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P08203 (ARAD_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 132. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
L-ribulose-5-phosphate 4-epimerase

EC=5.1.3.4
Alternative name(s):
Phosphoribulose isomerase
Gene names
Name:araD
Ordered Locus Names:b0061, JW0060
OrganismEscherichia coli (strain K12) [Reference proteome] [HAMAP]
Taxonomic identifier83333 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Protein attributes

Sequence length231 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Catalytic activity

L-ribulose 5-phosphate = D-xylulose 5-phosphate. HAMAP-Rule MF_00989

Cofactor

Binds 1 zinc ion per subunit. Ref.12

Pathway

Carbohydrate degradation; L-arabinose degradation via L-ribulose; D-xylulose 5-phosphate from L-arabinose (bacterial route): step 3/3. HAMAP-Rule MF_00989

Subunit structure

Homotetramer. Ref.10 Ref.12

Sequence similarities

Belongs to the aldolase class II family. AraD/FucA subfamily.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 231231L-ribulose-5-phosphate 4-epimerase HAMAP-Rule MF_00989
PRO_0000162919

Sites

Metal binding951Zinc
Metal binding971Zinc
Metal binding1711Zinc

Natural variations

Natural variant501V → I.
Natural variant701T → A.
Natural variant2161D → N.

Secondary structure

....................................... 231
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P08203 [UniParc].

Last modified August 1, 1991. Version 2.
Checksum: 1753F75958332163

FASTA23125,519
        10         20         30         40         50         60 
MLEDLKRQVL EANLALPKHN LVTLTWGNVS AVDRERGVFV IKPSGVDYSV MTADDMVVVS 

        70         80         90        100        110        120 
IETGEVVEGT KKPSSDTPTH RLLYQAFPSI GGIVHTHSRH ATIWAQAGQS IPATGTTHAD 

       130        140        150        160        170        180 
YFYGTIPCTR KMTDAEINGE YEWETGNVIV ETFEKQGIDA AQMPGVLVHS HGPFAWGKNA 

