Riboflavin biosynthesis protein ribD (P25539)

Identification
Name:Riboflavin biosynthesis protein ribD
Synonyms:
  • Diaminohydroxyphosphoribosylaminopyrimidine deaminase
  • DRAP deaminase
  • Riboflavin-specific deaminase
  • 5-amino-6-(5-phosphoribosylamino)uracil reductase
  • HTP reductase
Gene Name:ribD
Enzyme Class:
Biological Properties
General Function:Involved in zinc ion binding
Specific Function:Converts 2,5-diamino-6-(ribosylamino)-4(3h)-pyrimidinone 5'-phosphate into 5-amino-6-(ribosylamino)-2,4(1h,3h)- pyrimidinedione 5'-phosphate
Cellular Location:Cytoplasmic
SMPDB Pathways:
KEGG Pathways:
KEGG Reactions:
1.0Thumb+1.0Thumb+1.0Thumb → 1.0Thumb+1.0Thumb
1.05-Amino-6-(5'-phosphoribosylamino)uracil + 1.0Hydrogen ion + 1.0NADPH → 1.05-Amino-6-(5'-phosphoribitylamino)uracil + 1.0NADP
ReactionCard
1.0Thumb+1.0Thumb ↔ 1.0Thumb+1.0Thumb+1.0Thumb
1.05-Amino-6-(5'-phosphoribitylamino)uracil + 1.0NADP ↔ 1.05-Amino-6-(5'-phosphoribosylamino)uracil + 1.0NADPH + 1.0Hydrogen ion
ReactionCard
1.0Thumb+1.0Thumb+1.0Thumb ↔ 1.0Thumb+1.0Thumb
1.02,5-Diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine + 1.0Water + 1.02,5-diamino-6-hydroxy-4-(5-phospho-D-ribosylamino)pyrimidine ↔ 1.05-Amino-6-(5'-phosphoribosylamino)uracil + 1.0Ammonia
ReactionCard
SMPDB Reactions:
1.0Thumb+1.0Thumb+1.0Thumb → 1.0Thumb+1.0Thumb
1.02,5-Diamino-6-(5'-phosphoribosylamino)-4-pyrimidineone + 1.0Water + 1.0Hydrogen ion → 1.0Ammonium + 1.05-Amino-6-(5'-phosphoribosylamino)uracil
ReactionCard
1.0Thumb+1.0Thumb+1.0NADPH+1.0Thumb → 1.0Thumb+1.05-Amino-6-(5'-phosphoribitylamino)uracil+1.0Thumb
1.05-Amino-6-(5'-phosphoribosylamino)uracil + 1.0Hydrogen ion + 1.0NADPH + 1.0NADPH → 1.0NADP + 1.05-Amino-6-(5'-phosphoribitylamino)uracil + 1.05-Amino-6-(5'-phosphoribitylamino)uracil
ReactionCard
EcoCyc Reactions:
1.0Thumb+1.0Thumb+1.0Thumb → 1.0Thumb+1.0Thumb
1.05-Amino-6-(5'-phosphoribosylamino)uracil + 1.0Hydrogen ion + 1.0NADPH → 1.05-Amino-6-(5'-phosphoribitylamino)uracil + 1.0NADP
ReactionCard
1.0Thumb+1.0Thumb ↔ 1.0Thumb+1.0Thumb+1.0Thumb
1.05-Amino-6-(5'-phosphoribitylamino)uracil + 1.0NADP ↔ 1.05-Amino-6-(5'-phosphoribosylamino)uracil + 1.0NADPH + 1.0Hydrogen ion
ReactionCard
1.0Thumb+1.0Thumb+1.0Thumb ↔ 1.0Thumb+1.0Thumb
1.02,5-Diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine + 1.0Water + 1.02,5-diamino-6-hydroxy-4-(5-phospho-D-ribosylamino)pyrimidine ↔ 1.05-Amino-6-(5'-phosphoribosylamino)uracil + 1.0Ammonia
ReactionCard
Complex Reactions:
1.0Thumb+1.0Thumb+1.0Thumb → 1.0Thumb+1.0Thumb
