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P0A955 (ALKH_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified March 19, 2014. Version 78. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
KHG/KDPG aldolase

Including the following 2 domains:

  1. 4-hydroxy-2-oxoglutarate aldolase
    EC=4.1.3.16
    Alternative name(s):
    2-keto-4-hydroxyglutarate aldolase
    Short name=KHG-aldolase
  2. 2-dehydro-3-deoxy-phosphogluconate aldolase
    EC=4.1.2.14
    Alternative name(s):
    2-keto-3-deoxy-6-phosphogluconate aldolase
    Short name=KDPG-aldolase
    Phospho-2-dehydro-3-deoxygluconate aldolase
    Phospho-2-keto-3-deoxygluconate aldolase
Gene names
Name:eda
Synonyms:hga, kdgA
Ordered Locus Names:b1850, JW1839
OrganismEscherichia coli (strain K12) [Reference proteome] [HAMAP]
Taxonomic identifier83333 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Protein attributes

Sequence length213 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Involved in the degradation of glucose via the Entner-Doudoroff pathway. Catalyzes the reversible, stereospecific retro-aldol cleavage of 2-Keto-3-deoxy-6-phosphogluconate (KDPG) to pyruvate and D-glyceraldehyde-3-phosphate. In the synthetic direction, it catalyzes the addition of pyruvate to electrophilic aldehydes with si-facial selectivity. It accepts some nucleophiles other than pyruvate, including 2-oxobutanoate, phenylpyruvate, and fluorobutanoate. It has a preference for the S-configuration at C2 of the electrophile. Ref.2 Ref.11

Catalytic activity

4-hydroxy-2-oxoglutarate = pyruvate + glyoxylate. Ref.11

2-dehydro-3-deoxy-6-phosphate-D-gluconate = pyruvate + D-glyceraldehyde 3-phosphate. Ref.11

Pathway

Carbohydrate acid metabolism; 2-dehydro-3-deoxy-D-gluconate degradation; D-glyceraldehyde 3-phosphate and pyruvate from 2-dehydro-3-deoxy-D-gluconate: step 2/2.

Carbohydrate metabolism; glyoxylate and dicarboxylate metabolism.

Subunit structure

Homotrimer. Ref.12 Ref.13 Ref.14

Subcellular location

Cytoplasm By similarity.

Induction

Constitutive, three-fold induction occurs for growth on gluconate and two-fold for growth on hexuronic acids. Ref.11

Disruption phenotype

Cells lacking this gene lose KHG aldolase activity. Ref.2

Sequence similarities

Belongs to the KHG/KDPG aldolase family.

Biophysicochemical properties

Kinetic parameters:

Kcat is 80 sec(-1) for KDPG, 0.012 sec(-1) for pyruvate and 0.0004 sec(-1) for 2-oxobutyrate.

KM=0.1 mM for KDPG Ref.11 Ref.13

KM=9 mM for 2-oxobutyrate

KM=10 mM for pyruvate

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 213213KHG/KDPG aldolase
PRO_0000201037

Regions

Region8 – 92Substrate binding

Sites

Active site451Proton acceptor Ref.1 Ref.9
Active site491 Ref.1 Ref.9
Active site1331Schiff-base intermediate with substrate Ref.1 Ref.9
Binding site491Substrate
Binding site731Substrate
Binding site1331Substrate (covalent)
Binding site1611Substrate
Binding site1631Substrate; via amide nitrogen
Binding site1841Substrate
Site1611Plays a major role in determining the stereoselectivity

Experimental info

Mutagenesis451E → N: 50-fold decrease in catalytic efficiency and 6-fold decrease of binding affinity. Ref.11 Ref.14
Mutagenesis1331K → Q: Absence of aldolase activity. Shows a markedly altered substrate specificity relative to the wild-type, with an enhanced activity against pyridine carboxaldehyde, benzaldehyde, and alpha-ketobutyrate; when associated with k-161. Ref.13
Mutagenesis1611T → K: Shows activity significantly greater than wild-type. Shows a markedly altered substrate specificity relative to the wild-type, with an enhanced activity against pyridine carboxaldehyde, benzaldehyde, and alpha-ketobutyrate; when associated with Q-133. Ref.11 Ref.13
Mutagenesis1611T → V: Little stereoselectivity, accepting KDPG and KDPGal as substrate with roughly equal efficacy. It strongly diminishes the activity against KDPG and slightly increases activity against KDPGal. Ref.11 Ref.13
Mutagenesis1681N → S: Shows activity significantly greater than wild-type. Ref.13

Secondary structure

........................................ 213
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P0A955 [UniParc].

