P32170 (RHAA_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
L-rhamnose isomerase
EC=5.3.1.14

Gene names

Name:	rhaA
Ordered Locus Names:	b3903, JW5561

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	419 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Catalytic activity	L-rhamnose = L-rhamnulose. HAMAP-Rule MF_00541
Cofactor	Binds 1 manganese ion per subunit.
Pathway	Carbohydrate degradation; L-rhamnose degradation; glycerone phosphate from L-rhamnose: step 1/3. HAMAP-Rule MF_00541
Subunit structure	Homotetramer. Ref.8
Subcellular location	Cytoplasm Probable HAMAP-Rule MF_00541.
Induction	Induced by L-rhamnose via the RhaR-RhaS regulatory cascade. Binding of the cAMP receptor protein (CRP) is required for full expression. Ref.6 Ref.7
Miscellaneous	In the crystal structure, RhaA appears to bind a zinc ion at a structural site. However, the metal ion may be different in vivo. HAMAP-Rule MF_00541
Sequence similarities	Belongs to the rhamnose isomerase family.

Ontologies

Keywords
Biological process	Rhamnose metabolism
Cellular component	Cytoplasm
Ligand	Manganese Metal-binding Zinc
Molecular function	Isomerase
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	L-lyxose metabolic process Inferred from expression pattern PubMed 1650346. Source: EcoCyc rhamnose catabolic process Inferred from mutant phenotype PubMed 5341476. Source: EcoCyc
Cellular_component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	L-rhamnose isomerase activity Inferred from direct assay PubMed 1650346. Source: EcoCyc manganese ion binding Inferred from electronic annotation. Source: HAMAP
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 419

419

L-rhamnose isomerase HAMAP-Rule MF_00541

PRO_0000090552

Sites

Metal binding

226

1

Zinc

Metal binding

259

1

Zinc

Metal binding

262

1

Manganese

Metal binding

286

1

Zinc

Metal binding

294

1

Manganese

Metal binding

296

1

Manganese

Metal binding

326

1

Zinc

Experimental info

Sequence conflict

359 – 360

2

EL → DV in AAB03036. Ref.2

Sequence conflict

366

1

A → P in CAA43002. Ref.1

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

419

Helix Strand Turn

Details...

Helix

4 – 18

15

Helix

23 – 30

8

Beta strand

35 – 38

4

Helix

39 – 42

4

Turn

43 – 45

3

Beta strand

48 – 53

6

Helix

72 – 84

13

Beta strand

90 – 95

6

Helix

96 – 98

3

Helix

107 – 109

3

Helix

112 – 115

4

Helix

116 – 124

9

Beta strand

128 – 132

5

Beta strand

136 – 138

3

Helix

139 – 141

3

Helix

152 – 176

25

Beta strand

180 – 184

5

Beta strand

189 – 192

4

Helix

198 – 211

14

Turn

218 – 220

3

Beta strand

221 – 226

6

Beta strand

236 – 240

5

Helix

242 – 252

11

Beta strand

255 – 259

5

Helix

269 – 276

8

Turn

277 – 279

3

Beta strand

283 – 287

5

Beta strand

291 – 294

4

Helix

303 – 314

12

Turn

318 – 320

3

Beta strand

321 – 325

5

Helix

334 – 353

20

Helix

357 – 364

8

Turn

365 – 367

3

Helix

369 – 379

11

Helix

384 – 394

11

Helix

403 – 413

11

Turn

414 – 416

3

Sequences

	Sequence		Length	Mass (Da)
	P32170 [UniParc]. Last modified October 11, 2004. Version 2. Checksum: D237E95BD24999BA	FASTA	419	47,199
	10 20 30 40 50 60 MTTQLEQAWE LAKQRFAAVG IDVEEALRQL DRLPVSMHCW QGDDVSGFEN PEGSLTGGIQ 70 80 90 100 110 120 ATGNYPGKAR NASELRADLE QAMRLIPGPK RLNLHAIYLE SDTPVSRDQI KPEHFKNWVE 130 140 150 160 170 180 WAKANQLGLD FNPSCFSHPL SADGFTLSHA DDSIRQFWID HCKASRRVSA YFGEQLGTPS 190 200 210 220 230 240 VMNIWIPDGM KDITVDRLAP RQRLLAALDE VISEKLNPAH HIDAVESKLF GIGAESYTVG 250 260 270 280 290 300 SNEFYMGYAT SRQTALCLDA GHFHPTEVIS DKISAAMLYV PQLLLHVSRP VRWDSDHVVL 310 320 330 340 350 360 LDDETQAIAS EIVRHDLFDR VHIGLDFFDA SINRIAAWVI GTRNMKKALL RALLEPTAEL 370 380 390 400 410 RKLEAAGDYT ARLALLEEQK SLPWQAVWEM YCQRHDTPAG SEWLESVRAY EKEILSRRG

