P32169 (RHAD_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Rhamnulose-1-phosphate aldolase
EC=4.1.2.19

Gene names

Name:	rhaD
Synonyms:	rhuA
Ordered Locus Names:	b3902, JW3873

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

General annotation (Comments)

Function	Catalyzes the reversible cleavage of L-rhamnulose-1-phosphate to dihydroxyacetone phosphate (DHAP) and L-lactaldehyde. HAMAP-Rule MF_00770
Catalytic activity	L-rhamnulose 1-phosphate = glycerone phosphate + (S)-lactaldehyde. HAMAP-Rule MF_00770
Cofactor	Binds 1 zinc ion per subunit.
Pathway	Carbohydrate degradation; L-rhamnose degradation; glycerone phosphate from L-rhamnose: step 3/3. HAMAP-Rule MF_00770
Subunit structure	Homotetramer.
Subcellular location	Cytoplasm HAMAP-Rule MF_00770.
Induction	Induced by L-rhamnose via the RhaR-RhaS regulatory cascade. Binding of the cAMP receptor protein (CRP) is required for full expression. Ref.5 Ref.7
Sequence similarities	Belongs to the aldolase class II family. RhaD subfamily.

Ontologies

Keywords
Biological process	Rhamnose metabolism
Cellular component	Cytoplasm
Ligand	Metal-binding Zinc
Molecular function	Lyase
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	rhamnose catabolic process Inferred from mutant phenotype PubMed 5341476. Source: EcoCyc
Cellular_component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW rhamnulose-1-phosphate aldolase activity Inferred from direct assay PubMed 4975916. Source: EcoCyc
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 274

274

Rhamnulose-1-phosphate aldolase HAMAP-Rule MF_00770

PRO_0000209657

Sites

Active site

117

1

Metal binding

141

1

Zinc

Metal binding

143

1

Zinc

Metal binding

212

1

Zinc

Secondary structure

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274

Helix Strand Turn

Details...

Helix

4 – 6

3

Helix

8 – 22

15

Beta strand

31 – 36

6

Helix

39 – 42

4

Helix

43 – 48

6

Beta strand

54 – 57

4

Helix

63 – 65

3

Beta strand

69 – 74

6

Helix

79 – 81

3

Turn

82 – 84

3

Helix

86 – 89

4

Beta strand

90 – 95

6

Beta strand

99 – 107

9

Turn

109 – 111

3

Helix

113 – 115

3

Helix

118 – 131

14

Turn

132 – 134

3

Beta strand

138 – 142

5

Helix

145 – 150

6

Turn

151 – 153

3

Helix

158 – 167

10

Helix

172 – 175

4

Beta strand

180 – 182

3

Beta strand

188 – 190

3

Helix

191 – 201

11

Beta strand

205 – 209

5

Turn

210 – 212

3

Beta strand

213 – 220

8

Helix

221 – 243

23

Helix

256 – 263

8

Helix

269 – 272

4

Sequences

	Sequence		Length	Mass (Da)
	P32169 [UniParc]. Last modified October 1, 1993. Version 1. Checksum: F9FF0BE156F4E63D	FASTA	274	30,145
	10 20 30 40 50 60 MQNITQSWFV QGMIKATTDA WLKGWDERNG GNLTLRLDDA DIAPYHDNFH QQPRYIPLSQ 70 80 90 100 110 120 PMPLLANTPF IVTGSGKFFR NVQLDPAANL GIVKVDSDGA GYHILWGLTN EAVPTSELPA 130 140 150 160 170 180 HFLSHCERIK ATNGKDRVIM HCHATNLIAL TYVLENDTAV FTRQLWEGST ECLVVFPDGV 190 200 210 220 230 240 GILPWMVPGT DEIGQATAQE MQKHSLVLWP FHGVFGSGPT LDETFGLIDT AEKSAQVLVK 250 260 270 VYSMGGMKQT ISREELIALG KRFGVTPLAS ALAL

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]	"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.
[5]	"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.
[6]	"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.
[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 L-rhamnulose-1-phosphate aldolase (class II) solved by low-resolution SIR phasing and 20-fold NCS averaging." Kroemer M., Schulz G.E. Acta Crystallogr. D 58:824-832(2002) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS).
[9]	"Structure and catalytic mechanism of L-rhamnulose-1-phosphate aldolase." Kroemer M., Merkel I., Schulz G.E. Biochemistry 42:10560-10568(2003) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS).
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

X60472 Genomic DNA. Translation: CAA43003.1.
L19201 Genomic DNA. Translation: AAB03035.1.
U00096 Genomic DNA. Translation: AAC76884.1.
AP009048 Genomic DNA. Translation: BAE77407.1.

PIR

C48649.

RefSeq

NP_418338.1. NC_000913.2.
YP_491548.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1GT7	X-ray	2.70	A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P/Q/R/S/T	1-274	[»]
1OJR	X-ray	1.35	A	1-274	[»]
2UYU	X-ray	1.96	A/E	1-274	[»]
2UYV	X-ray	2.20	A/B/C/D	1-274	[»]
2V29	X-ray	2.03	A/B	1-274	[»]
2V2A	X-ray	1.75	A	1-274	[»]
2V2B	X-ray	1.50	A	1-274	[»]
2V9E	X-ray	1.58	A/B	1-272	[»]
2V9F	X-ray	2.10	A	1-272	[»]
2V9G	X-ray	2.70	A/B/C/D	1-274	[»]
2V9I	X-ray	1.80	A/B	1-273	[»]
2V9L	X-ray	1.23	A	1-274	[»]
2V9M	X-ray	1.30	A/B	1-274	[»]
2V9N	X-ray	1.40	A/B/C/D	1-274	[»]
2V9O	X-ray	1.95	A/E	1-274	[»]

ProteinModelPortal

P32169.

SMR

P32169. Positions 1-274.

ModBase

Search...

Protein-protein interaction databases

IntAct

P32169. 7 interactions.

STRING

511145.b3902.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC76884; AAC76884; b3902.
BAE77407; BAE77407; BAE77407.

GeneID

12931682.
948401.

KEGG

ecj:Y75_p3284.
eco:b3902.

PATRIC

32123313. VBIEscCol129921_4017.

Organism-specific databases

EchoBASE

EB1812.

EcoGene

EG11866. rhaD.

Phylogenomic databases

eggNOG

COG0235.

HOGENOM

HOG000279628.

KO

K01629.

OMA

DMWLKGW.

ProtClustDB

PRK03634.

Enzyme and pathway databases

BioCyc

EcoCyc:RHAMNULPALDOL-MONOMER.
ECOL316407:JW3873-MONOMER.
MetaCyc:RHAMNULPALDOL-MONOMER.

UniPathway

UPA00541; UER00603.

Gene expression databases

Genevestigator

P32169.

Family and domain databases

Gene3D

3.40.225.10. 1 hit.

HAMAP

MF_00770. RhaD.

InterPro

IPR001303. Aldolase_II/adducin_N.
IPR013447. Rhamnulose-1-P_Aldolase.
[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

TIGR02624. rhamnu_1P_ald. 1 hit.

ProtoNet

Search...

Other

EvolutionaryTrace

P32169.

Entry information

Entry name

RHAD_ECOLI

Accession

Primary (citable) accession number: P32169
Secondary accession number(s): Q2M8J9

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 1, 1993
Last sequence update:	October 1, 1993
Last modified:	May 1, 2013
This is version 108 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program