L-ribulose-5-phosphate 4-epimerase - Escherichia coli (strain K12)

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Reviewed, UniProtKB/Swiss-Prot P08203 (ARAD_ECOLI)

Last modified June 16, 2009. Version 92. History...

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Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents

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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) [Complete proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

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Protein attributes

Sequence length	231 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

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General annotation (Comments)

Catalytic activity	L-ribulose 5-phosphate = D-xylulose 5-phosphate.
Cofactor	Binds 1 zinc ion per subunit Potential.
Pathway	Carbohydrate degradation; L-arabinose degradation via L-ribulose; D-xylulose 5-phosphate from L-arabinose (bacteria route): step 3/3.
Subunit structure	Homotetramer. Ref.10
Sequence similarities	Belongs to the aldolase class II family. AraD/fucA subfamily.

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Ontologies

Keywords
Biological process	Arabinose catabolism Carbohydrate metabolism
Ligand	Metal-binding Zinc
Molecular function	Isomerase
Technical term	3D-structure Complete proteome Direct protein sequencing
Gene Ontology (GO)
Biological process	L-arabinose catabolic process Inferred from electronic annotation. Source: InterPro
Molecular function	L-ribulose-phosphate 4-epimerase activity Inferred from electronic annotation. Source: EC zinc ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

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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

Zinc By similarity

Metal binding

Zinc By similarity

Metal binding

Zinc By similarity

Metal binding

171

Zinc By similarity

Natural variations

Natural variant

V → I

Natural variant

T → A

Natural variant

216

D → N

Secondary structure

231

Helix Strand Turn

Details...

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Sequences

Sequence

Length

Mass (Da)

Tools

P08203-1 [UniParc].

Last modified August 1, 1991. Version 2.
Checksum: 1753F75958332163
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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

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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: 3549454] [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: 2261080] [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: 2251150] [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: 1630901] [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: 9278503] [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: 16738553] [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: 8520491] [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: 2034216] [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: 2217198] [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: 4879898] [Abstract] Cited for: SUBUNIT. Strain: B/R.
[11]	"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: 11732895] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS).

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Cross-references

Sequence databases

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

AP_000725.1.
NP_414603.1.

3D structure databases

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	[»]

ModBase

Search...

Protein-protein interaction databases

DIP

DIP:9126N.

2-D gel databases

ECO2DBASE

G028.1. 6TH EDITION.

Genome annotation databases

GeneID

945294.

GenomeReviews

Gene locus JW0060 in contig AP009048_GR.
Gene locus b0061 in contig U00096_GR.

KEGG

ecj:JW0060.
eco:b0061.

Organism-specific databases

EchoBASE

EB0053.

EcoGene

EG10055. araD.

CMR

Search...

Phylogenomic databases

HOGENOM

P08203.

OMA

P08203. ISKDRSY.

Enzyme and pathway databases

BioCyc

EcoCyc:RIBULPEPIM-MON.
MetaCyc:RIBULPEPIM-MON.

Family and domain databases

InterPro

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

Gene3D

G3DSA:3.40.225.10. Aldolase_II/adducin_N. 1 hit.

Pfam

PF00596. Aldolase_II. 1 hit.
[Graphical view]

TIGRFAMs

TIGR00760. araD. 1 hit.

ProtoNet

Search...

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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:	June 16, 2009
This is version 92 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)

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