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Protein

L-ribulose-5-phosphate 4-epimerase

Gene

araD

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

Zn2+UniRule annotation1 PublicationNote: Binds 1 zinc ion per subunit.UniRule annotation1 Publication

Pathway: L-arabinose degradation via L-ribulose

This protein is involved in step 3 of the subpathway that synthesizes D-xylulose 5-phosphate from L-arabinose (bacterial route).UniRule annotation
Proteins known to be involved in the 3 steps of the subpathway in this organism are:
  1. L-arabinose isomerase (araA), L-arabinose isomerase (araA)
  2. Ribulokinase (araB), Ribulokinase (araB)
  3. L-ribulose-5-phosphate 4-epimerase (araD)
This subpathway is part of the pathway L-arabinose degradation via L-ribulose, which is itself part of Carbohydrate degradation.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes D-xylulose 5-phosphate from L-arabinose (bacterial route), the pathway L-arabinose degradation via L-ribulose and in Carbohydrate degradation.

Sites

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

GO - Molecular functioni

  • L-ribulose-phosphate 4-epimerase activity Source: EcoCyc
  • zinc ion binding Source: InterPro

GO - Biological processi

  • L-arabinose catabolic process to xylulose 5-phosphate Source: EcoCyc
  • 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-epimeraseUniRule annotation (EC:5.1.3.4UniRule annotation)
Alternative name(s):
Phosphoribulose isomeraseUniRule annotation
Gene namesi
Name:araDUniRule annotation
Ordered Locus Names:b0061, JW0060
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
ProteomesiUP000000318 Componenti: Chromosome UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10055. araD.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 231231L-ribulose-5-phosphate 4-epimerasePRO_0000162919Add
BLAST

Interactioni

Subunit structurei

Homotetramer.UniRule annotation2 Publications

Protein-protein interaction databases

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

Structurei

Secondary structure

1
231
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi3 – 1816Combined sources
Beta strandi28 – 336Combined sources
Turni34 – 374Combined sources
Beta strandi38 – 414Combined sources
Beta strandi43 – 453Combined sources
Turni48 – 503Combined sources
Helixi53 – 553Combined sources
Beta strandi57 – 604Combined sources
Turni61 – 633Combined sources
Beta strandi66 – 683Combined sources
Helixi77 – 8610Combined sources
Beta strandi92 – 954Combined sources
Helixi99 – 1079Combined sources
Helixi116 – 1194Combined sources
Helixi134 – 1385Combined sources
Helixi141 – 15515Combined sources
Turni160 – 1623Combined sources
Beta strandi165 – 1684Combined sources
Turni169 – 1713Combined sources
Beta strandi172 – 1798Combined sources
Helixi180 – 20324Combined sources
Helixi212 – 22110Combined sources

3D structure databases

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

Miscellaneous databases

EvolutionaryTraceiP08203.

Family & Domainsi

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiCOG0235.
HOGENOMiHOG000218183.
InParanoidiP08203.
KOiK01786.
OMAiCTRLMTD.
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

        10         20         30         40         50
MLEDLKRQVL EANLALPKHN LVTLTWGNVS AVDRERGVFV IKPSGVDYSV
60 70 80 90 100
MTADDMVVVS IETGEVVEGT KKPSSDTPTH RLLYQAFPSI GGIVHTHSRH
110 120 130 140 150
ATIWAQAGQS IPATGTTHAD YFYGTIPCTR KMTDAEINGE YEWETGNVIV
160 170 180 190 200
ETFEKQGIDA AQMPGVLVHS HGPFAWGKNA EDAVHNAIVL EEVAYMGIFC
210 220 230
RQLAPQLPDM QQTLLDKHYL RKHGAKAYYG Q
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:
EMBLi
GenBanki
DDBJi
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.

Genome annotation databases

EnsemblBacteriaiAAC73172; AAC73172; b0061.
BAB96630; BAB96630; BAB96630.
GeneIDi945294.
KEGGiecj:Y75_p0061.
eco:b0061.
PATRICi32115223. VBIEscCol129921_0063.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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.

3D structure databases

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

Protein-protein interaction databases

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

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC73172; AAC73172; b0061.
BAB96630; BAB96630; BAB96630.
GeneIDi945294.
KEGGiecj:Y75_p0061.
eco:b0061.
PATRICi32115223. VBIEscCol129921_0063.

Organism-specific databases

EchoBASEiEB0053.
EcoGeneiEG10055. araD.

Phylogenomic databases

eggNOGiCOG0235.
HOGENOMiHOG000218183.
InParanoidiP08203.
KOiK01786.
OMAiCTRLMTD.
OrthoDBiEOG6358F1.
PhylomeDBiP08203.

Enzyme and pathway databases

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

Miscellaneous databases

EvolutionaryTraceiP08203.
PROiP08203.

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.
ProtoNetiSearch...

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: June 24, 2015
This is version 139 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

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.