1.02,5-Diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine + 1.0Hydrogen ion + 1.0Water → 1.05-Amino-6-(5'-phosphoribosylamino)uracil + 1.0Ammonium
ReactionCard
1.0Thumb+1.0Thumb → 1.05-amino-6-(5-phospho-D-ribosylamino)uracil+1.0Thumb
1.05-Amino-6-(5'-phosphoribitylamino)uracil + 1.0NADP → 1.05-amino-6-(5-phospho-D-ribosylamino)uracil + 1.0NADPH
ReactionCard
Metabolites:
ECMDB IDNameView
ECMDB200582,5-Diamino-6-(5'-phosphoribosylamino)-4-pyrimidineoneMetaboCard
ECMDB040522,5-Diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidineMetaboCard
ECMDB211775-Amino-6-(5'-phosphoribitylamino)uracilMetaboCard
ECMDB200995-Amino-6-(5'-phosphoribosylamino)uracilMetaboCard
ECMDB00051AmmoniaMetaboCard
ECMDB21186AmmoniumMetaboCard
ECMDB21225Hydrogen ionMetaboCard
ECMDB00217NADPMetaboCard
ECMDB04111NADPHMetaboCard
ECMDB00494WaterMetaboCard
GO Classification:
Function
5-amino-6-(5-phosphoribosylamino)uracil reductase activity
binding
catalytic activity
cation binding
diaminohydroxyphosphoribosylaminopyrimidine deaminase activity
hydrolase activity
hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds
hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines
ion binding
metal ion binding
NADP or NADPH binding
nucleotide binding
oxidoreductase activity
oxidoreductase activity, acting on CH-OH group of donors
oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
transition metal ion binding
zinc ion binding
Process
metabolic process
nitrogen compound metabolic process
oxidation reduction
riboflavin biosynthetic process
riboflavin metabolic process
Gene Properties
Blattner:b0414
Gene OrientationClockwise
Centisome Percentage:9.33
Left Sequence End432679
Right Sequence End433782
Gene Sequence:
>1104 bp
ATGAGTGACAGCCAGACGCTGGTGGTAAAACTCGGCACCAGTGTGCTAACAGGCGGATCG
CGCCGTCTGAACCGTGCCCATATCGTTGAACTTGTTCGCCAGTGCGCGCAGTTACATGCC
GCCGGGCATCGGATTGTTATTGTGACGTCGGGCGCGATCGCCGCCGGACGTGAGCACCTG
GGTTACCCGGAACTGCCAGCGACCATCGCCTCGAAACAACTGCTGGCGGCGGTAGGGCAG
AGTCGACTGATTCAACTGTGGGAACAGCTGTTTTCGATTTATGGCATTCACGTCGGGCAA
ATGCTGCTGACCCGTGCTGATATGGAAGACCGTGAACGCTTCCTGAACGCCCGCGACACC
CTGCGAGCGTTGCTCGATAACAATATCGTTCCGGTAATCAATGAGAACGATGCTGTCGCT
ACGGCAGAGATTAAGGTCGGCGATAACGATAACCTTTCTGCGCTGGCGGCGATTCTTGCG
GGTGCCGATAAACTGTTGCTGCTGACCGATCAAAAAGGTTTGTATACCGCTGACCCGCGC
AGCAATCCGCAGGCAGAACTGATTAAAGATGTTTACGGCATTGATGACGCACTGCGCGCG
ATTGCCGGTGACAGCGTTTCAGGCCTCGGAACTGGCGGCATGAGTACCAAATTGCAGGCC
GCTGACGTGGCTTGCCGTGCGGGTATCGACACCATTATTGCCGCGGGCAGCAAGCCGGGC
