eda Gene Review Notes

Core identity

• eda in Pseudomonas putida KT2440 is UniProt Q88P29 / locus tag PP_1024 and is annotated as 2-dehydro-3-deoxy-phosphogluconate aldolase with EC=4.1.2.14 [file:PSEPK/eda/eda-uniprot.txt "RecName: Full=2-dehydro-3-deoxy-phosphogluconate aldolase"; file:PSEPK/eda/eda-uniprot.txt "GN OrderedLocusNames=PP_1024"; file:PSEPK/eda/eda-uniprot.txt "DE EC=4.1.2.14"].
• UniProt gives the catalytic reaction as cleavage of 2-dehydro-3-deoxy-6-phospho-D-gluconate to D-glyceraldehyde 3-phosphate + pyruvate, which is the canonical KDPG aldolase reaction [file:PSEPK/eda/eda-uniprot.txt "Reaction=2-dehydro-3-deoxy-6-phospho-D-gluconate = D-glyceraldehyde 3-phosphate + pyruvate"].
• UniProt places the enzyme in 2-dehydro-3-deoxy-D-gluconate degradation step 2/2, consistent with the terminal carbon-splitting step of the Entner-Doudoroff route [file:PSEPK/eda/eda-uniprot.txt "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"].

Family / structure

• The protein is a member of the KHG/KDPG aldolase family and is predicted to form a homotrimer [file:PSEPK/eda/eda-uniprot.txt "SUBUNIT: Homotrimer."; file:PSEPK/eda/eda-uniprot.txt "SIMILARITY: Belongs to the KHG/KDPG aldolase family."].
• GOA for Q88P29 currently contains only two molecular function annotations: the specific aldolase term GO:0008675 and the broad parent GO:0016829 lyase activity [file:PSEPK/eda/eda-goa.tsv "GO:0008675"; file:PSEPK/eda/eda-goa.tsv "GO:0016829"].

Curation take

• GO:0008675 2-dehydro-3-deoxy-phosphogluconate aldolase activity should be retained as the core molecular function because it matches the named catalytic activity and reaction chemistry [file:PSEPK/eda/eda-uniprot.txt "RecName: Full=2-dehydro-3-deoxy-phosphogluconate aldolase"; file:PSEPK/eda/eda-uniprot.txt "Reaction=2-dehydro-3-deoxy-6-phospho-D-gluconate = D-glyceraldehyde 3-phosphate + pyruvate"].
• GO:0016829 lyase activity is accurate but too generic to represent the evolved core function on its own; it should be retained only as non-core [file:PSEPK/eda/eda-uniprot.txt "KW Lyase"].
• A missing process-level annotation is involvement in the Entner-Doudoroff pathway through 6-phosphogluconate (GO:0009255), supported by the explicit UniProt pathway statement [file:PSEPK/eda/eda-uniprot.txt "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"].

Context

• The KT2440 genome paper is useful for strain/background provenance but does not itself establish eda biochemistry beyond the genome context PMID:12534463.