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P25539 (RIBD_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 132. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Riboflavin biosynthesis protein RibD

Including the following 2 domains:

  1. Diaminohydroxyphosphoribosylaminopyrimidine deaminase
    Short name=DRAP deaminase
    EC=3.5.4.26
    Alternative name(s):
    Riboflavin-specific deaminase
  2. 5-amino-6-(5-phosphoribosylamino)uracil reductase
    EC=1.1.1.193
    Alternative name(s):
    HTP reductase
Gene names
Name:ribD
Synonyms:ribG, ybaE
Ordered Locus Names:b0414, JW0404
OrganismEscherichia coli (strain K12) [Reference proteome] [HAMAP]
Taxonomic identifier83333 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Protein attributes

Sequence length367 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Converts 2,5-diamino-6-(ribosylamino)-4(3h)-pyrimidinone 5'-phosphate into 5-amino-6-(ribosylamino)-2,4(1h,3h)-pyrimidinedione 5'-phosphate.

Catalytic activity

2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine + H2O = 5-amino-6-(5-phosphoribosylamino)uracil + NH3.

5-amino-6-(5-phospho-D-ribitylamino)uracil + NADP+ = 5-amino-6-(5-phospho-D-ribosylamino)uracil + NADPH.

Cofactor

Binds 1 zinc ion By similarity.

Pathway

Cofactor biosynthesis; riboflavin biosynthesis; 5-amino-6-(D-ribitylamino)uracil from GTP: step 2/4.

Cofactor biosynthesis; riboflavin biosynthesis; 5-amino-6-(D-ribitylamino)uracil from GTP: step 3/4.

Subunit structure

Homodimer. Ref.6

Sequence similarities

In the N-terminal section; belongs to the cytidine and deoxycytidylate deaminase family.

In the C-terminal section; belongs to the HTP reductase family.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 367367Riboflavin biosynthesis protein RibD
PRO_0000171721

Regions

Nucleotide binding161 – 1644NADP
Nucleotide binding301 – 3044NADP
Region1 – 145145Deaminase
Region146 – 367222Reductase

Sites

Active site521Proton donor By similarity
Metal binding501Zinc; catalytic By similarity
Metal binding751Zinc; catalytic By similarity
Metal binding841Zinc; catalytic By similarity
Binding site1681Substrate
Binding site1701NADP
Binding site1841Substrate
Binding site1961NADP
Binding site2001NADP
Binding site2041Substrate; via amide nitrogen
Binding site2071Substrate
Binding site2341NADP
Binding site2991Substrate

Secondary structure

................................................................. 367
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P25539 [UniParc].

Last modified May 1, 1992. Version 1.
Checksum: B19CEF474D48D14D

FASTA36740,338
        10         20         30         40         50         60 
MQDEYYMARA LKLAQRGRFT THPNPNVGCV IVKDGEIVGE GYHQRAGEPH AEVHALRMAG 

        70         80         90        100        110        120 
EKAKGATAYV TLEPCSHHGR TPPCCDALIA AGVARVVASM QDPNPQVAGR GLYRLQQAGI 

       130        140        150        160        170        180 
DVSHGLMMSE AEQLNKGFLK RMRTGFPYIQ LKLGASLDGR TAMASGESQW ITSPQARRDV 

       190        200        210        220        230        240 
QLLRAQSHAI LTSSATVLAD DPALTVRWSE LDEQTQALYP QQNLRQPIRI VIDSQNRVTP 

       250        260        270        280        290        300 
VHRIVQQPGE TWFARTQEDS REWPETVRTL LIPEHKGHLD LVVLMMQLGK QQINSIWVEA 

       310        320        330        340        350        360 
GPTLAGALLQ AGLVDELIVY IAPKLLGSDA RGLCTLPGLE KLADAPQFKF KEIRHVGPDV 