       190        200        210        220        230 
EDAVHNAIVL EEVAYMGIFC RQLAPQLPDM QQTLLDKHYL RKHGAKAYYG Q 

« Hide

References

« Hide 'large scale' references
[1]"The organization of the araBAD operon of Escherichia coli."
Lee N., Gielow W., Martin R., Hamilton E., Fowler A.
Gene 47:231-244(1986) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: B.
[2]"Nucleotide sequence and deletion analysis of the polB gene of Escherichia coli."
Chen H., Sun Y., Stark T., Beattie W., Moses R.E.
DNA Cell Biol. 9:631-635(1990) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: K12.
[3]"Nucleotide sequence of the araD gene of Escherichia coli K12 encoding the L-ribulose 5-phosphate 4-epimerase."
Mineno J., Fukui H., Ishino Y., Kato I., Shinagawa H.
Nucleic Acids Res. 18:6722-6722(1990) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: K12.
[4]"Systematic sequencing of the Escherichia coli genome: analysis of the 0-2.4 min region."
Yura T., Mori H., Nagai H., Nagata T., Ishihama A., Fujita N., Isono K., Mizobuchi K., Nakata A.
Nucleic Acids Res. 20:3305-3308(1992) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12.
[5]"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 277:1453-1462(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / MG1655 / ATCC 47076.
[6]"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.
[7]"Purification and preliminary X-ray crystallographic studies of recombinant L-ribulose-5-phosphate 4-epimerase from Escherichia coli."
Andersson A., Schneider G., Lindqvist Y.
Protein Sci. 4:1648-1650(1995) [PubMed] [Europe PMC] [Abstract]
Cited for: PROTEIN SEQUENCE OF 1-8, PRELIMINARY CRYSTALLIZATION.
[8]"Escherichia coli DNA polymerase II is homologous to alpha-like DNA polymerases."
Iwasaki H., Ishino Y., Toh H., Nakata A., Shinagawa H.
Mol. Gen. Genet. 226:24-33(1991) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 158-231.
Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[9]"DNA polymerase II is encoded by the DNA damage-inducible dinA gene of Escherichia coli."
Bonner C.A., Hays S., McEntee K., Goodman M.F.
Proc. Natl. Acad. Sci. U.S.A. 87:7663-7667(1990) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 222-231.
Strain: K12.
[10]"Crystalline L-ribulose 5-phosphate 4-epimerase from Escherichia coli."
Lee N., Patrick J.W., Masson M.
J. Biol. Chem. 243:4700-4705(1968) [PubMed] [Europe PMC] [Abstract]
Cited for: SUBUNIT.
Strain: B/R.
[11]"Escherichia coli proteome analysis using the gene-protein database."
VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C.
Electrophoresis 18:1243-1251(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY 2D-GEL.
[12]"The structure of L-ribulose-5-phosphate 4-epimerase: an aldolase-like platform for epimerization."
Luo Y., Samuel J., Mosimann S.C., Lee J.E., Tanner M.E., Strynadka N.C.
Biochemistry 40:14763-14771(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) IN COMPLEX WITH ZINC IONS, COFACTOR, SUBUNIT.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
M15263 Genomic DNA. Translation: AAA23464.1.
M35371 Genomic DNA. No translation available.
M62646 Genomic DNA. Translation: AAA24405.1.
U00096 Genomic DNA. Translation: AAC73172.1.
AP009048 Genomic DNA. Translation: BAB96630.1.
M37727 Genomic DNA. Translation: AAA23683.1.
M38283 Genomic DNA. Translation: AAA63763.1.
X56048 Genomic DNA. Translation: CAA39519.1.
PIRISECP4. E64727.
RefSeqNP_414603.1. NC_000913.3.
YP_488367.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1JDIX-ray2.40A/B/C/D/E/F1-231[»]
1K0WX-ray2.10A/B/C/D/E/F1-231[»]
ProteinModelPortalP08203.
SMRP08203. Positions 1-223.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

DIPDIP-9126N.
IntActP08203. 4 interactions.
STRING511145.b0061.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAC73172; AAC73172; b0061.
BAB96630; BAB96630; BAB96630.
GeneID12934049.
945294.
KEGGecj:Y75_p0061.
eco:b0061.
PATRIC32115223. VBIEscCol129921_0063.

Organism-specific databases

EchoBASEEB0053.
EcoGeneEG10055. araD.

Phylogenomic databases

eggNOGCOG0235.
HOGENOMHOG000218183.
KOK01786.
OMACTRLMTD.
OrthoDBEOG6358F1.
PhylomeDBP08203.
ProtClustDBPRK08193.

Enzyme and pathway databases

BioCycEcoCyc:RIBULPEPIM-MONOMER.
ECOL316407:JW0060-MONOMER.
MetaCyc:RIBULPEPIM-MONOMER.
SABIO-RKP08203.
UniPathwayUPA00145; UER00567.

Gene expression databases

GenevestigatorP08203.

Family and domain databases

Gene3D3.40.225.10. 1 hit.
HAMAPMF_00989. AraD_entero.
InterProIPR001303. Aldolase_II/adducin_N.
IPR004661. AraD.
[Graphical view]
PfamPF00596. Aldolase_II. 1 hit.
[Graphical view]
SMARTSM01007. Aldolase_II. 1 hit.
[Graphical view]
SUPFAMSSF53639. SSF53639. 1 hit.
TIGRFAMsTIGR00760. araD. 1 hit.
ProtoNetSearch...

Other

EvolutionaryTraceP08203.
PROP08203.

Entry information

Entry nameARAD_ECOLI
AccessionPrimary (citable) accession number: P08203
Entry history
Integrated into UniProtKB/Swiss-Prot: August 1, 1988
Last sequence update: August 1, 1991
Last modified: April 16, 2014
This is version 132 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

PATHWAY comments

Index of metabolic and biosynthesis pathways

Escherichia coli

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