM B-1378Imported.

Entry informationi

Entry nameiC7LSH6_DESBD
AccessioniPrimary (citable) accession number: C7LSH6
Entry historyi
Integrated into UniProtKB/TrEMBL: October 13, 2009
Last sequence update: October 13, 2009
Last modified: July 22, 2015
This is version 44 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.