Riboflavin biosynthesis protein RibD - Escherichia coli (strain K12)

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P25539 (RIBD_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 127. History...

Clusters with 100%, 90%, 50% identity |

Documents (4) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
Riboflavin biosynthesis protein RibD

Including the following 2 domains:

Diaminohydroxyphosphoribosylaminopyrimidine deaminase
Short name=DRAP deaminase
EC=3.5.4.26
Alternative name(s):
Riboflavin-specific deaminase
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

Organism

Escherichia coli (strain K12) [Reference proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia ›

Protein attributes

Sequence length	367 AA.
Sequence status	Complete.
Protein existence	Evidence 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.

Ontologies

Keywords
Biological process	Riboflavin biosynthesis
Ligand	Metal-binding NADP Zinc
Molecular function	Hydrolase Oxidoreductase
Technical term	3D-structure Complete proteome Multifunctional enzyme Reference proteome
Gene Ontology (GO)
Biological_process	riboflavin biosynthetic process Inferred from direct assay PubMed 18500821. Source: EcoCyc
Molecular_function	5-amino-6-(5-phosphoribosylamino)uracil reductase activity Inferred from direct assay PubMed 18500821 Ref.5. Source: EcoCyc NADP binding Inferred from direct assay PubMed 18500821. Source: EcoCyc diaminohydroxyphosphoribosylaminopyrimidine deaminase activity Inferred from direct assay PubMed 18500821 Ref.5. Source: EcoCyc zinc ion binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 367

367

Riboflavin biosynthesis protein RibD

PRO_0000171721

Regions

Nucleotide binding

161 – 164

NADP

Nucleotide binding

301 – 304

NADP

Region

1 – 145

145

Deaminase

Region

146 – 367

222

Reductase

Sites

Active site

Proton donor By similarity

Metal binding

Zinc; catalytic By similarity

Metal binding

Zinc; catalytic By similarity

Metal binding

Zinc; catalytic By similarity

Binding site

168

Substrate

Binding site

170

NADP

Binding site

184

Substrate

Binding site

196

NADP

Binding site

200

NADP

Binding site

204

Substrate; via amide nitrogen

Binding site

207

Substrate

Binding site

234

NADP

Binding site

299

Substrate

Secondary structure

367

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

P25539 [UniParc].

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

FASTA

367

40,338

        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' referencesShow '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 277:1453-1474(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.

PIR

S26201.

RefSeq

NP_414948.1. NC_000913.2.
YP_488706.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

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	[»]

ProteinModelPortal

P25539.

SMR

P25539. Positions 2-367.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-10708N.

IntAct

P25539. 30 interactions.

MINT

MINT-1221612.

STRING

511145.b0414.

Proteomic databases

PaxDb

P25539.

PRIDE

P25539.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC73517; AAC73517; b0414.
BAE76194; BAE76194; BAE76194.

GeneID

12934255.
945620.

KEGG

ecj:Y75_p0402.
eco:b0414.

PATRIC

32115977. VBIEscCol129921_0430.

Organism-specific databases

EchoBASE

EB1297.

EcoGene

EG11321. ribD.

Phylogenomic databases

eggNOG

COG0117.

HOGENOM

HOG000257442.

K11752.

OMA

LHVEAGF.

ProtClustDB

PRK10786.

Enzyme and pathway databases

BioCyc

EcoCyc:RIBOFLAVINSYNDEAM-MONOMER.
ECOL316407:JW0404-MONOMER.
MetaCyc:RIBOFLAVINSYNDEAM-MONOMER.

UniPathway

UPA00275; UER00401.
UPA00275; UER00402.

Gene expression databases

Genevestigator

P25539.

Family and domain databases

Gene3D

3.40.430.10. 1 hit.

InterPro

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]

Pfam

PF00383. dCMP_cyt_deam_1. 1 hit.
PF01872. RibD_C. 1 hit.
[Graphical view]

PIRSF

PIRSF006769. RibD. 1 hit.

SUPFAM

SSF53927. Cytidine_deaminase-like. 1 hit.
SSF53597. SSF53597. 1 hit.

TIGRFAMs

TIGR00326. eubact_ribD. 1 hit.
TIGR00227. ribD_Cterm. 1 hit.

PROSITE

PS00903. CYT_DCMP_DEAMINASES. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P25539.

Entry information

Entry name

RIBD_ECOLI

Accession

Primary (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:	May 1, 2013
This is version 127 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program

Relevant documents

Escherichia coli

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

PATHWAY comments

Index of metabolic and biosynthesis pathways

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Including the following 2 domains:

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Regions

Sites

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Other

Entry information

Relevant documents