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Protein

Riboflavin biosynthesis protein RibD

Gene

ribD

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: 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

Zn2+By similarityNote: Binds 1 zinc ion.By similarity

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi50 – 501Zinc; catalyticBy similarity
Active sitei52 – 521Proton donorBy similarity
Metal bindingi75 – 751Zinc; catalyticBy similarity
Metal bindingi84 – 841Zinc; catalyticBy 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. diaminohydroxyphosphoribosylaminopyrimidine deaminase activity Source: EcoCyc
  3. NADP binding Source: EcoCyc
  4. zinc ion binding Source: InterPro

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.
BRENDAi1.1.1.193. 2165.
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 Componenti: Chromosome UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG11321. ribD.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 367367Riboflavin biosynthesis protein RibDPRO_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

1
367
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi2 – 1413Combined sources
Helixi15 – 173Combined sources
Turni18 – 203Combined sources
Beta strandi28 – 336Combined sources
Beta strandi36 – 427Combined sources
Beta strandi46 – 483Combined sources
Helixi51 – 599Combined sources
Helixi60 – 634Combined sources
Beta strandi64 – 663Combined sources
Beta strandi68 – 725Combined sources
Helixi85 – 917Combined sources
Beta strandi96 – 1005Combined sources
Helixi111 – 1177Combined sources
Beta strandi122 – 1243Combined sources
Helixi128 – 1347Combined sources
Helixi136 – 1438Combined sources
Beta strandi144 – 1463Combined sources
Beta strandi148 – 1569Combined sources
Helixi174 – 18512Combined sources
Beta strandi187 – 1937Combined sources
Helixi194 – 2007Combined sources
Helixi208 – 2103Combined sources
Helixi214 – 2174Combined sources
Helixi221 – 2233Combined sources
Beta strandi228 – 2325Combined sources
Helixi243 – 2453Combined sources
Beta strandi247 – 2493Combined sources
Beta strandi251 – 2577Combined sources
Beta strandi267 – 2715Combined sources
Helixi281 – 29010Combined sources
Beta strandi295 – 2984Combined sources
Helixi302 – 31110Combined sources
Beta strandi315 – 3239Combined sources
Beta strandi349 – 3568Combined sources
Beta strandi359 – 3657Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP25539.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini1 – 123123CMP/dCMP-type deaminasePROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni1 – 145145DeaminaseAdd
BLAST
Regioni146 – 367222ReductaseAdd
BLAST

Sequence similaritiesi

In the N-terminal section; belongs to the cytidine and deoxycytidylate deaminase family.Curated
In the C-terminal section; belongs to the HTP reductase family.Curated
Contains 1 CMP/dCMP-type deaminase domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiCOG0117.
HOGENOMiHOG000257442.
InParanoidiP25539.
KOiK11752.
OMAiMRTGFPW.
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. 1 hit.
PS51747. CYT_DCMP_DEAMINASES_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P25539-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MQDEYYMARA LKLAQRGRFT THPNPNVGCV IVKDGEIVGE GYHQRAGEPH
60 70 80 90 100
AEVHALRMAG EKAKGATAYV TLEPCSHHGR TPPCCDALIA AGVARVVASM
110 120 130 140 150
QDPNPQVAGR GLYRLQQAGI DVSHGLMMSE AEQLNKGFLK RMRTGFPYIQ
160 170 180 190 200
LKLGASLDGR TAMASGESQW ITSPQARRDV QLLRAQSHAI LTSSATVLAD
210 220 230 240 250
DPALTVRWSE LDEQTQALYP QQNLRQPIRI VIDSQNRVTP VHRIVQQPGE
260 270 280 290 300
TWFARTQEDS REWPETVRTL LIPEHKGHLD LVVLMMQLGK QQINSIWVEA
310 320 330 340 350
GPTLAGALLQ AGLVDELIVY IAPKLLGSDA RGLCTLPGLE KLADAPQFKF
360
KEIRHVGPDV CLHLVGA
Length:367
Mass (Da):40,338
Last modified:May 1, 1992 - v1
Checksum:iB19CEF474D48D14D
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
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.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

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

Proteomic databases

PaxDbiP25539.
PRIDEiP25539.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

EchoBASEiEB1297.
EcoGeneiEG11321. ribD.

Phylogenomic databases

eggNOGiCOG0117.
HOGENOMiHOG000257442.
InParanoidiP25539.
KOiK11752.
OMAiMRTGFPW.
OrthoDBiEOG66F07R.
PhylomeDBiP25539.

Enzyme and pathway databases

UniPathwayiUPA00275; UER00401.
UPA00275; UER00402.
BioCyciEcoCyc:RIBOFLAVINSYNDEAM-MONOMER.
ECOL316407:JW0404-MONOMER.
MetaCyc:RIBOFLAVINSYNDEAM-MONOMER.
BRENDAi1.1.1.193. 2165.

Miscellaneous databases

EvolutionaryTraceiP25539.
PROiP25539.

Gene expression databases

GenevestigatoriP25539.

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. 1 hit.
PS51747. CYT_DCMP_DEAMINASES_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

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: April 1, 2015
This is version 138 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

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 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.