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P25539

- RIBD_ECOLI

UniProt

P25539 - RIBD_ECOLI

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Protein
Riboflavin biosynthesis protein RibD
Gene
ribD, ribG, ybaE, b0414, JW0404
Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

Functioni

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

Catalytic activityi

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.

Cofactori

Binds 1 zinc ion By similarity.

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi50 – 501Zinc; catalytic By similarity
Active sitei52 – 521Proton donor By similarity
Metal bindingi75 – 751Zinc; catalytic By similarity
Metal bindingi84 – 841Zinc; catalytic By similarity
Binding sitei168 – 1681Substrate
Binding sitei170 – 1701NADP
Binding sitei184 – 1841Substrate
Binding sitei196 – 1961NADP
Binding sitei200 – 2001NADP
Binding sitei204 – 2041Substrate; via amide nitrogen
Binding sitei207 – 2071Substrate
Binding sitei234 – 2341NADP
Binding sitei299 – 2991Substrate

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi161 – 1644NADP
Nucleotide bindingi301 – 3044NADP

GO - Molecular functioni

  1. 5-amino-6-(5-phosphoribosylamino)uracil reductase activity Source: EcoCyc
  2. NADP binding Source: EcoCyc
  3. diaminohydroxyphosphoribosylaminopyrimidine deaminase activity Source: EcoCyc
  4. zinc ion binding Source: InterPro
Complete GO annotation...

GO - Biological processi

  1. riboflavin biosynthetic process Source: EcoCyc
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase, Oxidoreductase

Keywords - Biological processi

Riboflavin biosynthesis

Keywords - Ligandi

Metal-binding, NADP, Zinc

Enzyme and pathway databases

BioCyciEcoCyc:RIBOFLAVINSYNDEAM-MONOMER.
ECOL316407:JW0404-MONOMER.
MetaCyc:RIBOFLAVINSYNDEAM-MONOMER.
UniPathwayiUPA00275; UER00401.
UPA00275; UER00402.

Names & Taxonomyi

Protein namesi
Recommended name:
Riboflavin biosynthesis protein RibD
Including the following 2 domains:
Diaminohydroxyphosphoribosylaminopyrimidine deaminase (EC:3.5.4.26)
Short name:
DRAP deaminase
Alternative name(s):
Riboflavin-specific deaminase
5-amino-6-(5-phosphoribosylamino)uracil reductase (EC:1.1.1.193)
Alternative name(s):
HTP reductase
Gene namesi
Name:ribD
Synonyms:ribG, ybaE
Ordered Locus Names:b0414, JW0404
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

Organism-specific databases

EcoGeneiEG11321. ribD.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 367367Riboflavin biosynthesis protein RibD
PRO_0000171721Add
BLAST

Proteomic databases

PaxDbiP25539.
PRIDEiP25539.

Expressioni

Gene expression databases

GenevestigatoriP25539.

Interactioni

Subunit structurei

Homodimer.1 Publication

Protein-protein interaction databases

DIPiDIP-10708N.
IntActiP25539. 34 interactions.
MINTiMINT-1221612.
STRINGi511145.b0414.

Structurei

Secondary structure

Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi2 – 1413
Helixi15 – 173
Turni18 – 203
Beta strandi28 – 336
Beta strandi36 – 427
Beta strandi46 – 483
Helixi51 – 599
Helixi60 – 634
Beta strandi64 – 663
Beta strandi68 – 725
Helixi85 – 917
Beta strandi96 – 1005
Helixi111 – 1177
Beta strandi122 – 1243
Helixi128 – 1347
Helixi136 – 1438
Beta strandi144 – 1463
Beta strandi148 – 1569
Helixi174 – 18512
Beta strandi187 – 1937
Helixi194 – 2007
Helixi208 – 2103
Helixi214 – 2174
Helixi221 – 2233
Beta strandi228 – 2325
Helixi243 – 2453
Beta strandi247 – 2493
Beta strandi251 – 2577
Beta strandi267 – 2715
Helixi281 – 29010
Beta strandi295 – 2984
Helixi302 – 31110
Beta strandi315 – 3239
Beta strandi349 – 3568
Beta strandi359 – 3657

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2G6VX-ray2.60A/B2-367[»]
2O7PX-ray3.00A/B2-367[»]
2OBCX-ray3.00A/B2-367[»]
ProteinModelPortaliP25539.
SMRiP25539. Positions 2-367.

Miscellaneous databases

EvolutionaryTraceiP25539.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni1 – 145145Deaminase
Add
BLAST
Regioni146 – 367222Reductase
Add
BLAST

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiCOG0117.
HOGENOMiHOG000257442.
KOiK11752.
OMAiQINSVWV.
OrthoDBiEOG66F07R.
PhylomeDBiP25539.

