UniProtKB - P08203 (ARAD_ECOLI)
Protein
L-ribulose-5-phosphate 4-epimerase AraD
Gene
araD
Organism
Escherichia coli (strain K12)
Status
Functioni
Involved in the degradation of L-arabinose (PubMed:13890280). Catalyzes the interconversion of L-ribulose 5-phosphate (LRu5P) and D-xylulose 5-phosphate (D-Xu5P) via a retroaldol/aldol mechanism (carbon-carbon bond cleavage analogous to a class II aldolase reaction).UniRule annotation6 Publications
Catalytic activityi
- EC:5.1.3.4UniRule annotation5 Publications
Cofactori
Zn2+UniRule annotation4 PublicationsNote: Binds 1 zinc ion per subunit (PubMed:9548961, PubMed:10769139, PubMed:11732895, PubMed:11732896). Also able to use cobalt and manganese ions, but less efficiently (PubMed:10769139).UniRule annotation4 Publications
Activity regulationi
Inhibited by glycolohydroxamate at concentration above 0.1 mM.1 Publication
Kineticsi
Kcat is 20.4 sec(-1) for L-ribulose 5-phosphate (LRu5P) as substrate (PubMed:9548961). Kcat is 19.4 sec(-1) for L-ribulose 5-phosphate (LRu5P) as substrate (PubMed:11732896). Kcat is 17.3 sec(-1) for L-ribulose 5-phosphate (LRu5P) as substrate (PubMed:10769139). Kcat is 10.6 sec(-1) for L-ribulose 5-phosphate (LRu5P) as substrate (at pH 7) (PubMed:10769138). Kcat is 4.23 sec(-1) for L-ribulose 5-phosphate (LRu5P) as substrate (at pH 5.5) (PubMed:10769138).4 Publications
- KM=0.17 µM for Zn2+1 Publication
- KM=0.29 µM for Co2+1 Publication
- KM=0.54 µM for Mn2+1 Publication
- KM=47 µM for L-ribulose 5-phosphate (LRu5P) (with zinc ion)2 Publications
- KM=87 µM for L-ribulose 5-phosphate (LRu5P) (with zinc ion)1 Publication
- KM=95 µM for L-ribulose 5-phosphate (LRu5P) (with zinc ion)1 Publication
- KM=110 µM for L-ribulose 5-phosphate (LRu5P) (with cobalt ion)1 Publication
- KM=425 µM for L-ribulose 5-phosphate (LRu5P) (with manganese ion)1 Publication
pH dependencei
Optimum pH is 7.1 Publication
: L-arabinose degradation via L-ribulose Pathwayi
This protein is involved in step 3 of the subpathway that synthesizes D-xylulose 5-phosphate from L-arabinose (bacterial route).UniRule annotation1 PublicationProteins known to be involved in the 3 steps of the subpathway in this organism are:
- L-arabinose isomerase (araA), L-arabinose isomerase (araA)
- Ribulokinase (araB), Ribulokinase (araB)
- L-ribulose-5-phosphate 4-epimerase (araD), L-ribulose-5-phosphate 4-epimerase AraD (araD)
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 key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Metal bindingi | 76 | ZincUniRule annotation2 Publications | 1 | |
Metal bindingi | 95 | Zinc; via tele nitrogenUniRule annotationCombined sources2 Publications2 Publications | 1 | |
Metal bindingi | 97 | Zinc; via tele nitrogenUniRule annotationCombined sources2 Publications2 Publications | 1 | |
Active sitei | 120 | Proton donor/acceptorUniRule annotation1 Publication | 1 | |
Metal bindingi | 171 | Zinc; via tele nitrogenUniRule annotationCombined sources1 Publication2 Publications | 1 | |
Active sitei | 229 | Proton donor/acceptorUniRule annotation1 Publication | 1 |
GO - Molecular functioni
- aldehyde-lyase activity Source: GO_Central
- L-ribulose-phosphate 4-epimerase activity Source: UniProtKB
- zinc ion binding Source: UniProtKB
GO - Biological processi
- L-arabinose catabolic process to xylulose 5-phosphate Source: UniProtKB
- L-lyxose metabolic process Source: EcoCyc
- pentose catabolic process Source: GO_Central
- protein homotetramerization Source: EcoCyc
Keywordsi
Molecular function | Isomerase |
Biological process | Arabinose catabolism, Carbohydrate metabolism |
Ligand | Cobalt, Manganese, Metal-binding, Zinc |
Enzyme and pathway databases
BioCyci | EcoCyc:RIBULPEPIM-MONOMER MetaCyc:RIBULPEPIM-MONOMER |
SABIO-RKi | P08203 |
UniPathwayi | UPA00145;UER00567 |
Names & Taxonomyi
Protein namesi | Recommended name: L-ribulose-5-phosphate 4-epimerase AraD1 PublicationUniRule annotation (EC:5.1.3.4UniRule annotation5 Publications)Alternative name(s): Phosphoribulose isomeraseUniRule annotation |
Gene namesi | Name:araD1 PublicationUniRule annotation Ordered Locus Names:b0061, JW0060 |
Organismi | Escherichia coli (strain K12) |
Taxonomic identifieri | 83333 [NCBI] |
Taxonomic lineagei | Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacterales › Enterobacteriaceae › Escherichia › |
Proteomesi |
|
Pathology & Biotechi
Disruption phenotypei
Cells lacking this gene accumulate large amount of L-ribulose 5-phosphate when incubated with L-arabinose.1 Publication
Mutagenesis
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Mutagenesisi | 28 | N → A: Strong decrease of the affinity for L-ribulose 5-phosphate (LRu5P). 1 Publication | 1 | |
Mutagenesisi | 42 | K → M: Strong decrease of the affinity for L-ribulose 5-phosphate (LRu5P). 1 Publication | 1 | |
Mutagenesisi | 76 | D → N: Mutant shows a strong decrease of the catalytic efficiency, but it retains considerable epimerase activity. The affinity for L-ribulose 5-phosphate (LRu5P) is relatively unaffected. 2 Publications | 1 | |
Mutagenesisi | 95 | H → N: Mutant shows a strong decrease of the catalytic efficiency and a reduced affinity for Zn(2+). 2 Publications | 1 | |
Mutagenesisi | 97 | H → N: Mutant shows a strong decrease of the catalytic efficiency and a reduced affinity for Zn(2+). Inhibited by glycolaldehyde phosphate. 2 Publications | 1 | |
Mutagenesisi | 116 | T → E or Y: Loss of the epimerase activity due to an increased steric bulk introduced by the mutation which causes a conformational change that is incompatible with catalysis. 1 Publication | 1 | |
Mutagenesisi | 120 | D → N: Loss of the epimerase activity. 1 Publication | 1 | |
Mutagenesisi | 142 | E → Q: Mutant shows a strong decrease of the catalytic efficiency, but it retains considerable epimerase activity. The affinity for L-ribulose 5-phosphate (LRu5P) is relatively unaffected. 1 Publication | 1 | |
Mutagenesisi | 218 | H → N: Mutant shows a strong decrease of the catalytic efficiency, but it retains considerable epimerase activity. The affinity for L-ribulose 5-phosphate (LRu5P) is relatively unaffected. 1 Publication | 1 | |
Mutagenesisi | 229 | Y → F: Loss of the epimerase activity. 2 Publications | 1 |
PTM / Processingi
Molecule processing
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
ChainiPRO_0000162919 | 1 – 231 | L-ribulose-5-phosphate 4-epimerase AraDAdd BLAST | 231 |
Proteomic databases
PaxDbi | P08203 |
PRIDEi | P08203 |
Expressioni
Inductioni
Interactioni
Subunit structurei
Homotetramer.
UniRule annotation4 PublicationsProtein-protein interaction databases
BioGRIDi | 4263043, 1 interactor |
DIPi | DIP-9126N |
IntActi | P08203, 4 interactors |
STRINGi | 511145.b0061 |
Structurei
Secondary structure
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details3D structure databases
SMRi | P08203 |
ModBasei | Search... |
PDBe-KBi | Search... |
Miscellaneous databases
EvolutionaryTracei | P08203 |
Family & Domainsi
Region
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Regioni | 27 – 28 | Substrate bindingUniRule annotationBy similarity | 2 | |
Regioni | 44 – 45 | Substrate bindingUniRule annotationBy similarity | 2 | |
Regioni | 74 – 75 | Substrate bindingUniRule annotationBy similarity | 2 |
Sequence similaritiesi
Phylogenomic databases
eggNOGi | COG0235, Bacteria |
HOGENOMi | CLU_006033_5_0_6 |
InParanoidi | P08203 |
PhylomeDBi | P08203 |
Family and domain databases
Gene3Di | 3.40.225.10, 1 hit |
HAMAPi | MF_00989, AraD_entero, 1 hit |
InterProi | View protein in InterPro IPR001303, Aldolase_II/adducin_N IPR036409, Aldolase_II/adducin_N_sf IPR004661, AraD IPR033748, AraD_entero |
Pfami | View protein in Pfam PF00596, Aldolase_II, 1 hit |
SMARTi | View protein in SMART SM01007, Aldolase_II, 1 hit |
SUPFAMi | SSF53639, SSF53639, 1 hit |
TIGRFAMsi | TIGR00760, araD, 1 hit |
i Sequence
Sequence statusi: Complete.
