Kgu-locus oxidoreductase assigned as the KguD candidate that reduces 2-dehydro-6-phospho-D-gluconate to 6-phospho-D-gluconate in the cytosolic arm of the 2-ketogluconate pathway. Its sequence classification and conserved locus context are consistent with EC 1.1.1.43.
Definition: The chemical reactions and pathways resulting in the breakdown of 2-dehydro-D-gluconate, including its conversion to 6-phospho-D-gluconate.
Justification: GO:0019521 covers D-gluconate generally but does not distinguish the phosphorylative 2-dehydro-D-gluconate pathway completed by KguD.
Parent term: monocarboxylic acid catabolic process
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005829 cytosol | IEA GO_REF:0000118 | KEEP AS NON CORE | Summary: Cytosolic localization is compatible with the intracellular KguK-KguD arm but is inherited from TreeGrafter rather than directly shown for Q88HI1. Reason: Retain the plausible localization as ancillary; pathway order supports intracellular action but does not directly resolve cytosol versus broader cytoplasm. Supporting Evidence: PMID:39770733 2KGA in the periplasmic space is transported into the cell by the 2KGA transporter KguT and phosphorylated into 2-keto-6-phosphogluconate by the 2-keto-6-phosphogluconate kinase KguK, which is then reduced to 6-phosphogluconate by the 2-keto-6-phosphogluconate reductase KguD |
| GO:0016491 oxidoreductase activity | IEA GO_REF:0000117 | MARK AS OVER ANNOTATED | Summary: This generic term is consistent with a dehydrogenase but lacks reaction specificity. Reason: GO:0008114 is the appropriate pathway-grounded molecular function. |
| GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor | IEA GO_REF:0000002 | MODIFY | Summary: The broad chemistry is compatible with KguD but should be replaced by the specific EC 1.1.1.43 term. Reason: Direct locus genetics and conserved pathway order support phosphogluconate 2-dehydrogenase activity more specifically. Proposed replacements: phosphogluconate 2-dehydrogenase activity Supporting Evidence: PMID:39770733 which is then reduced to 6-phosphogluconate by the 2-keto-6-phosphogluconate reductase KguD |
| GO:0016618 hydroxypyruvate reductase [NAD(P)H] activity | IEA GO_REF:0000118 | REMOVE | Summary: This TreeGrafter transfer conflicts with the direct kgu-locus genetics and pathway assignment. Reason: There is no target-specific hydroxypyruvate-reductase evidence. Supporting Evidence: file:PSEPK/ptxD/ptxD-uniprot.txt DR GO; GO:0016618; F:hydroxypyruvate reductase [NAD(P)H] activity; IEA:TreeGrafter. PMID:39770733 which is then reduced to 6-phosphogluconate by the 2-keto-6-phosphogluconate reductase KguD |
| GO:0030267 glyoxylate reductase (NADPH) activity | IEA GO_REF:0000118 | REMOVE | Summary: This TreeGrafter transfer conflicts with the direct kgu-locus genetics and pathway assignment. Reason: There is no target-specific glyoxylate-reductase evidence. Supporting Evidence: file:PSEPK/ptxD/ptxD-uniprot.txt DR GO; GO:0030267; F:glyoxylate reductase (NADPH) activity; IEA:TreeGrafter. PMID:39770733 which is then reduced to 6-phosphogluconate by the 2-keto-6-phosphogluconate reductase KguD |
| GO:0050609 phosphonate dehydrogenase activity | IEA GO_REF:0000003 | REMOVE | Summary: The EC mapping follows the legacy ptxD name; no direct Q88HI1 phosphite assay was found. Reason: The D-isomer-specific 2-hydroxyacid dehydrogenase fold is shared with genuine PtxD and does not discriminate the activities. Removal rests on the kgu-locus/pathway assignment and absence of a Q88HI1 phosphite assay. Supporting Evidence: file:PSEPK/ptxD/ptxD-deep-research-openscientist.md dedicated literature searches for *P. putida* KT2440–specific phosphite oxidation / PP_3376 characterization returned **no direct studies** |
| GO:0051287 NAD binding | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: The NAD-binding domain supports dinucleotide binding, but Q88HI1 cofactor preference is not established. Reason: EC 1.1.1.43 is NAD(P)-dependent and InterPro IPR006140 supports an NAD-binding fold; retain this as ancillary pending target-protein cofactor measurements. Supporting Evidence: file:PSEPK/ptxD/ptxD-uniprot.txt DR InterPro; IPR006140; D-isomer_DH_NAD-bd. |
| GO:0019521 D-gluconate metabolic process | ISS | NEW | Summary: PP_3376 disruption and the ordered kgu pathway place this protein in the 2-ketogluconate loop. Reason: This process covers the intracellular phosphorylative use of 2-ketogluconate without misclassifying it as a non-phosphorylated reaction. Supporting Evidence: PMID:39770733 which is then reduced to 6-phosphogluconate by the 2-keto-6-phosphogluconate reductase KguD PMID:29607620 kguT, kguK and kguD that form another operon with ptxS |
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Download this section (compressed HTML)Q: Does purified Q88HI1 prefer 2-dehydro-6-phospho-D-gluconate/NADPH, and is any phosphite oxidation detectable?
Experiment: Compare purified Q88HI1 kinetics for the KguD reaction and phosphite/NAD+ oxidation, then complement a PP_3376 deletion and quantify pathway intermediates.
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