ALKH_ECOLI
ID ALKH_ECOLI Reviewed; 213 AA.
AC P0A955; P10177;
DT 19-JUL-2005, integrated into UniProtKB/Swiss-Prot.
DT 19-JUL-2005, sequence version 1.
DT 03-AUG-2022, entry version 130.
DE RecName: Full=KHG/KDPG aldolase;
DE Includes:
DE RecName: Full=4-hydroxy-2-oxoglutarate aldolase;
DE EC=4.1.3.16;
DE AltName: Full=2-keto-4-hydroxyglutarate aldolase;
DE Short=KHG-aldolase;
DE Includes:
DE RecName: Full=2-dehydro-3-deoxy-phosphogluconate aldolase;
DE EC=4.1.2.14;
DE AltName: Full=2-keto-3-deoxy-6-phosphogluconate aldolase;
DE Short=KDPG-aldolase;
DE AltName: Full=Phospho-2-dehydro-3-deoxygluconate aldolase;
DE AltName: Full=Phospho-2-keto-3-deoxygluconate aldolase;
GN Name=eda; Synonyms=hga, kdgA; OrderedLocusNames=b1850, JW1839;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP PROTEIN SEQUENCE, AND ACTIVE SITE.
RC STRAIN=K12;
RX PubMed=3136164; DOI=10.1016/s0021-9258(18)37838-4;
RA Vlahos C.J., Dekker E.E.;
RT "The complete amino acid sequence and identification of the active-site
RT arginine peptide of Escherichia coli 2-keto-4-hydroxyglutarate aldolase.";
RL J. Biol. Chem. 263:11683-11691(1988).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION AS A KHG-ALDOLASE, AND
RP DISRUPTION PHENOTYPE.
RX PubMed=1339418; DOI=10.1128/jb.174.1.102-107.1992;
RA Patil R.V., Dekker E.E.;
RT "Cloning, nucleotide sequence, overexpression, and inactivation of the
RT Escherichia coli 2-keto-4-hydroxyglutarate aldolase gene.";
RL J. Bacteriol. 174:102-107(1992).
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=1624451; DOI=10.1128/jb.174.14.4638-4646.1992;
RA Egan S.E., Fliege R., Tong S., Shibata A., Wolf R.E. Jr., Conway T.;
RT "Molecular characterization of the Entner-Doudoroff pathway in Escherichia
RT coli: sequence analysis and localization of promoters for the edd-eda
RT operon.";
RL J. Bacteriol. 174:4638-4646(1992).
RN [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12;
RA Smith J.M., Nygaard P.;
RT "Purine and one-carbon metabolism in Escherichia coli K12: DNA sequence of
RT a second GAR transformylase.";
RL Submitted (JUL-1993) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12;
RX PubMed=8344525; DOI=10.1016/0378-1119(93)90362-7;
RA Carter A.T., Pearson B.M., Dickinson J.R., Lancashire W.E.;
RT "Sequence of the Escherichia coli K-12 edd and eda genes of the Entner-
RT Doudoroff pathway.";
RL Gene 130:155-156(1993).
RN [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=9097040; DOI=10.1093/dnares/3.6.379;
RA Itoh T., Aiba H., Baba T., Fujita K., Hayashi K., Inada T., Isono K.,
RA Kasai H., Kimura S., Kitakawa M., Kitagawa M., Makino K., Miki T.,
RA Mizobuchi K., Mori H., Mori T., Motomura K., Nakade S., Nakamura Y.,
RA Nashimoto H., Nishio Y., Oshima T., Saito N., Sampei G., Seki Y.,
RA Sivasundaram S., Tagami H., Takeda J., Takemoto K., Wada C., Yamamoto Y.,
RA Horiuchi T.;
RT "A 460-kb DNA sequence of the Escherichia coli K-12 genome corresponding to
RT the 40.1-50.0 min region on the linkage map.";
RL DNA Res. 3:379-392(1996).
RN [7]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [8]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [9]
RP ACTIVE SITE.
RX PubMed=1978721; DOI=10.1016/s0021-9258(17)30515-x;
RA Vlahos C.J., Dekker E.E.;
RT "Active-site residues of 2-keto-4-hydroxyglutarate aldolase from
RT Escherichia coli. Bromopyruvate inactivation and labeling of glutamate
RT 45.";
RL J. Biol. Chem. 265:20384-20389(1990).
RN [10]
RP IDENTIFICATION BY 2D-GEL.
RX PubMed=9298644; DOI=10.1002/elps.1150180805;
RA VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C.;
RT "Escherichia coli proteome analysis using the gene-protein database.";
RL Electrophoresis 18:1243-1251(1997).
RN [11]
RP FUNCTION AS A KDPG-ALDOLASE, CATALYTIC ACTIVITY, MUTAGENESIS OF GLU-45 AND
RP THR-161, BIOPHYSICOCHEMICAL PROPERTIES, SUBSTRATE SPECIFICITY, AND
RP INDUCTION.
RX PubMed=17981470; DOI=10.1016/j.bmc.2007.10.043;
RA Walters M.J., Srikannathasan V., McEwan A.R., Naismith J.H., Fierke C.A.,
RA Toone E.J.;
RT "Characterization and crystal structure of Escherichia coli KDPGal
RT aldolase.";
RL Bioorg. Med. Chem. 16:710-720(2008).
RN [12]
RP X-RAY CRYSTALLOGRAPHY (1.95 ANGSTROMS) IN COMPLEX WITH SUBSTRATE, REACTION
RP MECHANISM, AND SUBUNIT.
RX PubMed=11274385; DOI=10.1073/pnas.071380898;
RA Allard J., Grochulski P., Sygusch J.;
RT "Covalent intermediate trapped in 2-keto-3-deoxy-6-phosphogluconate (KDPG)
RT aldolase structure at 1.95-A resolution.";
RL Proc. Natl. Acad. Sci. U.S.A. 98:3679-3684(2001).
RN [13]
RP X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF WILD-TYPE AND DOUBLE MUTANT IN
RP COMPLEX WITH SUBSTRATE, MUTAGENESIS OF LYS-133; THR-161 AND ASN-168,
RP BIOPHYSICOCHEMICAL PROPERTIES, AND SUBUNIT.
RX PubMed=11342129; DOI=10.1016/s0969-2126(00)00555-4;
RA Wymer N., Buchanan L.V., Henderson D., Mehta N., Botting C.H.,
RA Pocivavsek L., Fierke C.A., Toone E.J., Naismith J.H.;
RT "Directed evolution of a new catalytic site in 2-keto-3-deoxy-6-
RT phosphogluconate aldolase from Escherichia coli.";
RL Structure 9:1-9(2001).
RN [14]
RP X-RAY CRYSTALLOGRAPHY (1.55 ANGSTROMS) OF WILD-TYPE AND MUTANT IN COMPLEX
RP WITH SUBSTRATE, MUTAGENESIS OF GLU-45, REACTION MECHANISM, AND SUBUNIT.
RX PubMed=16403639; DOI=10.1016/j.bmc.2005.12.022;
RA Fullerton S.W., Griffiths J.S., Merkel A.B., Cheriyan M., Wymer N.J.,
RA Hutchins M.J., Fierke C.A., Toone E.J., Naismith J.H.;
RT "Mechanism of the Class I KDPG aldolase.";
RL Bioorg. Med. Chem. 14:3002-3010(2006).
CC -!- FUNCTION: Involved in the degradation of glucose via the Entner-
CC Doudoroff pathway. Catalyzes the reversible, stereospecific retro-aldol
CC cleavage of 2-Keto-3-deoxy-6-phosphogluconate (KDPG) to pyruvate and D-
CC glyceraldehyde-3-phosphate. In the synthetic direction, it catalyzes
CC the addition of pyruvate to electrophilic aldehydes with si-facial
CC selectivity. It accepts some nucleophiles other than pyruvate,
CC including 2-oxobutanoate, phenylpyruvate, and fluorobutanoate. It has a
CC preference for the S-configuration at C2 of the electrophile.
CC {ECO:0000269|PubMed:1339418, ECO:0000269|PubMed:17981470}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(4S)-4-hydroxy-2-oxoglutarate = glyoxylate + pyruvate;
CC Xref=Rhea:RHEA:35639, ChEBI:CHEBI:15361, ChEBI:CHEBI:36655,
CC ChEBI:CHEBI:71685; EC=4.1.3.16;
CC Evidence={ECO:0000269|PubMed:17981470};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(4R)-4-hydroxy-2-oxoglutarate = glyoxylate + pyruvate;
CC Xref=Rhea:RHEA:30687, ChEBI:CHEBI:15361, ChEBI:CHEBI:36655,
CC ChEBI:CHEBI:62213; EC=4.1.3.16;
CC Evidence={ECO:0000269|PubMed:17981470};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2-dehydro-3-deoxy-6-phospho-D-gluconate = D-glyceraldehyde 3-
CC phosphate + pyruvate; Xref=Rhea:RHEA:17089, ChEBI:CHEBI:15361,
CC ChEBI:CHEBI:57569, ChEBI:CHEBI:59776; EC=4.1.2.14;
CC Evidence={ECO:0000269|PubMed:17981470};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.1 mM for KDPG {ECO:0000269|PubMed:11342129,
CC ECO:0000269|PubMed:17981470};
CC KM=9 mM for 2-oxobutyrate {ECO:0000269|PubMed:11342129,
CC ECO:0000269|PubMed:17981470};
CC KM=10 mM for pyruvate {ECO:0000269|PubMed:11342129,
CC ECO:0000269|PubMed:17981470};
CC Note=kcat is 80 sec(-1) for KDPG, 0.012 sec(-1) for pyruvate and
CC 0.0004 sec(-1) for 2-oxobutyrate.;
CC -!- PATHWAY: Carbohydrate acid metabolism; 2-dehydro-3-deoxy-D-gluconate
CC degradation; D-glyceraldehyde 3-phosphate and pyruvate from 2-dehydro-
CC 3-deoxy-D-gluconate: step 2/2.
CC -!- PATHWAY: Carbohydrate metabolism; glyoxylate and dicarboxylate
CC metabolism.
CC -!- SUBUNIT: Homotrimer. {ECO:0000269|PubMed:11274385,
CC ECO:0000269|PubMed:11342129, ECO:0000269|PubMed:16403639}.
CC -!- INTERACTION:
CC P0A955; P0A955: eda; NbExp=3; IntAct=EBI-558114, EBI-558114;
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250}.
CC -!- INDUCTION: Constitutive, three-fold induction occurs for growth on
CC gluconate and two-fold for growth on hexuronic acids.
CC {ECO:0000269|PubMed:17981470}.
CC -!- DISRUPTION PHENOTYPE: Cells lacking this gene lose KHG aldolase
CC activity. {ECO:0000269|PubMed:1339418}.
CC -!- SIMILARITY: Belongs to the KHG/KDPG aldolase family. {ECO:0000305}.
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DR EMBL; X68871; CAA48732.1; -; Genomic_DNA.
DR EMBL; M87458; AAA23723.1; -; Genomic_DNA.
DR EMBL; L20897; AAA23862.1; -; Genomic_DNA.
DR EMBL; X63694; CAA45222.1; -; Genomic_DNA.
DR EMBL; U00096; AAC74920.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA15658.1; -; Genomic_DNA.
DR PIR; B42986; ADECOG.
DR RefSeq; NP_416364.1; NC_000913.3.
DR RefSeq; WP_000800512.1; NZ_STEB01000009.1.
DR PDB; 1EUA; X-ray; 1.95 A; A/B/C=1-213.
DR PDB; 1EUN; X-ray; 2.00 A; A/B/C=1-213.
DR PDB; 1FQ0; X-ray; 2.10 A; A/B/C=1-213.
DR PDB; 1FWR; X-ray; 2.70 A; A/B/C=1-213.
DR PDB; 1WAU; X-ray; 2.80 A; A=1-213.
DR PDB; 1WBH; X-ray; 1.55 A; A/B/C=1-213.
DR PDB; 2C0A; X-ray; 1.55 A; A/B/C=1-213.
DR PDBsum; 1EUA; -.
DR PDBsum; 1EUN; -.
DR PDBsum; 1FQ0; -.
DR PDBsum; 1FWR; -.
DR PDBsum; 1WAU; -.
DR PDBsum; 1WBH; -.
DR PDBsum; 2C0A; -.
DR AlphaFoldDB; P0A955; -.
DR SMR; P0A955; -.
DR BioGRID; 4259153; 29.
DR BioGRID; 850724; 2.
DR DIP; DIP-36196N; -.
DR IntAct; P0A955; 10.
DR STRING; 511145.b1850; -.
DR ChEMBL; CHEMBL4296292; -.
DR SWISS-2DPAGE; P0A955; -.
DR jPOST; P0A955; -.
DR PaxDb; P0A955; -.
DR PRIDE; P0A955; -.
DR EnsemblBacteria; AAC74920; AAC74920; b1850.
DR EnsemblBacteria; BAA15658; BAA15658; BAA15658.
DR GeneID; 66674260; -.
DR GeneID; 946367; -.
DR KEGG; ecj:JW1839; -.
DR KEGG; eco:b1850; -.
DR PATRIC; fig|1411691.4.peg.399; -.
DR EchoBASE; EB0252; -.
DR eggNOG; COG0800; Bacteria.
DR HOGENOM; CLU_077795_1_1_6; -.
DR InParanoid; P0A955; -.
DR OMA; FFPAEYC; -.
DR PhylomeDB; P0A955; -.
DR BioCyc; EcoCyc:KDPGALDOL-4OH2OXOGLUTARALDOL-MON; -.
DR BioCyc; MetaCyc:KDPGALDOL-4OH2OXOGLUTARALDOL-MON; -.
DR BRENDA; 4.1.2.14; 2026.
DR BRENDA; 4.1.3.16; 2026.
DR BRENDA; 4.1.3.42; 2026.
DR UniPathway; UPA00227; -.
DR UniPathway; UPA00856; UER00829.
DR EvolutionaryTrace; P0A955; -.
DR PRO; PR:P0A955; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0016020; C:membrane; HDA:UniProtKB.
DR GO; GO:0106009; F:(4S)-4-hydroxy-2-oxoglutarate aldolase activity; IDA:EcoCyc.
DR GO; GO:0008675; F:2-dehydro-3-deoxy-phosphogluconate aldolase activity; IDA:EcoCyc.
DR GO; GO:0008700; F:4-hydroxy-2-oxoglutarate aldolase activity; IDA:UniProtKB.
DR GO; GO:0042802; F:identical protein binding; IPI:IntAct.
DR GO; GO:0008948; F:oxaloacetate decarboxylase activity; IDA:EcoCyc.
DR GO; GO:0016833; F:oxo-acid-lyase activity; IDA:EcoCyc.
DR GO; GO:0008152; P:metabolic process; IEA:UniProtKB-KW.
DR CDD; cd00452; KDPG_aldolase; 1.
DR Gene3D; 3.20.20.70; -; 1.
DR InterPro; IPR000887; Aldlse_KDPG_KHG.
DR InterPro; IPR013785; Aldolase_TIM.
DR InterPro; IPR031337; KDPG/KHG_AS_1.
DR InterPro; IPR031338; KDPG/KHG_AS_2.
DR PANTHER; PTHR30246; PTHR30246; 1.
DR Pfam; PF01081; Aldolase; 1.
DR TIGRFAMs; TIGR01182; eda; 1.
DR PROSITE; PS00159; ALDOLASE_KDPG_KHG_1; 1.
DR PROSITE; PS00160; ALDOLASE_KDPG_KHG_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Direct protein sequencing; Lyase;
KW Multifunctional enzyme; Reference proteome; Schiff base.
FT CHAIN 1..213
FT /note="KHG/KDPG aldolase"
FT /id="PRO_0000201037"
FT ACT_SITE 45
FT /note="Proton acceptor"
FT ACT_SITE 49
FT ACT_SITE 133
FT /note="Schiff-base intermediate with substrate"
FT BINDING 8..9
FT /ligand="substrate"
FT BINDING 49
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:16403639"
FT BINDING 73
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:16403639"
FT BINDING 133
FT /ligand="substrate"
FT /note="covalent"
FT /evidence="ECO:0000269|PubMed:16403639"
FT BINDING 161
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:16403639"
FT BINDING 163
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:16403639"
FT BINDING 184
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:16403639"
FT SITE 161
FT /note="Plays a major role in determining the
FT stereoselectivity"
FT MUTAGEN 45
FT /note="E->N: 50-fold decrease in catalytic efficiency and
FT 6-fold decrease of binding affinity."
FT /evidence="ECO:0000269|PubMed:16403639,
FT ECO:0000269|PubMed:17981470"
FT MUTAGEN 133
FT /note="K->Q: Absence of aldolase activity. Shows a markedly
FT altered substrate specificity relative to the wild-type,
FT with an enhanced activity against pyridine carboxaldehyde,
FT benzaldehyde, and alpha-ketobutyrate; when associated with
FT k-161."
FT /evidence="ECO:0000269|PubMed:11342129"
FT MUTAGEN 161
FT /note="T->K: Shows activity significantly greater than
FT wild-type. Shows a markedly altered substrate specificity
FT relative to the wild-type, with an enhanced activity
FT against pyridine carboxaldehyde, benzaldehyde, and alpha-
FT ketobutyrate; when associated with Q-133."
FT /evidence="ECO:0000269|PubMed:11342129,
FT ECO:0000269|PubMed:17981470"
FT MUTAGEN 161
FT /note="T->V: Little stereoselectivity, accepting KDPG and
FT KDPGal as substrate with roughly equal efficacy. It
FT strongly diminishes the activity against KDPG and slightly
FT increases activity against KDPGal."
FT /evidence="ECO:0000269|PubMed:11342129,
FT ECO:0000269|PubMed:17981470"
FT MUTAGEN 168
FT /note="N->S: Shows activity significantly greater than
FT wild-type."
FT /evidence="ECO:0000269|PubMed:11342129"
FT HELIX 8..13
FT /evidence="ECO:0007829|PDB:1WBH"
FT STRAND 16..21
FT /evidence="ECO:0007829|PDB:1WBH"
FT HELIX 26..28
FT /evidence="ECO:0007829|PDB:1WBH"
FT HELIX 29..38
FT /evidence="ECO:0007829|PDB:1WBH"
FT STRAND 43..48
FT /evidence="ECO:0007829|PDB:1WBH"
FT HELIX 53..63
FT /evidence="ECO:0007829|PDB:1WBH"
FT STRAND 67..73
FT /evidence="ECO:0007829|PDB:1WBH"
FT HELIX 77..86
FT /evidence="ECO:0007829|PDB:1WBH"
FT STRAND 91..95
FT /evidence="ECO:0007829|PDB:1WBH"
FT HELIX 98..106
FT /evidence="ECO:0007829|PDB:1WBH"
FT STRAND 107..109
FT /evidence="ECO:0007829|PDB:1WBH"
FT STRAND 111..117
FT /evidence="ECO:0007829|PDB:1WBH"
FT HELIX 118..126
FT /evidence="ECO:0007829|PDB:1WBH"
FT STRAND 131..134
FT /evidence="ECO:0007829|PDB:1WBH"
FT TURN 135..141
FT /evidence="ECO:0007829|PDB:1WBH"
FT HELIX 142..150
FT /evidence="ECO:0007829|PDB:1WBH"
FT STRAND 157..163
FT /evidence="ECO:0007829|PDB:1WBH"
FT TURN 166..168
FT /evidence="ECO:0007829|PDB:1WBH"
FT HELIX 169..173
FT /evidence="ECO:0007829|PDB:1WBH"
FT STRAND 181..183
FT /evidence="ECO:0007829|PDB:1WBH"
FT HELIX 184..186
FT /evidence="ECO:0007829|PDB:1WBH"
FT HELIX 189..194
FT /evidence="ECO:0007829|PDB:1WBH"
FT HELIX 197..210
FT /evidence="ECO:0007829|PDB:1WBH"
SQ SEQUENCE 213 AA; 22284 MW; CC8D51B50480D0B7 CRC64;
MKNWKTSAES ILTTGPVVPV IVVKKLEHAV PMAKALVAGG VRVLEVTLRT ECAVDAIRAI
AKEVPEAIVG AGTVLNPQQL AEVTEAGAQF AISPGLTEPL LKAATEGTIP LIPGISTVSE
LMLGMDYGLK EFKFFPAEAN GGVKALQAIA GPFSQVRFCP TGGISPANYR DYLALKSVLC
IGGSWLVPAD ALEAGDYDRI TKLAREAVEG AKL