P08203-1 [UniParc]FASTAAdd to basket
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
Mass spectrometryi
Molecular mass is 25522 Da. Determined by ESI. 1 Publication
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 |
PIRi | E64727, ISECP4 |
RefSeqi | NP_414603.1, NC_000913.3 WP_000888666.1, NZ_STEB01000010.1 |
Genome annotation databases
EnsemblBacteriai | AAC73172; AAC73172; b0061 BAB96630; BAB96630; BAB96630 |
GeneIDi | 57730861 945294 |
KEGGi | ecj:JW0060 eco:b0061 |
PATRICi | fig|1411691.4.peg.2222 |
Similar proteinsi
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 |
PIRi | E64727, ISECP4 |
RefSeqi | NP_414603.1, NC_000913.3 WP_000888666.1, NZ_STEB01000010.1 |
3D structure databases
Select the link destinations: PDBei RCSB PDBi PDBji Links Updated | PDB 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 | [»] | |
SMRi | P08203 | |||||
ModBasei | Search... | |||||
PDBe-KBi | Search... |
Protein-protein interaction databases
BioGRIDi | 4263043, 1 interactor |
DIPi | DIP-9126N |
IntActi | P08203, 4 interactors |
STRINGi | 511145.b0061 |
Proteomic databases
PaxDbi | P08203 |
PRIDEi | P08203 |
Genome annotation databases
EnsemblBacteriai | AAC73172; AAC73172; b0061 BAB96630; BAB96630; BAB96630 |
GeneIDi | 57730861 945294 |
KEGGi | ecj:JW0060 eco:b0061 |
PATRICi | fig|1411691.4.peg.2222 |
Organism-specific databases
EchoBASEi | EB0053 |
Phylogenomic databases
eggNOGi | COG0235, Bacteria |
HOGENOMi | CLU_006033_5_0_6 |
InParanoidi | P08203 |
PhylomeDBi | P08203 |
Enzyme and pathway databases
UniPathwayi | UPA00145;UER00567 |
BioCyci | EcoCyc:RIBULPEPIM-MONOMER MetaCyc:RIBULPEPIM-MONOMER |
SABIO-RKi | P08203 |
Miscellaneous databases
EvolutionaryTracei | P08203 |
PROi | PR:P08203 |
Family and domain databases
Gene3Di | 3.40.225.10, 1 hit |
HAMAPi | MF_00989, AraD_entero, 1 hit |
InterProi | View protein in InterPro IPR001303, Aldolase_II/adducin_N IPR036409, Aldolase_II/adducin_N_sf IPR004661, AraD IPR033748, AraD_entero |
Pfami | View protein in Pfam PF00596, Aldolase_II, 1 hit |
SMARTi | View protein in SMART SM01007, Aldolase_II, 1 hit |
SUPFAMi | SSF53639, SSF53639, 1 hit |
TIGRFAMsi | TIGR00760, araD, 1 hit |
ProtoNeti | Search... |
MobiDBi | Search... |
Entry informationi
Entry namei | ARAD_ECOLI | |
Accessioni | P08203Primary (citable) accession number: P08203 | |
Entry historyi | Integrated into UniProtKB/Swiss-Prot: | August 1, 1988 |
Last sequence update: | August 1, 1991 | |
Last modified: | April 7, 2021 | |
This is version 179 of the entry and version 2 of the sequence. See complete history. | ||
Entry statusi | Reviewed (UniProtKB/Swiss-Prot) | |
Annotation program | Prokaryotic Protein Annotation Program |
Miscellaneousi
Keywords - Technical termi
3D-structure, Direct protein sequencing, Reference proteomeDocuments
- 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