Glyceraldehyde-3-phosphate dehydrogenase (GAPDH; gapA, locus PP_1009) of Pseudomonas putida KT2440. It is a homotetrameric, NAD-dependent oxidoreductase that catalyzes the reversible oxidative phosphorylation of D-glyceraldehyde-3-phosphate with inorganic phosphate to 1,3-bisphosphoglycerate, reducing NAD+ to NADH. This reaction is the central energy-conserving step of the lower glycolytic (Embden-Meyerhof-Parnas) segment. In P. putida, which catabolizes glucose primarily through the Entner-Doudoroff pathway, GAPDH acts at the node where the triose phosphate produced by the ED and EMP routes is channeled toward 3-phosphoglycerate, pyruvate and the TCA cycle. The enzyme is cytoplasmic and is a member of the NAD-dependent glyceraldehyde-3-phosphate dehydrogenase (type I, GAPDH-I) family, with a Rossmann-fold NAD(P)-binding domain and a catalytic cysteine active site.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0006006 glucose metabolic process | IEA GO_REF:0000002 | ACCEPT | Summary: GAPDH catalyzes a core step of glucose catabolism (lower glycolysis), converting glyceraldehyde-3-phosphate to 1,3-bisphosphoglycerate. In P. putida this node integrates Entner-Doudoroff-derived triose phosphate with lower EMP flux. The annotation is biologically correct and represents a core function. Reason: Family/domain-based IEA annotation consistent with the well-established role of GAPDH in glucose metabolism; supported by P. putida pathway literature. Supporting Evidence: PMID:18245293 PP_1009 (gap-1/gapA) encodes glyceraldehyde-3-phosphate dehydrogenase acting in KT2440 glucose catabolism, repressed by the glucose-catabolism regulator HexR (4.89-fold derepression in a hexR mutant). |
| GO:0016620 oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor | IEA GO_REF:0000002 | MODIFY | Summary: This is the correct parent molecular function for GAPDH, which oxidizes the aldehyde group of glyceraldehyde-3-phosphate using NAD as acceptor. A more specific child term exists (glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity, GO:0004365), which better captures the precise reaction catalyzed by this enzyme. Reason: The term is correct but too general. The protein is a canonical phosphorylating, NAD-dependent GAPDH (TIGR01534 GAPDH-I, PROSITE PS00071, with catalytic Cys at position 154 and bound NAD+), so the specific child term is warranted. Proposed replacements: glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity |
| GO:0050661 NADP binding | IEA GO_REF:0000002 | REMOVE | Summary: This annotation derives from the broad NAD(P)-binding Rossmann-fold InterPro signature (IPR006424). However, all cofactor-binding residues modeled in the UniProt record bind NAD+ (CHEBI:57540), and the protein is classified as GAPDH-I (TIGR01534), the NAD-specific form of the family. There is no P. putida-specific evidence of NADP usage; NADP-dependent GAPDH is the distinct GapN/GapC/non-phosphorylating class. Reason: Over-propagated electronic inference from a generic NAD(P)-binding domain signature. The structural evidence (NAD+-only binding sites) and GAPDH-I family membership argue against NADP binding for this specific protein. NAD binding is already captured separately. |
| GO:0051287 NAD binding | IEA GO_REF:0000002 | ACCEPT | Summary: GAPDH binds NAD+ as its catalytic cofactor. The UniProt record annotates multiple NAD+-binding residues (positions 12-13, 37, 81, 123, 314) via the Rossmann-fold NAD(P)-binding domain. This is correct and a core feature. Reason: Strongly supported by domain architecture and conserved NAD+-binding residues; consistent with NAD-dependent GAPDH-I family membership. |
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