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P08203

- ARAD_ECOLI

UniProt

P08203 - ARAD_ECOLI

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Protein
L-ribulose-5-phosphate 4-epimerase
Gene
araD, b0061, JW0060
Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 4 out of 5 - Experimental evidence at protein leveli

Functioni

Catalytic activityi

L-ribulose 5-phosphate = D-xylulose 5-phosphate.UniRule annotation

Cofactori

Binds 1 zinc ion per subunit.1 Publication

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi95 – 951Zinc
Metal bindingi97 – 971Zinc
Metal bindingi171 – 1711Zinc

GO - Molecular functioni

  1. L-ribulose-phosphate 4-epimerase activity Source: EcoCyc
  2. zinc ion binding Source: InterPro

GO - Biological processi

  1. L-arabinose catabolic process to xylulose 5-phosphate Source: EcoCyc
  2. L-lyxose metabolic process Source: EcoCyc
Complete GO annotation...

Keywords - Molecular functioni

Isomerase

Keywords - Biological processi

Arabinose catabolism, Carbohydrate metabolism

Keywords - Ligandi

Metal-binding, Zinc

Enzyme and pathway databases

BioCyciEcoCyc:RIBULPEPIM-MONOMER.
ECOL316407:JW0060-MONOMER.
MetaCyc:RIBULPEPIM-MONOMER.
SABIO-RKP08203.
UniPathwayiUPA00145; UER00567.

Names & Taxonomyi

Protein namesi
Recommended name:
L-ribulose-5-phosphate 4-epimerase (EC:5.1.3.4)
Alternative name(s):
Phosphoribulose isomerase
Gene namesi
Name:araD
Ordered Locus Names:b0061, JW0060
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

Organism-specific databases

EcoGeneiEG10055. araD.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 231231L-ribulose-5-phosphate 4-epimeraseUniRule annotation
PRO_0000162919Add
BLAST

Expressioni

Gene expression databases

GenevestigatoriP08203.

Interactioni

Subunit structurei

Homotetramer.2 Publications

Protein-protein interaction databases

DIPiDIP-9126N.
IntActiP08203. 4 interactions.
STRINGi511145.b0061.

Structurei

Secondary structure

Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi3 – 1816
Beta strandi28 – 336
Turni34 – 374
Beta strandi38 – 414
Beta strandi43 – 453
Turni48 – 503
Helixi53 – 553
Beta strandi57 – 604
Turni61 – 633
Beta strandi66 – 683
Helixi77 – 8610
Beta strandi92 – 954
Helixi99 – 1079
Helixi116 – 1194
Helixi134 – 1385
Helixi141 – 15515
Turni160 – 1623
Beta strandi165 – 1684
Turni169 – 1713
Beta strandi172 – 1798
Helixi180 – 20324
Helixi212 – 22110

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1JDIX-ray2.40A/B/C/D/E/F1-231[»]
1K0WX-ray2.10A/B/C/D/E/F1-231[»]
ProteinModelPortaliP08203.
SMRiP08203. Positions 1-223.

Miscellaneous databases

EvolutionaryTraceiP08203.

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0235.
HOGENOMiHOG000218183.
KOiK01786.
OMAiLALPQHN.
OrthoDBiEOG6358F1.
PhylomeDBiP08203.

Family and domain databases

Gene3Di3.40.225.10. 1 hit.
HAMAPiMF_00989. AraD_entero.
InterProiIPR001303. Aldolase_II/adducin_N.
IPR004661. AraD.
[Graphical view]
PfamiPF00596. Aldolase_II. 1 hit.
[Graphical view]
SMARTiSM01007. Aldolase_II. 1 hit.
[Graphical view]
SUPFAMiSSF53639. SSF53639. 1 hit.
TIGRFAMsiTIGR00760. araD. 1 hit.

Sequencei

Sequence statusi: Complete.

P08203-1 [UniParc]FASTAAdd to Basket

« Hide

MLEDLKRQVL EANLALPKHN LVTLTWGNVS AVDRERGVFV IKPSGVDYSV    50
MTADDMVVVS IETGEVVEGT KKPSSDTPTH RLLYQAFPSI GGIVHTHSRH 100
ATIWAQAGQS IPATGTTHAD YFYGTIPCTR KMTDAEINGE YEWETGNVIV 150
ETFEKQGIDA AQMPGVLVHS HGPFAWGKNA EDAVHNAIVL EEVAYMGIFC 200
RQLAPQLPDM QQTLLDKHYL RKHGAKAYYG Q 231
Length:231
Mass (Da):25,519
Last modified:August 1, 1991 - v2
Checksum:i1753F75958332163
GO

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti50 – 501V → I.
Natural varianti70 – 701T → A.
Natural varianti216 – 2161D → N.

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
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.
PIRiE64727. ISECP4.
RefSeqiNP_414603.1. NC_000913.3.
YP_488367.1. NC_007779.1.

Genome annotation databases

EnsemblBacteriaiAAC73172; AAC73172; b0061.
BAB96630; BAB96630; BAB96630.
GeneIDi12934049.
945294.
KEGGiecj:Y75_p0061.
eco:b0061.
PATRICi32115223. VBIEscCol129921_0063.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
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 .
PIRi E64727. ISECP4.
RefSeqi NP_414603.1. NC_000913.3.
YP_488367.1. NC_007779.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1JDI X-ray 2.40 A/B/C/D/E/F 1-231 [» ]
1K0W X-ray 2.10 A/B/C/D/E/F 1-231 [» ]
ProteinModelPortali P08203.
SMRi P08203. Positions 1-223.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

DIPi DIP-9126N.
IntActi P08203. 4 interactions.
STRINGi 511145.b0061.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAC73172 ; AAC73172 ; b0061 .
BAB96630 ; BAB96630 ; BAB96630 .
GeneIDi 12934049.
945294.
KEGGi ecj:Y75_p0061.
eco:b0061.
PATRICi 32115223. VBIEscCol129921_0063.

Organism-specific databases

EchoBASEi EB0053.
EcoGenei EG10055. araD.

Phylogenomic databases

eggNOGi COG0235.
HOGENOMi HOG000218183.
KOi K01786.
OMAi LALPQHN.
OrthoDBi EOG6358F1.
PhylomeDBi P08203.

Enzyme and pathway databases

UniPathwayi UPA00145 ; UER00567 .
BioCyci EcoCyc:RIBULPEPIM-MONOMER.
ECOL316407:JW0060-MONOMER.
MetaCyc:RIBULPEPIM-MONOMER.
SABIO-RK P08203.

Miscellaneous databases

EvolutionaryTracei P08203.
PROi P08203.

Gene expression databases

Genevestigatori P08203.

Family and domain databases

Gene3Di 3.40.225.10. 1 hit.
HAMAPi MF_00989. AraD_entero.
InterProi IPR001303. Aldolase_II/adducin_N.
IPR004661. AraD.
[Graphical view ]
Pfami PF00596. Aldolase_II. 1 hit.
[Graphical view ]
SMARTi SM01007. Aldolase_II. 1 hit.
[Graphical view ]
SUPFAMi SSF53639. SSF53639. 1 hit.
TIGRFAMsi TIGR00760. araD. 1 hit.
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  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. 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.

Entry informationi

Entry nameiARAD_ECOLI
AccessioniPrimary (citable) accession number: P08203
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 1, 1988
Last sequence update: August 1, 1991
Last modified: May 14, 2014
This is version 133 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, 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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