Last modified July 19, 2005. Version 1.
Checksum: CC8D51B50480D0B7

FASTA21322,284
        10         20         30         40         50         60 
MKNWKTSAES ILTTGPVVPV IVVKKLEHAV PMAKALVAGG VRVLEVTLRT ECAVDAIRAI 

        70         80         90        100        110        120 
AKEVPEAIVG AGTVLNPQQL AEVTEAGAQF AISPGLTEPL LKAATEGTIP LIPGISTVSE 

       130        140        150        160        170        180 
LMLGMDYGLK EFKFFPAEAN GGVKALQAIA GPFSQVRFCP TGGISPANYR DYLALKSVLC 

       190        200        210 
IGGSWLVPAD ALEAGDYDRI TKLAREAVEG AKL 

« Hide

References

« Hide 'large scale' references
[1]"The complete amino acid sequence and identification of the active-site arginine peptide of Escherichia coli 2-keto-4-hydroxyglutarate aldolase."
Vlahos C.J., Dekker E.E.
J. Biol. Chem. 263:11683-11691(1988) [PubMed] [Europe PMC] [Abstract]
Cited for: PROTEIN SEQUENCE, ACTIVE SITE.
Strain: K12.
[2]"Cloning, nucleotide sequence, overexpression, and inactivation of the Escherichia coli 2-keto-4-hydroxyglutarate aldolase gene."
Patil R.V., Dekker E.E.
J. Bacteriol. 174:102-107(1992) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION AS A KHG-ALDOLASE, DISRUPTION PHENOTYPE.
[3]"Molecular characterization of the Entner-Doudoroff pathway in Escherichia coli: sequence analysis and localization of promoters for the edd-eda operon."
Egan S.E., Fliege R., Tong S., Shibata A., Wolf R.E. Jr., Conway T.
J. Bacteriol. 174:4638-4646(1992) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[4]"Purine and one-carbon metabolism in Escherichia coli K12: DNA sequence of a second GAR transformylase."
Smith J.M., Nygaard P.
Submitted (JUL-1993) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: K12.
[5]"Sequence of the Escherichia coli K-12 edd and eda genes of the Entner-Doudoroff pathway."
Carter A.T., Pearson B.M., Dickinson J.R., Lancashire W.E.
Gene 130:155-156(1993) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: K12.
[6]"A 460-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 40.1-50.0 min region on the linkage map."
Itoh T., Aiba H., Baba T., Fujita K., Hayashi K., Inada T., Isono K., Kasai H., Kimura S., Kitakawa M., Kitagawa M., Makino K., Miki T., Mizobuchi K., Mori H., Mori T., Motomura K., Nakade S. expand/collapse author list , Nakamura Y., Nashimoto H., Nishio Y., Oshima T., Saito N., Sampei G., Seki Y., Sivasundaram S., Tagami H., Takeda J., Takemoto K., Wada C., Yamamoto Y., Horiuchi T.
DNA Res. 3:379-392(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[7]"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 277:1453-1462(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / MG1655 / ATCC 47076.
[8]"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.
[9]"Active-site residues of 2-keto-4-hydroxyglutarate aldolase from Escherichia coli. Bromopyruvate inactivation and labeling of glutamate 45."
Vlahos C.J., Dekker E.E.
J. Biol. Chem. 265:20384-20389(1990) [PubMed] [Europe PMC] [Abstract]
Cited for: ACTIVE SITE.
[10]"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.
[11]"Characterization and crystal structure of Escherichia coli KDPGal aldolase."
Walters M.J., Srikannathasan V., McEwan A.R., Naismith J.H., Fierke C.A., Toone E.J.
Bioorg. Med. Chem. 16:710-720(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION AS A KDPG-ALDOLASE, CATALYTIC ACTIVITY, MUTAGENESIS OF GLU-45 AND THR-161, BIOPHYSICOCHEMICAL PROPERTIES, SUBSTRATE SPECIFICITY, INDUCTION.
[12]"Covalent intermediate trapped in 2-keto-3-deoxy-6-phosphogluconate (KDPG) aldolase structure at 1.95-A resolution."
Allard J., Grochulski P., Sygusch J.
Proc. Natl. Acad. Sci. U.S.A. 98:3679-3684(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.95 ANGSTROMS) IN COMPLEX WITH SUSBTRATE, REACTION MECHANISM, SUBUNIT.
[13]"Directed evolution of a new catalytic site in 2-keto-3-deoxy-6-phosphogluconate aldolase from Escherichia coli."
Wymer N., Buchanan L.V., Henderson D., Mehta N., Botting C.H., Pocivavsek L., Fierke C.A., Toone E.J., Naismith J.H.
Structure 9:1-9(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF WILD-TYPE AND DOUBLE MUTANT IN COMPLEX WITH SUSBTRATE, MUTAGENESIS OF LYS-133; THR-161 AND ASN-168, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT.
[14]"Mechanism of the Class I KDPG aldolase."
Fullerton S.W., Griffiths J.S., Merkel A.B., Cheriyan M., Wymer N.J., Hutchins M.J., Fierke C.A., Toone E.J., Naismith J.H.
Bioorg. Med. Chem. 14:3002-3010(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.55 ANGSTROMS) OF WILD-TYPE AND MUTANT IN COMPLEX WITH SUBSTRATE, MUTAGENESIS OF GLU-45, REACTION MECHANISM, SUBUNIT.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
X68871 Genomic DNA. Translation: CAA48732.1.
M87458 Genomic DNA. Translation: AAA23723.1.
L20897 Genomic DNA. Translation: AAA23862.1.
X63694 Genomic DNA. Translation: CAA45222.1.
U00096 Genomic DNA. Translation: AAC74920.1.
AP009048 Genomic DNA. Translation: BAA15658.1.
PIRADECOG. B42986.
RefSeqNP_416364.1. NC_000913.3.
YP_490112.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1EUAX-ray1.95A/B/C1-213[»]
1EUNX-ray2.00A/B/C1-213[»]
1FQ0X-ray2.10A/B/C1-213[»]
1FWRX-ray2.70A/B/C1-213[»]
1WAUX-ray2.80A1-213[»]
1WBHX-ray1.55A/B/C1-213[»]
2C0AX-ray1.55A/B/C1-213[»]
ProteinModelPortalP0A955.
SMRP0A955. Positions 1-213.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