CLHLVGA 

« Hide

References

« Hide 'large scale' references
[1]"Insertional disruption of the nusB (ssyB) gene leads to cold-sensitive growth of Escherichia coli and suppression of the secY24 mutation."
Taura T., Ueguchi C., Shiba K., Ito K.
Mol. Gen. Genet. 234:429-432(1992) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: K12.
[2]"Sequence of minutes 4-25 of Escherichia coli."
Chung E., Allen E., Araujo R., Aparicio A.M., Davis K., Duncan M., Federspiel N., Hyman R., Kalman S., Komp C., Kurdi O., Lew H., Lin D., Namath A., Oefner P., Roberts D., Schramm S., Davis R.W.
Submitted (JAN-1997) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / MG1655 / ATCC 47076.
[3]"The complete genome sequence of Escherichia coli K-12."
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y.
Science 277:1453-1462(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / MG1655 / ATCC 47076.
[4]"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[5]"Biosynthesis of riboflavin: characterization of the bifunctional deaminase-reductase of Escherichia coli and Bacillus subtilis."
Richter G., Fischer M., Krieger C., Eberhardt S., Luttgen H., Gerstenschlager I., Bacher A.
J. Bacteriol. 179:2022-2028(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: CHARACTERIZATION.
[6]"The crystal structure of the bifunctional deaminase/reductase RibD of the riboflavin biosynthetic pathway in Escherichia coli: implications for the reductive mechanism."
Stenmark P., Moche M., Gurmu D., Nordlund P.
J. Mol. Biol. 373:48-64(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS) IN COMPLEXES WITH RIBOSE-5-PHOSPHATE AND NADP, SUBUNIT.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
X64395 Genomic DNA. Translation: CAA45735.1.
U82664 Genomic DNA. Translation: AAB40170.1.
U00096 Genomic DNA. Translation: AAC73517.1.
AP009048 Genomic DNA. Translation: BAE76194.1.
PIRS26201.
RefSeqNP_414948.1. NC_000913.3.
YP_488706.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2G6VX-ray2.60A/B2-367[»]
2O7PX-ray3.00A/B2-367[»]
2OBCX-ray3.00A/B2-367[»]
ProteinModelPortalP25539.
SMRP25539. Positions 2-367.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

DIPDIP-10708N.
IntActP25539. 34 interactions.
MINTMINT-1221612.
STRING511145.b0414.

Proteomic databases

PaxDbP25539.
PRIDEP25539.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAC73517; AAC73517; b0414.
BAE76194; BAE76194; BAE76194.
GeneID12934255.
945620.
KEGGecj:Y75_p0402.
eco:b0414.
PATRIC32115977. VBIEscCol129921_0430.

Organism-specific databases

EchoBASEEB1297.
EcoGeneEG11321. ribD.

Phylogenomic databases

eggNOGCOG0117.
HOGENOMHOG000257442.
KOK11752.
OMAQINSVWV.
OrthoDBEOG66F07R.
PhylomeDBP25539.
ProtClustDBPRK10786.

Enzyme and pathway databases

BioCycEcoCyc:RIBOFLAVINSYNDEAM-MONOMER.
ECOL316407:JW0404-MONOMER.
MetaCyc:RIBOFLAVINSYNDEAM-MONOMER.
UniPathwayUPA00275; UER00401.
UPA00275; UER00402.

Gene expression databases

GenevestigatorP25539.

Family and domain databases

Gene3D3.40.430.10. 1 hit.
InterProIPR016192. APOBEC/CMP_deaminase_Zn-bd.
IPR002125. CMP_dCMP_Zn-bd.
IPR016193. Cytidine_deaminase-like.
IPR024072. DHFR-like_dom.
IPR004794. Eubact_RibD.
IPR011549. RibD_C.
IPR002734. RibDG_C.
[Graphical view]
PfamPF00383. dCMP_cyt_deam_1. 1 hit.
PF01872. RibD_C. 1 hit.
[Graphical view]
PIRSFPIRSF006769. RibD. 1 hit.
SUPFAMSSF53597. SSF53597. 1 hit.
SSF53927. SSF53927. 1 hit.
TIGRFAMsTIGR00326. eubact_ribD. 1 hit.
TIGR00227. ribD_Cterm. 1 hit.
PROSITEPS00903. CYT_DCMP_DEAMINASES. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP25539.
PROP25539.

Entry information

Entry nameRIBD_ECOLI
AccessionPrimary (citable) accession number: P25539
Secondary accession number(s): Q2MC12
Entry history
Integrated into UniProtKB/Swiss-Prot: May 1, 1992
Last sequence update: May 1, 1992
Last modified: April 16, 2014
This is version 132 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

PATHWAY comments

Index of metabolic and biosynthesis pathways

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene