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P0A955

- ALKH_ECOLI

UniProt

P0A955 - ALKH_ECOLI

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Protein

KHG/KDPG aldolase

Gene

eda

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-oxobutyrate2 Publications
  3. KM=10 mM for pyruvate2 Publications

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei45 – 451Proton acceptor
Active sitei49 – 491
Binding sitei49 – 491Substrate1 Publication
Binding sitei73 – 731Substrate1 Publication
Active sitei133 – 1331Schiff-base intermediate with substrate
Binding sitei133 – 1331Substrate (covalent)1 Publication
Binding sitei161 – 1611Substrate1 Publication
Sitei161 – 1611Plays a major role in determining the stereoselectivity
Binding sitei163 – 1631Substrate; via amide nitrogen1 Publication
Binding sitei184 – 1841Substrate1 Publication

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 aldolasePRO_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

1
213
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.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0A955.

Family & Domainsi

Region

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

Sequence similaritiesi

Belongs to the KHG/KDPG aldolase family.Curated

Phylogenomic databases

eggNOGiCOG0800.
HOGENOMiHOG000233114.
InParanoidiP0A955.
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

        10         20         30         40         50
MKNWKTSAES ILTTGPVVPV IVVKKLEHAV PMAKALVAGG VRVLEVTLRT
60 70 80 90 100
ECAVDAIRAI AKEVPEAIVG AGTVLNPQQL AEVTEAGAQF AISPGLTEPL
110 120 130 140 150
LKAATEGTIP LIPGISTVSE LMLGMDYGLK EFKFFPAEAN GGVKALQAIA
160 170 180 190 200
GPFSQVRFCP TGGISPANYR DYLALKSVLC IGGSWLVPAD ALEAGDYDRI
210
TKLAREAVEG AKL
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.
InParanoidi P0A955.
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: October 29, 2014
This is version 82 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