dapB encodes 4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8), which reduces the DapA product to tetrahydrodipicolinate in the second dedicated reaction of the diaminopimelate route to L-lysine. DapB-family enzymes can use NADPH or NADH as the reducing cofactor.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005737 cytoplasm | IEA GO_REF:0000120 | KEEP AS NON CORE | Summary: DapB is a soluble cytoplasmic biosynthetic enzyme. Reason: The location is valid but secondary to the reaction. |
| GO:0005829 cytosol | IEA GO_REF:0000118 | KEEP AS NON CORE | Summary: This duplicates the retained bacterial cytoplasm annotation. Reason: Relaxed from MARK_AS_OVER_ANNOTATED on re-review, per the rule that broad-but-true terms are not over-annotations. DapB is a soluble cytoplasmic enzyme with no signal peptide, transmembrane segment or lipobox, so the cytosol is where it resides; carrying the broader cytoplasm term on another row makes this one redundant, not incorrect. |
| GO:0008839 4-hydroxy-tetrahydrodipicolinate reductase activity | IEA GO_REF:0000120 | ACCEPT | Summary: This is the defining DapB molecular function. Reason: The HAMAP MF_00102 curated function statement and DapB family membership (HAMAP, NCBIfam TIGR00036) agree on HTPA reduction; this is a family-rule inference, as Q88DU4 itself has not been assayed. Supporting Evidence: file:PSEPK/dapB/dapB-uniprot.txt Catalyzes the conversion of 4-hydroxy-tetrahydrodipicolinate file:PSEPK/dapB/dapB-uniprot.txt DR NCBIfam; TIGR00036; dapB; 1. |
| GO:0009085 L-lysine biosynthetic process | IEA GO_REF:0000002 | ACCEPT | Summary: DapB performs the reduction step of the lysine DAP pathway. Reason: UniProt assigns Q88DU4 to L-lysine biosynthesis via the DAP pathway. |
| GO:0016726 oxidoreductase activity, acting on CH or CH2 groups, NAD or NADP as acceptor | IEA GO_REF:0000104 | MARK AS OVER ANNOTATED | Summary: This broad redox term is redundant with the specific DapB activity. Reason: GO:0008839 captures the substrate-specific reaction. |
| GO:0050661 NADP binding | IEA GO_REF:0000104 | KEEP AS NON CORE | Summary: NADP binding is valid cofactor context for DapB. Reason: The reviewed reaction permits NADPH, but cofactor binding is less informative than catalysis. |
| GO:0051287 NAD binding | IEA GO_REF:0000104 | KEEP AS NON CORE | Summary: NAD binding is valid cofactor context for DapB. Reason: The reviewed reaction permits NADH, but cofactor binding is less informative than catalysis. |
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Download this section (compressed HTML)What is not known — curated, literature-grounded statements of the open unknowns (the inverse of core functions).
Gap: Q88DU4 has not been assayed directly, so its cofactor preference, kinetics, and physiological contribution have not been established in KT2440.
BIOLOGYCURATION
What is known: The exact reaction and dual NADPH/NADH capability are strongly supported by the reviewed record and conserved DapB-family evidence; target-specific quantitative properties remain inference-based.
Provenance (the field's own admissions):
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Download this section (compressed HTML)The gene-level OpenScientist request for Q88DU4/PP_4725 reached the provider's
3600-second ceiling, was cancelled, and produced no report. No provider-named
deep-research file was created. This first-pass review therefore remains
grounded in the exact UniProt and GOA records, DapB-specific HAMAP and NCBIfam
assignments, Rhea reaction mappings, and the curated lysine-pathway context.
Direct biochemical or genetic evidence for this specific KT2440 protein was not
established in this pass.
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