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Protein

Riboflavin biosynthesis protein RibBA

Gene

ribBA

Organism
Bacillus subtilis (strain 168)
Status
Reviewed-Annotation score: Annotation score: 5 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 annotation
Catalyzes the conversion of GTP to 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate (DARP), formate and pyrophosphate.UniRule 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 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

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 annotation
Proteins known to be involved in this subpathway in this organism are:
  1. 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.

Pathwayi: riboflavin biosynthesis

This protein is involved in step 1 of the subpathway that synthesizes 5-amino-6-(D-ribitylamino)uracil from GTP.UniRule 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 (ribD)
  3. Riboflavin biosynthesis protein RibD (ribD)
  4. 5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase YitU (yitU), 5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase YwtE (ywtE), 5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase YcsE (ycsE)
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 bindingi27 – 271Magnesium or manganese 1UniRule annotation
Metal bindingi27 – 271Magnesium or manganese 2UniRule annotation
Binding sitei31 – 311D-ribulose 5-phosphateUniRule annotation
Sitei124 – 1241Essential for DHBP synthase activityUniRule annotation
Metal bindingi141 – 1411Magnesium or manganese 2UniRule annotation
Binding sitei162 – 1621D-ribulose 5-phosphateUniRule annotation
Sitei162 – 1621Essential for DHBP synthase activityUniRule annotation
Metal bindingi256 – 2561Zinc; catalyticUniRule annotation
Metal bindingi267 – 2671Zinc; catalyticUniRule annotation
Metal bindingi269 – 2691Zinc; catalyticUniRule annotation
Binding sitei272 – 2721GTPUniRule annotation
Binding sitei316 – 3161GTPUniRule annotation
Active sitei328 – 3281Proton acceptor; for GTP cyclohydrolase activityUniRule annotation
Active sitei330 – 3301Nucleophile; for GTP cyclohydrolase activityUniRule annotation
Binding sitei351 – 3511GTPUniRule annotation
Binding sitei356 – 3561GTPUniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi251 – 2555GTPUniRule annotation
Nucleotide bindingi294 – 2963GTPUniRule annotation

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Hydrolase, Lyase

Keywords - Biological processi

Riboflavin biosynthesis

Keywords - Ligandi

GTP-binding, Magnesium, Manganese, Metal-binding, Nucleotide-binding, Zinc

Enzyme and pathway databases

BioCyciBSUB:BSU23260-MONOMER.
UniPathwayiUPA00275; UER00399.
UPA00275; UER00400.

Names & Taxonomyi

Protein namesi
Recommended name:
Riboflavin biosynthesis protein RibBAUniRule annotation
Including the following 2 domains:
3,4-dihydroxy-2-butanone 4-phosphate synthaseUniRule annotation (EC:4.1.99.12UniRule annotation)
Short name:
DHBP synthaseUniRule annotation
GTP cyclohydrolase-2UniRule annotation (EC:3.5.4.25UniRule annotation)
Alternative name(s):
GTP cyclohydrolase IIUniRule annotation
Gene namesi
Name:ribBAUniRule annotation
Synonyms:ribA
Ordered Locus Names:BSU23260
OrganismiBacillus subtilis (strain 168)
Taxonomic identifieri224308 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
Proteomesi
  • UP000001570 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 398398Riboflavin biosynthesis protein RibBAPRO_0000151721Add
BLAST

Proteomic databases

PaxDbiP17620.

Interactioni

Protein-protein interaction databases

IntActiP17620. 1 interaction.
MINTiMINT-8366770.
STRINGi224308.Bsubs1_010100012771.

Structurei

3D structure databases

ProteinModelPortaliP17620.
SMRiP17620. Positions 2-375.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni1 – 199199DHBP synthaseAdd
BLAST
Regioni26 – 272D-ribulose 5-phosphate bindingUniRule annotation
Regioni138 – 1425D-ribulose 5-phosphate bindingUniRule annotation
Regioni200 – 398199GTP cyclohydrolase IIAdd
BLAST

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiENOG4105C66. Bacteria.
COG0108. LUCA.
COG0807. LUCA.
HOGENOMiHOG000115440.
InParanoidiP17620.
KOiK14652.
OMAiLMVDRNT.
PhylomeDBiP17620.

Family and domain databases

CDDicd00641. GTP_cyclohydro2. 1 hit.
Gene3Di3.90.870.10. 1 hit.
HAMAPiMF_00179. RibA. 1 hit.
MF_00180. RibB. 1 hit.
MF_01283. RibBA. 1 hit.
InterProiIPR017945. DHBP_synth_RibB-like_a/b_dom.
IPR000422. DHBP_synthase_RibB.
IPR032677. GTP_cyclohydro_II.
IPR000926. RibA.
IPR016299. Riboflavin_synth_RibBA.
[Graphical view]
PfamiPF00926. DHBP_synthase. 1 hit.
PF00925. GTP_cyclohydro2. 1 hit.
[Graphical view]
SUPFAMiSSF142695. SSF142695. 1 hit.
SSF55821. SSF55821. 1 hit.
TIGRFAMsiTIGR00505. ribA. 1 hit.
TIGR00506. ribB. 1 hit.

