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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

Pathwayi: 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)
  2. 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)DescriptionActionsGraphical viewLength
Metal bindingi95ZincUniRule annotation1 Publication1
Metal bindingi97ZincUniRule annotation1 Publication1
Metal bindingi171ZincUniRule annotation1 Publication1

GO - Molecular functioni

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

Organism-specific databases

EcoGeneiEG10055. araD.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: EcoCyc
Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001629191 – 231L-ribulose-5-phosphate 4-epimeraseAdd BLAST231

Proteomic databases

PaxDbiP08203.
PRIDEiP08203.

Interactioni

Subunit structurei

Homotetramer.UniRule annotation2 Publications

Protein-protein interaction databases

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

Structurei

Secondary structure

1231
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi3 – 18Combined sources16
Beta strandi28 – 33Combined sources6
Turni34 – 37Combined sources4
Beta strandi38 – 41Combined sources4
Beta strandi43 – 45Combined sources3
Turni48 – 50Combined sources3
Helixi53 – 55Combined sources3
Beta strandi57 – 60Combined sources4
Turni61 – 63Combined sources3
Beta strandi66 – 68Combined sources3
Helixi77 – 86Combined sources10
Beta strandi92 – 95Combined sources4
Helixi99 – 107Combined sources9
Helixi116 – 119Combined sources4
Helixi134 – 138Combined sources5
Helixi141 – 155Combined sources15
Turni160 – 162Combined sources3
Beta strandi165 – 168Combined sources4
Turni169 – 171Combined sources3
Beta strandi172 – 179Combined sources8
Helixi180 – 203Combined sources24
Helixi212 – 221Combined sources10

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1JDIX-ray2.40A/B/C/D/E/F1-231[»]
1K0WX-ray2.10A/B/C/D/E/F1-231[»]
ProteinModelPortaliP08203.
SMRiP08203.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP08203.

Family & Domainsi

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiENOG4107R0P. Bacteria.
COG0235. LUCA.
HOGENOMiHOG000218183.
InParanoidiP08203.
KOiK01786.
OMAiHSPWAVS.
PhylomeDBiP08203.

Family and domain databases

Gene3Di3.40.225.10. 1 hit.
HAMAPiMF_00989. AraD_entero. 1 hit.
InterProiIPR001303. Aldolase_II/adducin_N.
IPR004661. AraD.
IPR033748. AraD_entero.
[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)DescriptionActionsGraphical viewLength
Natural varianti50V → I.1
Natural varianti70T → A.1
Natural varianti216D → N.1

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.
WP_000888666.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC73172; AAC73172; b0061.
BAB96630; BAB96630; BAB96630.
GeneIDi945294.
KEGGiecj:JW0060.
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.
WP_000888666.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1JDIX-ray2.40A/B/C/D/E/F1-231[»]
1K0WX-ray2.10A/B/C/D/E/F1-231[»]
ProteinModelPortaliP08203.
SMRiP08203.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

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

Proteomic databases

PaxDbiP08203.
PRIDEiP08203.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC73172; AAC73172; b0061.
BAB96630; BAB96630; BAB96630.
GeneIDi945294.
KEGGiecj:JW0060.
eco:b0061.
PATRICi32115223. VBIEscCol129921_0063.

Organism-specific databases

EchoBASEiEB0053.
EcoGeneiEG10055. araD.

Phylogenomic databases

eggNOGiENOG4107R0P. Bacteria.
COG0235. LUCA.
HOGENOMiHOG000218183.
InParanoidiP08203.
KOiK01786.
OMAiHSPWAVS.
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. 1 hit.
InterProiIPR001303. Aldolase_II/adducin_N.
IPR004661. AraD.
IPR033748. AraD_entero.
[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...

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: November 30, 2016
This is version 149 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

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.