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Q5YTP3 (RIBBA_NOCFA) Reviewed, UniProtKB/Swiss-Prot

Last modified January 25, 2012. Version 53. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
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Names and origin

Protein namesRecommended name:
Riboflavin biosynthesis protein ribBA

Including the following 2 domains:

  1. 3,4-dihydroxy-2-butanone 4-phosphate synthase
    Short name=DHBP synthase
    EC=4.1.99.12
  2. GTP cyclohydrolase-2
    EC=3.5.4.25
    Alternative name(s):
    GTP cyclohydrolase II
Gene names
Name:ribBA
Ordered Locus Names:NFA_36000
OrganismNocardia farcinica (strain IFM 10152) [Complete proteome] [HAMAP]
Taxonomic identifier247156 [NCBI]
Taxonomic lineageBacteria › Actinobacteria › Actinobacteridae › Actinomycetales › Corynebacterineae › Nocardiaceae › Nocardia

Protein attributes

Sequence length414 AA.
Sequence statusComplete.
Protein existenceInferred from homology

General annotation (Comments)

Function

Catalyzes the conversion of D-ribulose 5-phosphate to formate and 3,4-dihydroxy-2-butanone 4-phosphate By similarity. HAMAP MF_01283

Catalyzes the conversion of GTP to 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate (DARP), formate and pyrophosphate By similarity. HAMAP MF_01283

Catalytic activity

D-ribulose 5-phosphate = formate + L-3,4-dihydroxybutan-2-one 4-phosphate. HAMAP MF_01283

GTP + 3 H2O = formate + 2,5-diamino-6-hydroxy-4-(5-phospho-D-ribosylamino)pyrimidine + diphosphate. HAMAP MF_01283

Cofactor

Binds 2 divalent metal cations per subunit. Magnesium or manganese By similarity.

Binds 1 zinc ion per subunit By similarity. HAMAP MF_01283

Pathway

Cofactor biosynthesis; riboflavin biosynthesis; 2-hydroxy-3-oxobutyl phosphate from D-ribulose 5-phosphate: step 1/1. HAMAP MF_01283

Cofactor biosynthesis; riboflavin biosynthesis; 5-amino-6-(D-ribitylamino)uracil from GTP: step 1/4. HAMAP MF_01283

Sequence similarities

In the N-terminal section; belongs to the DHBP synthase family.

In the C-terminal section; belongs to the GTP cyclohydrolase II family.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 414414Riboflavin biosynthesis protein ribBA HAMAP MF_01283
PRO_1000067429

Regions

Nucleotide binding255 – 2595GTP By similarity
Nucleotide binding299 – 3013GTP By similarity
Region1 – 204204DHBP synthase HAMAP MF_01283
Region28 – 292D-ribulose 5-phosphate binding By similarity
Region141 – 1455D-ribulose 5-phosphate binding By similarity
Region205 – 414210GTP cyclohydrolase II HAMAP MF_01283

Sites

Active site3331Proton acceptor; for GTP cyclohydrolase activity Potential
Active site3351Nucleophile; for GTP cyclohydrolase activity By similarity
Metal binding291Magnesium or manganese 1 By similarity
Metal binding291Magnesium or manganese 2 By similarity
Metal binding1441Magnesium or manganese 2 By similarity
Metal binding2601Zinc; catalytic By similarity
Metal binding2711Zinc; catalytic By similarity
Metal binding2731Zinc; catalytic By similarity
Binding site331D-ribulose 5-phosphate By similarity
Binding site1651D-ribulose 5-phosphate By similarity
Binding site2761GTP By similarity
Binding site3211GTP By similarity
Binding site3561GTP By similarity
Binding site3611GTP By similarity
Site1271Essential for DHBP synthase activity By similarity
Site1651Essential for DHBP synthase activity By similarity

Sequences

Sequence LengthMass (Da)Tools
Q5YTP3 [UniParc].

Last modified November 23, 2004. Version 1.
Checksum: 4723E65A226608DC

FASTA41445,052
        10         20         30         40         50         60 
MTRFDTIERA VADIAAGKAV VVVDDEDREN EGDLIFAAEK ATPELVAFMI RYTSGYICVP 

        70         80         90        100        110        120 
LTGEDCDRLG LPPMYATNQD KHGTAYTVSV DAREGITTGI SAADRATTMR LLADADAKAD 

       130        140        150        160        170        180 
DLTRPGHVVP LRAKDGGVLR RPGHTEAAVD LARMAGLRPA GVICEIVSQK DEGHMARTEE 

       190        200        210        220        230        240 
LRVFADDHDL ALISIADMIA WRRKHEKQVV RVAEARIPTA HGAFTAVGYQ SIYDDVEHVA 

       250        260        270        280        290        300 
LVRGDIGDGE DVLVRVHSEC LTGDVFGSLR CDCGPQLDAA LEMVDQEGRG VVLYMRGHEG 

       310        320        330        340        350        360 
RGIGLMHKLQ AYQLQDSGRD TVDANLDLGL PADARDYGTG AQILVDLGIR SMRLLTNNPA 

       370        380        390        400        410 
KRVGLDGYGL TITERVPMPL RANAENLRYL RTKRDRMGHD LVGLDDLDLG ETAQ

« Hide

References

[1]"The complete genomic sequence of Nocardia farcinica IFM 10152."
Ishikawa J., Yamashita A., Mikami Y., Hoshino Y., Kurita H., Hotta K., Shiba T., Hattori M.
Proc. Natl. Acad. Sci. U.S.A. 101:14925-14930(2004) [PubMed: 15466710] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: IFM 10152.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		AP006618 Genomic DNA. Translation: BAD58448.1.
RefSeqYP_119812.1. NC_006361.1.

3D structure databases

HSSPHSSP built from PDB template 2BZ0 based on UniProtKB P0A7I7.
ProteinModelPortalQ5YTP3.
SMRQ5YTP3. Positions 208-379.
ModBaseSearch...

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

GeneID3111454.
GenomeReviewsGene locus NFA_36000 in contig AP006618_GR.
KEGGnfa:nfa36000.
NMPDRfig|247156.1.peg.3513.
PATRIC22736816. VBINocFar94200_3644.

Organism-specific databases

CMRSearch...

Phylogenomic databases

HOGENOMHBG735778.
OMARCDCRMQ.
ProtClustDBPRK09311.

Enzyme and pathway databases

BioCycNFAR247156:NFA36000-MONOMER.

Family and domain databases

HAMAPMF_01283. RibBA.
[Tree]
InterProIPR017945. DHBP_synth_RibB-like_a/b_dom.
IPR000422. DHBP_synthase_RibB.
IPR000926. GTP_CycHdrlaseII_RibA.
IPR016299. Riboflavin_synth_RibBA.
[Graphical view]
Gene3DG3DSA:3.90.870.10. DHBP_synth_RibB-like_a/b_dom. 1 hit.
KOK14652.
PfamPF00926. DHBP_synthase. 1 hit.
PF00925. GTP_cyclohydro2. 1 hit.
[Graphical view]
PIRSFPIRSF001259. RibA. 1 hit.
SUPFAMSSF55821. DHBP_synth_RibB-like_a/b_dom. 1 hit.
TIGRFAMsTIGR00505. RibA. 1 hit.
TIGR00506. RibB. 1 hit.
ProtoNetSearch...

Entry information

Entry nameRIBBA_NOCFA
AccessionPrimary (citable) accession number: Q5YTP3
Entry history
Integrated into UniProtKB/Swiss-Prot: February 5, 2008
Last sequence update: November 23, 2004
Last modified: January 25, 2012
This is version 53 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

PATHWAY comments

Index of metabolic and biosynthesis pathways

SIMILARITY comments

Index of protein domains and families

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