DIPDIP-36196N.
IntActP0A955. 8 interactions.
STRING511145.b1850.

2D gel databases

SWISS-2DPAGEP0A955.

Proteomic databases

PaxDbP0A955.
PRIDEP0A955.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAC74920; AAC74920; b1850.
BAA15658; BAA15658; BAA15658.
GeneID12930159.
946367.
KEGGecj:Y75_p1826.
eco:b1850.
PATRIC32119021. VBIEscCol129921_1928.

Organism-specific databases

EchoBASEEB0252.
EcoGeneEG10256. eda.

Phylogenomic databases

eggNOGCOG0800.
HOGENOMHOG000233114.
KOK01625.
OMAKFFPAEY.
OrthoDBEOG67DPKT.
ProtClustDBPRK05718.

Enzyme and pathway databases

BioCycEcoCyc:KDPGALDOL-4OH2OXOGLUTARALDOL-MONOMER.
ECOL316407:JW1839-MONOMER.
MetaCyc:KDPGALDOL-4OH2OXOGLUTARALDOL-MONOMER.
UniPathwayUPA00227.
UPA00856; UER00829.

Gene expression databases

GenevestigatorP0A955.

Family and domain databases

Gene3D3.20.20.70. 1 hit.
InterProIPR000887. Aldlse_KDPG_KHG.
IPR013785. Aldolase_TIM.
[Graphical view]
PfamPF01081. Aldolase. 1 hit.
[Graphical view]
TIGRFAMsTIGR01182. eda. 1 hit.
PROSITEPS00159. ALDOLASE_KDPG_KHG_1. 1 hit.
PS00160. ALDOLASE_KDPG_KHG_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP0A955.
PROP0A955.

Entry information

Entry nameALKH_ECOLI
AccessionPrimary (citable) accession number: P0A955
Secondary accession number(s): P10177
Entry history
Integrated into UniProtKB/Swiss-Prot: July 19, 2005
Last sequence update: July 19, 2005
Last modified: March 19, 2014
This is version 78 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

PATHWAY comments

Index of metabolic and biosynthesis pathways

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene