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P0A955

- ALKH_ECOLI

UniProt

P0A955 - ALKH_ECOLI

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Protein
KHG/KDPG aldolase
Gene
eda, hga, kdgA, b1850, JW1839
Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

Functioni

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.2 Publications

Catalytic activityi

4-hydroxy-2-oxoglutarate = pyruvate + glyoxylate.1 Publication
2-dehydro-3-deoxy-6-phosphate-D-gluconate = pyruvate + D-glyceraldehyde 3-phosphate.1 Publication

Kineticsi

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

  1. KM=0.1 mM for KDPG2 Publications
  2. KM=9 mM for 2-oxobutyrate
  3. KM=10 mM for pyruvate

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei45 – 451Proton acceptor2 Publications
Active sitei49 – 4912 Publications
Binding sitei49 – 491Substrate
Binding sitei73 – 731Substrate
Active sitei133 – 1331Schiff-base intermediate with substrate2 Publications
Binding sitei133 – 1331Substrate (covalent)
Binding sitei161 – 1611Substrate
Sitei161 – 1611Plays a major role in determining the stereoselectivity
Binding sitei163 – 1631Substrate; via amide nitrogen
Binding sitei184 – 1841Substrate

GO - Molecular functioni

  1. 2-dehydro-3-deoxy-phosphogluconate aldolase activity Source: EcoliWiki
  2. 4-hydroxy-2-oxoglutarate aldolase activity Source: UniProtKB
  3. identical protein binding Source: IntAct
Complete GO annotation...

Keywords - Molecular functioni

Lyase

Keywords - Ligandi

Schiff base

Enzyme and pathway databases

BioCyciEcoCyc:KDPGALDOL-4OH2OXOGLUTARALDOL-MONOMER.
ECOL316407:JW1839-MONOMER.
MetaCyc:KDPGALDOL-4OH2OXOGLUTARALDOL-MONOMER.
UniPathwayiUPA00227.
UPA00856; UER00829.

Names & Taxonomyi

Protein namesi
Recommended name:
KHG/KDPG aldolase
Including the following 2 domains:
4-hydroxy-2-oxoglutarate aldolase (EC:4.1.3.16)
Alternative name(s):
2-keto-4-hydroxyglutarate aldolase
Short name:
KHG-aldolase
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 namesi
Name:eda
Synonyms:hga, kdgA
Ordered Locus Names:b1850, JW1839
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

Organism-specific databases

EcoGeneiEG10256. eda.

Subcellular locationi

Cytoplasm By similarity

GO - Cellular componenti

  1. cytosol Source: UniProtKB
  2. membrane Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Disruption phenotypei

Cells lacking this gene lose KHG aldolase activity.1 Publication

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi45 – 451E → N: 50-fold decrease in catalytic efficiency and 6-fold decrease of binding affinity. 2 Publications
Mutagenesisi133 – 1331K → 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. 1 Publication
Mutagenesisi161 – 1611T → 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. 2 Publications
Mutagenesisi161 – 1611T → 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. 2 Publications
Mutagenesisi168 – 1681N → S: Shows activity significantly greater than wild-type. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 213213KHG/KDPG aldolase
PRO_0000201037Add
BLAST

Proteomic databases

PaxDbiP0A955.
PRIDEiP0A955.

2D gel databases

SWISS-2DPAGEP0A955.

Expressioni

Inductioni

Constitutive, three-fold induction occurs for growth on gluconate and two-fold for growth on hexuronic acids.1 Publication

Gene expression databases

GenevestigatoriP0A955.

Interactioni

Subunit structurei

Homotrimer.3 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
itself3EBI-558114,EBI-558114

Protein-protein interaction databases

DIPiDIP-36196N.
IntActiP0A955. 9 interactions.
STRINGi511145.b1850.

Structurei

Secondary structure

Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi8 – 136
Beta strandi16 – 216
Helixi26 – 283
Helixi29 – 3810
Beta strandi43 – 486
Helixi53 – 6311
Beta strandi67 – 737
Helixi77 – 8610
Beta strandi91 – 955
Helixi98 – 1069
Beta strandi107 – 1093
Beta strandi111 – 1177
Helixi118 – 1269
Beta strandi131 – 1344
Turni135 – 1417
Helixi142 – 1509
Beta strandi157 – 1637
Turni166 – 1683
Helixi169 – 1735
Beta strandi181 – 1833
Helixi184 – 1863
Helixi189 – 1946
Helixi197 – 21014

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
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[»]
ProteinModelPortaliP0A955.
SMRiP0A955. Positions 1-213.

Miscellaneous databases

EvolutionaryTraceiP0A955.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni8 – 92Substrate binding

Sequence similaritiesi

Belongs to the KHG/KDPG aldolase family.

Phylogenomic databases

eggNOGiCOG0800.
HOGENOMiHOG000233114.
KOiK01625.
OMAiSWLVPND.
OrthoDBiEOG67DPKT.
PhylomeDBiP0A955.

Family and domain databases

Gene3Di3.20.20.70. 1 hit.
InterProiIPR000887. Aldlse_KDPG_KHG.
IPR013785. Aldolase_TIM.
[Graphical view]
PfamiPF01081. Aldolase. 1 hit.
[Graphical view]
TIGRFAMsiTIGR01182. eda. 1 hit.
PROSITEiPS00159. ALDOLASE_KDPG_KHG_1. 1 hit.
PS00160. ALDOLASE_KDPG_KHG_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P0A955-1 [UniParc]FASTAAdd to Basket

« Hide

MKNWKTSAES ILTTGPVVPV IVVKKLEHAV PMAKALVAGG VRVLEVTLRT    50
ECAVDAIRAI AKEVPEAIVG AGTVLNPQQL AEVTEAGAQF AISPGLTEPL 100
LKAATEGTIP LIPGISTVSE LMLGMDYGLK EFKFFPAEAN GGVKALQAIA 150
GPFSQVRFCP TGGISPANYR DYLALKSVLC IGGSWLVPAD ALEAGDYDRI 200
TKLAREAVEG AKL 213
Length:213
Mass (Da):22,284
Last modified:July 19, 2005 - v1
Checksum:iCC8D51B50480D0B7
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
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.
PIRiB42986. ADECOG.
RefSeqiNP_416364.1. NC_000913.3.
YP_490112.1. NC_007779.1.

Genome annotation databases

EnsemblBacteriaiAAC74920; AAC74920; b1850.
BAA15658; BAA15658; BAA15658.
GeneIDi12930159.
946367.
KEGGiecj:Y75_p1826.
eco:b1850.
PATRICi32119021. VBIEscCol129921_1928.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
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 .
PIRi B42986. ADECOG.
RefSeqi NP_416364.1. NC_000913.3.
YP_490112.1. NC_007779.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1EUA X-ray 1.95 A/B/C 1-213 [» ]
1EUN X-ray 2.00 A/B/C 1-213 [» ]
1FQ0 X-ray 2.10 A/B/C 1-213 [» ]
1FWR X-ray 2.70 A/B/C 1-213 [» ]
1WAU X-ray 2.80 A 1-213 [» ]
1WBH X-ray 1.55 A/B/C 1-213 [» ]
2C0A X-ray 1.55 A/B/C 1-213 [» ]
ProteinModelPortali P0A955.
SMRi P0A955. Positions 1-213.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

DIPi DIP-36196N.
IntActi P0A955. 9 interactions.
STRINGi 511145.b1850.

2D gel databases

SWISS-2DPAGE P0A955.

Proteomic databases

PaxDbi P0A955.
PRIDEi P0A955.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAC74920 ; AAC74920 ; b1850 .
BAA15658 ; BAA15658 ; BAA15658 .
GeneIDi 12930159.
946367.
KEGGi ecj:Y75_p1826.
eco:b1850.
PATRICi 32119021. VBIEscCol129921_1928.

Organism-specific databases

EchoBASEi EB0252.
EcoGenei EG10256. eda.

Phylogenomic databases

eggNOGi COG0800.
HOGENOMi HOG000233114.
KOi K01625.
OMAi SWLVPND.
OrthoDBi EOG67DPKT.
PhylomeDBi P0A955.

Enzyme and pathway databases

UniPathwayi UPA00227 .
UPA00856 ; UER00829 .
BioCyci EcoCyc:KDPGALDOL-4OH2OXOGLUTARALDOL-MONOMER.
ECOL316407:JW1839-MONOMER.
MetaCyc:KDPGALDOL-4OH2OXOGLUTARALDOL-MONOMER.

Miscellaneous databases

EvolutionaryTracei P0A955.
PROi P0A955.

Gene expression databases

Genevestigatori P0A955.

Family and domain databases

Gene3Di 3.20.20.70. 1 hit.
InterProi IPR000887. Aldlse_KDPG_KHG.
IPR013785. Aldolase_TIM.
[Graphical view ]
Pfami PF01081. Aldolase. 1 hit.
[Graphical view ]
TIGRFAMsi TIGR01182. eda. 1 hit.
PROSITEi PS00159. ALDOLASE_KDPG_KHG_1. 1 hit.
PS00160. ALDOLASE_KDPG_KHG_2. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  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. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  7. 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. Cited for: X-RAY CRYSTALLOGRAPHY (1.55 ANGSTROMS) OF WILD-TYPE AND MUTANT IN COMPLEX WITH SUBSTRATE, MUTAGENESIS OF GLU-45, REACTION MECHANISM, SUBUNIT.

Entry informationi

Entry nameiALKH_ECOLI
AccessioniPrimary (citable) accession number: P0A955
Secondary accession number(s): P10177
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 19, 2005
Last sequence update: July 19, 2005
Last modified: May 14, 2014
This is version 80 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Multifunctional enzyme, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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