Family and domain databases

Gene3Di3.40.430.10. 1 hit.
InterProiIPR016192. 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]
PfamiPF00383. dCMP_cyt_deam_1. 1 hit.
PF01872. RibD_C. 1 hit.
[Graphical view]
PIRSFiPIRSF006769. RibD. 1 hit.
SUPFAMiSSF53597. SSF53597. 1 hit.
SSF53927. SSF53927. 1 hit.
TIGRFAMsiTIGR00326. eubact_ribD. 1 hit.
TIGR00227. ribD_Cterm. 1 hit.
PROSITEiPS00903. CYT_DCMP_DEAMINASES. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P25539-1 [UniParc]FASTAAdd to Basket

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MQDEYYMARA LKLAQRGRFT THPNPNVGCV IVKDGEIVGE GYHQRAGEPH    50
AEVHALRMAG EKAKGATAYV TLEPCSHHGR TPPCCDALIA AGVARVVASM 100
QDPNPQVAGR GLYRLQQAGI DVSHGLMMSE AEQLNKGFLK RMRTGFPYIQ 150
LKLGASLDGR TAMASGESQW ITSPQARRDV QLLRAQSHAI LTSSATVLAD 200
DPALTVRWSE LDEQTQALYP QQNLRQPIRI VIDSQNRVTP VHRIVQQPGE 250
TWFARTQEDS REWPETVRTL LIPEHKGHLD LVVLMMQLGK QQINSIWVEA 300
GPTLAGALLQ AGLVDELIVY IAPKLLGSDA RGLCTLPGLE KLADAPQFKF 350
KEIRHVGPDV CLHLVGA 367
Length:367
Mass (Da):40,338
Last modified:May 1, 1992 - v1
Checksum:iB19CEF474D48D14D
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
X64395 Genomic DNA. Translation: CAA45735.1.
U82664 Genomic DNA. Translation: AAB40170.1.
U00096 Genomic DNA. Translation: AAC73517.1.
AP009048 Genomic DNA. Translation: BAE76194.1.
PIRiS26201.
RefSeqiNP_414948.1. NC_000913.3.
YP_488706.1. NC_007779.1.

Genome annotation databases

EnsemblBacteriaiAAC73517; AAC73517; b0414.
BAE76194; BAE76194; BAE76194.
GeneIDi12934255.
945620.
KEGGiecj:Y75_p0402.
eco:b0414.
PATRICi32115977. VBIEscCol129921_0430.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
X64395 Genomic DNA. Translation: CAA45735.1 .
U82664 Genomic DNA. Translation: AAB40170.1 .
U00096 Genomic DNA. Translation: AAC73517.1 .
AP009048 Genomic DNA. Translation: BAE76194.1 .
PIRi S26201.
RefSeqi NP_414948.1. NC_000913.3.
YP_488706.1. NC_007779.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
2G6V X-ray 2.60 A/B 2-367 [» ]
2O7P X-ray 3.00 A/B 2-367 [» ]
2OBC X-ray 3.00 A/B 2-367 [» ]
ProteinModelPortali P25539.
SMRi P25539. Positions 2-367.
ModBasei Search...

Protein-protein interaction databases

DIPi DIP-10708N.
IntActi P25539. 34 interactions.
MINTi MINT-1221612.
STRINGi 511145.b0414.

Proteomic databases

PaxDbi P25539.
PRIDEi P25539.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAC73517 ; AAC73517 ; b0414 .
BAE76194 ; BAE76194 ; BAE76194 .
GeneIDi 12934255.
945620.
KEGGi ecj:Y75_p0402.
eco:b0414.
PATRICi 32115977. VBIEscCol129921_0430.

Organism-specific databases

EchoBASEi EB1297.
EcoGenei EG11321. ribD.

Phylogenomic databases

eggNOGi COG0117.
HOGENOMi HOG000257442.
KOi K11752.
OMAi QINSVWV.
OrthoDBi EOG66F07R.
PhylomeDBi P25539.

Enzyme and pathway databases

UniPathwayi UPA00275 ; UER00401 .
UPA00275 ; UER00402 .
BioCyci EcoCyc:RIBOFLAVINSYNDEAM-MONOMER.
ECOL316407:JW0404-MONOMER.
MetaCyc:RIBOFLAVINSYNDEAM-MONOMER.

Miscellaneous databases

EvolutionaryTracei P25539.
PROi P25539.

Gene expression databases

Genevestigatori P25539.

Family and domain databases

Gene3Di 3.40.430.10. 1 hit.
InterProi IPR016192. 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 ]
Pfami PF00383. dCMP_cyt_deam_1. 1 hit.
PF01872. RibD_C. 1 hit.
[Graphical view ]
PIRSFi PIRSF006769. RibD. 1 hit.
SUPFAMi SSF53597. SSF53597. 1 hit.
SSF53927. SSF53927. 1 hit.
TIGRFAMsi TIGR00326. eubact_ribD. 1 hit.
TIGR00227. ribD_Cterm. 1 hit.
PROSITEi PS00903. CYT_DCMP_DEAMINASES. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  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. 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.

Entry informationi

Entry nameiRIBD_ECOLI
AccessioniPrimary (citable) accession number: P25539
Secondary accession number(s): Q2MC12
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 1, 1992
Last sequence update: May 1, 1992
Last modified: May 14, 2014
This is version 133 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

3D-structure, Complete proteome, Multifunctional enzyme, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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