NADP-dependent isocitrate dehydrogenase (EC 1.1.1.42) of Pseudomonas putida KT2440 (locus PP_4011). It catalyzes the divalent-metal-dependent (Mg2+/Mn2+) oxidative decarboxylation of D-threo-isocitrate to 2-oxoglutarate and CO2 with the concomitant reduction of NADP+ to NADPH. The enzyme is a soluble cytoplasmic homodimer belonging to the isocitrate/isopropylmalate dehydrogenase family. It acts at the isocitrate node of the tricarboxylic acid cycle, where it both supplies 2-oxoglutarate for amino-acid biosynthesis and is a major source of anabolic reducing power (NADPH) for central metabolism and redox balance. In KT2440, biochemical assays of cell-free extracts show a strong (~89%) preference for NADP+ over NAD+. Activity at this branch point is subject to post-translational regulation (phosphorylation of a conserved serine), partitioning carbon between the TCA cycle and the glyoxylate shunt.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000287 magnesium ion binding | IEA GO_REF:0000002 | ACCEPT | Summary: NADP-IDH requires a divalent metal ion (Mg2+ or Mn2+) per subunit for catalysis, and UniProt annotates a Mg2+-binding residue (position 309). Magnesium ion binding is well supported for this family. Reason: Consistent with the IDH/IMDH family requirement for a divalent metal cofactor; UniProt records both Mg2+ and Mn2+ cofactors and a Mg2+-binding site. |
| GO:0004450 isocitrate dehydrogenase (NADP+) activity | IEA GO_REF:0000120 | ACCEPT | Summary: This is the core molecular function. The enzyme catalyzes oxidative decarboxylation of D-threo-isocitrate to 2-oxoglutarate + CO2 with reduction of NADP+ (EC 1.1.1.42, RHEA:19629). KT2440-specific biochemistry confirms strong NADP+ preference (~89% NADP+ vs ~11% NAD+ in cell-free extracts). Reason: Directly matches UniProt catalytic activity and is corroborated by organism-specific biochemical measurements of NADP cofactor preference (Nikel et al. 2015, PMID:26350459). |
| GO:0006099 tricarboxylic acid cycle | IEA GO_REF:0000120 | ACCEPT | Summary: Isocitrate dehydrogenase catalyzes the isocitrate to 2-oxoglutarate step of the TCA cycle. This is the appropriate biological process for the core function. Reason: Standard, well-supported placement of IDH within the TCA cycle; consistent with central carbon metabolism studies in KT2440. |
| GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor | IEA GO_REF:0000002 | MARK AS OVER ANNOTATED | Summary: This is a generic parent term of the specific and more informative GO:0004450 (isocitrate dehydrogenase (NADP+) activity), which is already annotated. It is not incorrect but adds no information beyond the specific child. Reason: Redundant grandparent of the specific MF term GO:0004450 that is already present; provides no additional specificity. |
| GO:0051287 NAD binding | IEA GO_REF:0000002 | REMOVE | Summary: This enzyme is NADP+-specific, not NAD+-binding. UniProt annotates multiple NADP(+)-binding residues (positions 106, 341-347, 354, 393, 397) and no NAD-binding site, and KT2440 biochemistry shows ~89% NADP+ preference. The InterPro2GO mapping to NAD binding is a mis-propagation for this NADP-specific family member; the correct cofactor binding is NADP, not NAD. Reason: Contradicted by cofactor specificity. The enzyme binds NADP+, not NAD+; this is an over-propagated InterPro IEA inference. NADP binding (GO:0050661) would be the correct term. Proposed replacements: NADP binding |
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