GTTATTGGTGATGTGATGGAAGGCATTTCCGTCGGTACGCTGTTCCATGCCCAGGCGACT
CCGCTTGAAAACCGTAAACGCTGGATTTTCGGTGCGCCGCCGGCGGGTGAAATCACGGTA
GATGAAGGGGCAACTGCCGCCATTCTGGAACGCGGCAGCTCCCTGTTGCCGAAAGGCATT
AAAAGCGTGACTGGCAATTTCTCGCGTGGTGAAGTCATCCGCATTTGCAACCTCGAAGGC
CGCGATATCGCCCACGGCGTCAGTCGTTACAACAGCGATGCATTACGCCGTATTGCCGGA
CACCACTCGCAAGAAATTGATGCAATACTGGGATATGAATACGGCCCGGTTGCCGTTCAC
CGTGATGACATGATTACCCGTTAA
Protein Properties
Pfam Domain Function:
Protein Residues:367
Protein Molecular Weight:40338
Protein Theoretical pI:8
Signaling Regions:
  • None
Transmembrane Regions:
  • None
Protein Sequence:
>Riboflavin biosynthesis protein ribD
MQDEYYMARALKLAQRGRFTTHPNPNVGCVIVKDGEIVGEGYHQRAGEPHAEVHALRMAG
EKAKGATAYVTLEPCSHHGRTPPCCDALIAAGVARVVASMQDPNPQVAGRGLYRLQQAGI
DVSHGLMMSEAEQLNKGFLKRMRTGFPYIQLKLGASLDGRTAMASGESQWITSPQARRDV
QLLRAQSHAILTSSATVLADDPALTVRWSELDEQTQALYPQQNLRQPIRIVIDSQNRVTP
VHRIVQQPGETWFARTQEDSREWPETVRTLLIPEHKGHLDLVVLMMQLGKQQINSIWVEA
GPTLAGALLQAGLVDELIVYIAPKLLGSDARGLCTLPGLEKLADAPQFKFKEIRHVGPDV
CLHLVGA
References
External Links:
ResourceLink
Uniprot ID:P25539
Uniprot Name:RIBD_ECOLI
GenBank Gene ID:AP009048
Genebank Protein ID:85674394
Ecogene ID:EG11321
Ecocyc:EG11321
ColiBase:b0414
Kegg Gene:b0414
EchoBASE ID:EB1297
CCDB:RIBD_ECOLI
BacMap:16128399
General Reference:
  • Blattner, F. R., Plunkett, G. 3rd, 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. (1997). "The complete genome sequence of Escherichia coli K-12." Science 277:1453-1462. Pubmed: 9278503
  • Hayashi, K., Morooka, N., Yamamoto, Y., Fujita, K., Isono, K., Choi, S., Ohtsubo, E., Baba, T., Wanner, B. L., Mori, H., Horiuchi, T. (2006). "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110." Mol Syst Biol 2:2006.0007. Pubmed: 16738553
  • Richter, G., Fischer, M., Krieger, C., Eberhardt, S., Luttgen, H., Gerstenschlager, I., Bacher, A. (1997). "Biosynthesis of riboflavin: characterization of the bifunctional deaminase-reductase of Escherichia coli and Bacillus subtilis." J Bacteriol 179:2022-2028. Pubmed: 9068650
  • Stenmark, P., Moche, M., Gurmu, D., Nordlund, P. (2007). "The crystal structure of the bifunctional deaminase/reductase RibD of the riboflavin biosynthetic pathway in Escherichia coli: implications for the reductive mechanism." J Mol Biol 373:48-64. Pubmed: 17765262
  • Taura, T., Ueguchi, C., Shiba, K., Ito, K. (1992). "Insertional disruption of the nusB (ssyB) gene leads to cold-sensitive growth of Escherichia coli and suppression of the secY24 mutation." Mol Gen Genet 234:429-432. Pubmed: 1406588