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Sequencing and characterization of a gene cluster encoding the enzymes for L-rhamnose metabolism in Escherichia coli." Moralejo P., Egan S.M., Hidalgo E.F., Aguilar J. J. Bacteriol. 175:5585-5594(1993) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12.
[2]	"Analysis of the Escherichia coli genome. III. DNA sequence of the region from 87.2 to 89.2 minutes." Plunkett G. III, Burland V., Daniels D.L., Blattner F.R. Nucleic Acids Res. 21:3391-3398(1993) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[3]	"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.
[4]	"Escherichia coli K-12: a cooperatively developed annotation snapshot -- 2005." Riley M., Abe T., Arnaud M.B., Berlyn M.K.B., Blattner F.R., Chaudhuri R.R., Glasner J.D., Horiuchi T., Keseler I.M., Kosuge T., Mori H., Perna N.T., Plunkett G. III, Rudd K.E., Serres M.H., Thomas G.H., Thomson N.R., Wishart D., Wanner B.L. Nucleic Acids Res. 34:1-9(2006) [PubMed] [Europe PMC] [Abstract] Cited for: SEQUENCE REVISION TO 359-360.
[5]	"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.
[6]	"A regulatory cascade in the induction of rhaBAD." Egan S.M., Schleif R.F. J. Mol. Biol. 234:87-98(1993) [PubMed] [Europe PMC] [Abstract] Cited for: INDUCTION. Strain: ECL116.
[7]	"Roles of cyclic AMP receptor protein and the carboxyl-terminal domain of the alpha subunit in transcription activation of the Escherichia coli rhaBAD operon." Holcroft C.C., Egan S.M. J. Bacteriol. 182:3529-3535(2000) [PubMed] [Europe PMC] [Abstract] Cited for: INDUCTION.
[8]	"The structure of rhamnose isomerase from Escherichia coli and its relation with xylose isomerase illustrates a change between inter and intra-subunit complementation during evolution." Korndoerfer I.P., Fessner W.-D., Matthews B.W. J. Mol. Biol. 300:917-933(2000) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS), SUBUNIT.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

X60472 Genomic DNA. Translation: CAA43002.1.
L19201 Genomic DNA. Translation: AAB03036.1.
U00096 Genomic DNA. Translation: AAT48234.1.
AP009048 Genomic DNA. Translation: BAE77406.1.

PIR

S40847.

RefSeq

YP_026276.1. NC_000913.2.
YP_491547.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1D8W	X-ray	1.60	A/B/C/D	1-419	[»]
1DE5	X-ray	2.20	A/B/C/D	1-419	[»]
1DE6	X-ray	2.10	A/B/C/D	1-419	[»]

DisProt

DP00429.

ProteinModelPortal

P32170.

SMR

P32170. Positions 3-418.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-10690N.

STRING

511145.b3903.

Proteomic databases

PRIDE

P32170.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAT48234; AAT48234; b3903.
BAE77406; BAE77406; BAE77406.

GeneID

12931684.
948400.

KEGG

ecj:Y75_p3283.
eco:b3903.

PATRIC

32123315. VBIEscCol129921_4018.

Organism-specific databases

EchoBASE

EB1813.

EcoGene

EG11867. rhaA.

Phylogenomic databases

eggNOG

COG4806.

HOGENOM

HOG000269679.

KO

K01813.

OMA

VNLHAIY.

ProtClustDB

PRK01076.

Enzyme and pathway databases

BioCyc

EcoCyc:RHAMNISOM-MONOMER.
ECOL316407:JW5561-MONOMER.
MetaCyc:RHAMNISOM-MONOMER.

BRENDA

5.3.1.14. 2026.

UniPathway

UPA00541; UER00601.

Gene expression databases

Genevestigator

P32170.

Family and domain databases

Gene3D

3.20.20.150. 1 hit.

HAMAP

MF_00541. RhaA.

InterPro

IPR009308. Rhamnose_isomerase.
IPR013022. Xyl_isomerase-like_TIM-brl.
[Graphical view]

Pfam

PF06134. RhaA. 1 hit.
[Graphical view]

SUPFAM

SSF51658. Xyl_isomerase-like_TIM-brl. 1 hit.

TIGRFAMs

TIGR01748. rhaA. 1 hit.

ProtoNet

Search...

Other

EvolutionaryTrace

P32170.

Entry information

Entry name

RHAA_ECOLI

Accession

Primary (citable) accession number: P32170
Secondary accession number(s): Q2M8K0, Q6BEY0

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 1, 1993
Last sequence update:	October 11, 2004
Last modified:	May 1, 2013
This is version 116 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program