P08203 (ARAD_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended 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

Organism

Escherichia coli (strain K12) [Reference proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia › Escherichia coli

Protein attributes

Sequence length	231 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Catalytic activity	L-ribulose 5-phosphate = D-xylulose 5-phosphate.
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.
Subunit structure	Homotetramer. Ref.10 Ref.12
Sequence similarities	Belongs to the aldolase class II family. AraD/FucA subfamily.

Ontologies

Keywords
Biological process	Arabinose catabolism Carbohydrate metabolism
Ligand	Metal-binding Zinc
Molecular function	Isomerase
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	L-arabinose catabolic process to xylulose 5-phosphate Inferred from expression pattern PubMed 7768852. Source: EcoCyc L-lyxose metabolic process Inferred from mutant phenotype PubMed 10913097. Source: EcoCyc
Molecular_function	L-ribulose-phosphate 4-epimerase activity Inferred from direct assay PubMed 9548961. Source: EcoCyc zinc ion binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 231

231

L-ribulose-5-phosphate 4-epimerase

PRO_0000162919

Sites

Metal binding

95

1

Zinc

Metal binding

97

1

Zinc

Metal binding

171

1

Zinc

Natural variations

Natural variant

50

1

V → I.

Natural variant

70

1

T → A.

Natural variant

216

1

D → N.

Secondary structure

1

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231

Helix Strand Turn

Details...

Helix

3 – 18

16

Beta strand

28 – 33

6

Turn

34 – 37

4

Beta strand

38 – 41

4

Beta strand

43 – 45

3

Turn

48 – 50

3

Helix

53 – 55

3

Beta strand

57 – 60

4

Turn

61 – 63

3

Beta strand

66 – 68

3

Helix

77 – 86

10

Beta strand

92 – 95

4

Helix

99 – 107

9

Helix

116 – 119

4

Helix

134 – 138

5

Helix

141 – 155

15

Turn

160 – 162

3

Beta strand

165 – 168

4

Turn

169 – 171

3

Beta strand

172 – 179

8

Helix

180 – 203

24

Helix

212 – 221

10

Sequences

	Sequence		Length	Mass (Da)
	P08203 [UniParc]. Last modified August 1, 1991. Version 2. Checksum: 1753F75958332163	FASTA	231	25,519
	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

References

	« Hide 'large scale' referencesShow '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 277:1453-1474(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.

PIR

ISECP4. E64727.

RefSeq

NP_414603.1. NC_000913.2.
YP_488367.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

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	[»]

ProteinModelPortal

P08203.

SMR

P08203. Positions 1-223.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-9126N.

IntAct

P08203. 4 interactions.

STRING

511145.b0061.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC73172; AAC73172; b0061.
BAB96630; BAB96630; BAB96630.

GeneID

12934049.
945294.

KEGG

ecj:Y75_p0061.
eco:b0061.

PATRIC

32115223. VBIEscCol129921_0063.

Organism-specific databases

EchoBASE

EB0053.

EcoGene

EG10055. araD.

Phylogenomic databases

eggNOG

COG0235.

HOGENOM

HOG000218183.

KO

K01786.

OMA

CTRLMTD.

ProtClustDB

PRK08193.

Enzyme and pathway databases

BioCyc

EcoCyc:RIBULPEPIM-MONOMER.
ECOL316407:JW0060-MONOMER.
MetaCyc:RIBULPEPIM-MONOMER.

SABIO-RK

P08203.

UniPathway

UPA00145; UER00567.

Gene expression databases

Genevestigator

P08203.

Family and domain databases

Gene3D

3.40.225.10. 1 hit.

InterPro

IPR001303. Aldolase_II/adducin_N.
IPR004661. AraD.
[Graphical view]

Pfam

PF00596. Aldolase_II. 1 hit.
[Graphical view]

SMART

SM01007. Aldolase_II. 1 hit.
[Graphical view]

SUPFAM

SSF53639. Aldolase_II_N. 1 hit.

TIGRFAMs

TIGR00760. araD. 1 hit.

ProtoNet

Search...

Other

EvolutionaryTrace

P08203.

Entry information

Entry name

ARAD_ECOLI

Accession

Primary (citable) accession number: P08203

Entry history

Integrated into UniProtKB/Swiss-Prot:	August 1, 1988
Last sequence update:	August 1, 1991
Last modified:	May 1, 2013
This is version 127 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program