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 27-MAR-2024, entry version 138. 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; Pseudomonadota; 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}. CC --------------------------------------------------------------------------- CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms CC Distributed under the Creative Commons Attribution (CC BY 4.0) License CC --------------------------------------------------------------------------- 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 jPOST; P0A955; -. DR PaxDb; 511145-b1850; -. DR EnsemblBacteria; AAC74920; AAC74920; b1850. DR GeneID; 83576924; -. 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 OrthoDB; 9805177at2; -. DR PhylomeDB; P0A955; -. DR BioCyc; EcoCyc:KDPGALDOL-4OH2OXOGLUTARALDOL-MONOMER; -. DR BioCyc; MetaCyc:KDPGALDOL-4OH2OXOGLUTARALDOL-MONOMER; -. 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; Aldolase class I; 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 NCBIfam; TIGR01182; eda; 1. DR PANTHER; PTHR30246; 2-KETO-3-DEOXY-6-PHOSPHOGLUCONATE ALDOLASE; 1. DR PANTHER; PTHR30246:SF2; KHG_KDPG ALDOLASE; 1. DR Pfam; PF01081; Aldolase; 1. DR SUPFAM; SSF51569; Aldolase; 1. DR PROSITE; PS00159; ALDOLASE_KDPG_KHG_1; 1. DR PROSITE; PS00160; ALDOLASE_KDPG_KHG_2; 1. DR SWISS-2DPAGE; P0A955; -. 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 FT alpha-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 //