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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: riboflavin biosynthesis

This protein is involved in step 2 and 3 of the subpathway that synthesizes 5-amino-6-(D-ribitylamino)uracil from GTP.
Proteins known to be involved in the 4 steps of the subpathway in this organism are:
  1. GTP cyclohydrolase-2 (ribA)
  2. Riboflavin biosynthesis protein RibD (ribD)
  3. Riboflavin biosynthesis protein RibD (ribD)
  4. 5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase YbjI (ybjI), 5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase YigB (yigB)
This subpathway is part of the pathway riboflavin biosynthesis, which is itself part of Cofactor biosynthesis.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes 5-amino-6-(D-ribitylamino)uracil from GTP, the pathway riboflavin biosynthesis and in Cofactor biosynthesis.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi50Zinc; catalyticBy similarity1
Active sitei52Proton donorBy similarity1
Metal bindingi75Zinc; catalyticBy similarity1
Metal bindingi84Zinc; catalyticBy similarity1
Binding sitei168Substrate1
Binding sitei170NADP1
Binding sitei184Substrate1
Binding sitei196NADP1
Binding sitei200NADP1
Binding sitei204Substrate; via amide nitrogen1
Binding sitei207Substrate1
Binding sitei234NADP1
Binding sitei299Substrate1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi161 – 164NADP4
Nucleotide bindingi301 – 304NADP4

GO - Molecular functioni

  • 5-amino-6-(5-phosphoribosylamino)uracil reductase activity Source: EcoCyc
  • diaminohydroxyphosphoribosylaminopyrimidine deaminase activity Source: EcoCyc
  • NADP binding Source: EcoCyc
  • zinc ion binding Source: InterPro

GO - Biological processi

  • riboflavin biosynthetic process Source: EcoCyc
  • RNA modification Source: GO_Central

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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG11321. ribD.

Subcellular locationi

GO - Cellular componenti

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001717211 – 367Riboflavin biosynthesis protein RibDAdd BLAST367

Proteomic databases

PaxDbiP25539.
PRIDEiP25539.

Interactioni

Subunit structurei

Homodimer.1 Publication

Protein-protein interaction databases

BioGridi4263249. 17 interactors.
DIPiDIP-10708N.
IntActiP25539. 34 interactors.
MINTiMINT-1221612.
STRINGi511145.b0414.

Structurei

Secondary structure

1367
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi2 – 14Combined sources13
Helixi15 – 17Combined sources3
Turni18 – 20Combined sources3
Beta strandi28 – 33Combined sources6
Beta strandi36 – 42Combined sources7
Beta strandi46 – 48Combined sources3
Helixi51 – 59Combined sources9
Helixi60 – 63Combined sources4
Beta strandi64 – 66Combined sources3
Beta strandi68 – 72Combined sources5
Helixi85 – 91Combined sources7
Beta strandi96 – 100Combined sources5
Helixi111 – 117Combined sources7
Beta strandi122 – 124Combined sources3
Helixi128 – 134Combined sources7
Helixi136 – 143Combined sources8
Beta strandi144 – 146Combined sources3
Beta strandi148 – 156Combined sources9
Beta strandi164 – 166Combined sources3
Helixi174 – 185Combined sources12
Beta strandi187 – 193Combined sources7
Helixi194 – 200Combined sources7
Helixi208 – 210Combined sources3
Helixi214 – 217Combined sources4
Helixi221 – 223Combined sources3
Beta strandi228 – 232Combined sources5
Helixi243 – 245Combined sources3
Beta strandi247 – 249Combined sources3
Beta strandi251 – 257Combined sources7
Beta strandi267 – 271Combined sources5
Helixi281 – 290Combined sources10
Beta strandi295 – 298Combined sources4
Helixi302 – 311Combined sources10
Beta strandi315 – 323Combined sources9
Beta strandi349 – 356Combined sources8
Beta strandi359 – 365Combined sources7

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2G6VX-ray2.60A/B2-367[»]
2O7PX-ray3.00A/B2-367[»]
2OBCX-ray3.00A/B2-367[»]
ProteinModelPortaliP25539.
SMRiP25539.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP25539.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini1 – 123CMP/dCMP-type deaminasePROSITE-ProRule annotationAdd BLAST123

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni1 – 145DeaminaseAdd BLAST145
Regioni146 – 367ReductaseAdd BLAST222

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

eggNOGiENOG4105D1W. Bacteria.
COG0117. LUCA.
COG1985. LUCA.
HOGENOMiHOG000257442.
InParanoidiP25539.
KOiK11752.
OMAiGHRWRAR.
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.
WP_001150457.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC73517; AAC73517; b0414.
BAE76194; BAE76194; BAE76194.
GeneIDi945620.
KEGGiecj:JW0404.
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.
WP_001150457.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2G6VX-ray2.60A/B2-367[»]
2O7PX-ray3.00A/B2-367[»]
2OBCX-ray3.00A/B2-367[»]
ProteinModelPortaliP25539.
SMRiP25539.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4263249. 17 interactors.
DIPiDIP-10708N.
IntActiP25539. 34 interactors.
MINTiMINT-1221612.
STRINGi511145.b0414.

Proteomic databases

PaxDbiP25539.
PRIDEiP25539.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC73517; AAC73517; b0414.
BAE76194; BAE76194; BAE76194.
GeneIDi945620.
KEGGiecj:JW0404.
eco:b0414.
PATRICi32115977. VBIEscCol129921_0430.

Organism-specific databases

EchoBASEiEB1297.
EcoGeneiEG11321. ribD.

Phylogenomic databases

eggNOGiENOG4105D1W. Bacteria.
COG0117. LUCA.
COG1985. LUCA.
HOGENOMiHOG000257442.
InParanoidiP25539.
KOiK11752.
OMAiGHRWRAR.
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.

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...

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: November 2, 2016
This is version 146 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

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 one 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.