Sequencei

Sequence statusi: Complete.

P17620-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MFHPIEEALD ALKKGEVIIV VDDEDRENEG DFVALAEHAT PEVINFMATH
60 70 80 90 100
GRGLICTPLS EEIADRLDLH PMVEHNTDSH HTAFTVSIDH RETKTGISAQ
110 120 130 140 150
ERSFTVQALL DSKSVPSDFQ RPGHIFPLIA KKGGVLKRAG HTEAAVDLAE
160 170 180 190 200
ACGSPGAGVI CEIMNEDGTM ARVPELIEIA KKHQLKMITI KDLIQYRYNL
210 220 230 240 250
TTLVEREVDI TLPTDFGTFK VYGYTNEVDG KEHVAFVMGD VPFGEEPVLV
260 270 280 290 300
RVHSECLTGD VFGSHRCDCG PQLHAALNQI AAEGRGVLLY LRQEGRGIGL
310 320 330 340 350
INKLKAYKLQ EQGYDTVEAN EALGFLPDLR NYGIGAQILR DLGVRNMKLL
360 370 380 390
TNNPRKIAGL EGYGLSISER VPLQMEAKEH NKKYLQTKMN KLGHLLHF
Length:398
Mass (Da):44,121
Last modified:August 1, 1990 - v1
Checksum:iD9162EA7DAE611AA
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L09228 Genomic DNA. Translation: AAA67483.1.
X51510 Genomic DNA. Translation: CAA35880.1.
AL009126 Genomic DNA. Translation: CAB14258.1.
PIRiS45545.
RefSeqiNP_390207.1. NC_000964.3.
WP_004398484.1. NZ_JNCM01000036.1.

Genome annotation databases

EnsemblBacteriaiCAB14258; CAB14258; BSU23260.
GeneIDi938946.
KEGGibsu:BSU23260.
PATRICi18976469. VBIBacSub10457_2425.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L09228 Genomic DNA. Translation: AAA67483.1.
X51510 Genomic DNA. Translation: CAA35880.1.
AL009126 Genomic DNA. Translation: CAB14258.1.
PIRiS45545.
RefSeqiNP_390207.1. NC_000964.3.
WP_004398484.1. NZ_JNCM01000036.1.

3D structure databases

ProteinModelPortaliP17620.
SMRiP17620. Positions 2-375.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiP17620. 1 interaction.
MINTiMINT-8366770.
STRINGi224308.Bsubs1_010100012771.

Proteomic databases

PaxDbiP17620.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAB14258; CAB14258; BSU23260.
GeneIDi938946.
KEGGibsu:BSU23260.
PATRICi18976469. VBIBacSub10457_2425.

Phylogenomic databases

eggNOGiENOG4105C66. Bacteria.
COG0108. LUCA.
COG0807. LUCA.
HOGENOMiHOG000115440.
InParanoidiP17620.
KOiK14652.
OMAiLMVDRNT.
PhylomeDBiP17620.

Enzyme and pathway databases

UniPathwayiUPA00275; UER00399.
UPA00275; UER00400.
BioCyciBSUB:BSU23260-MONOMER.

Family and domain databases

CDDicd00641. GTP_cyclohydro2. 1 hit.
Gene3Di3.90.870.10. 1 hit.
HAMAPiMF_00179. RibA. 1 hit.
MF_00180. RibB. 1 hit.
MF_01283. RibBA. 1 hit.
InterProiIPR017945. DHBP_synth_RibB-like_a/b_dom.
IPR000422. DHBP_synthase_RibB.
IPR032677. GTP_cyclohydro_II.
IPR000926. RibA.
IPR016299. Riboflavin_synth_RibBA.
[Graphical view]
PfamiPF00926. DHBP_synthase. 1 hit.
PF00925. GTP_cyclohydro2. 1 hit.
[Graphical view]
SUPFAMiSSF142695. SSF142695. 1 hit.
SSF55821. SSF55821. 1 hit.
TIGRFAMsiTIGR00505. ribA. 1 hit.
TIGR00506. ribB. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiRIBBA_BACSU
AccessioniPrimary (citable) accession number: P17620
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 1, 1990
Last sequence update: August 1, 1990
Last modified: September 7, 2016
This is version 129 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Multifunctional enzyme, Reference proteome

Documents

  1. Bacillus subtilis
    Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. SIMILARITY comments
    Index of protein domains and families

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.