EryCV is an iron-sulfur, S-adenosyl-L-methionine-dependent (radical-SAM-type) enzyme of the TDP-D-desosamine biosynthetic pathway in Saccharopolyspora erythraea (UniProt/EMBL/MIBiG name: NDP-4,6-dideoxyhexose 3,4-enoyl reductase; the DesII-type member of the cluster's deoxysugar enzymes). It carries a [4Fe-4S] cluster and uses SAM, consistent with a radical-SAM mechanism; the precise catalytic outcome on the TDP-deoxysugar intermediate is not experimentally resolved in the records available.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003824 catalytic activity | IEA GO_REF:0000002 | MARK AS OVER ANNOTATED | Summary: Root-level "catalytic activity" - uninformative; EryCV is a specific iron-sulfur/SAM enzyme. Reason: Generic catalytic-activity term provides no functional information; a specific MF is preferable. |
| GO:0016841 ammonia-lyase activity | IEA GO_REF:0000002 | UNDECIDED | Summary: Ammonia-lyase activity from an InterPro signature. This conflicts with the enzyme's name (3,4-enoyl reductase) and its radical-SAM (Fe-S/SAM) cofactor profile; DesII-type radical-SAM enzymes can catalyze dehydration/deamination, but the precise reaction here is unverified. Reason: Conflicting electronic assignments (ammonia-lyase vs 3,4-enoyl reductase) with no accessible experimental characterization; the radical-SAM cofactor binding is, however, well supported. |
| GO:0033068 macrolide biosynthetic process | IEA GO_REF:0000002 | ACCEPT | Summary: Involvement in macrolide (erythromycin) biosynthesis via the desosamine pathway. Correct; a more specific child (GO:1901115) is captured in core_functions. Reason: Accurate biological process. |
| GO:0051536 iron-sulfur cluster binding | IEA GO_REF:0000002 | ACCEPT | Summary: Iron-sulfur cluster binding; supported by the UniProt iron-sulfur keywords. Reason: Correct cofactor binding for this radical-SAM-type enzyme. Supporting Evidence: file:SACEN/eryCV/eryCV-uniprot.txt EryCV NDP-4,6-dideoxyhexose 3,4-enoyl reductase |
| GO:0051539 4 iron, 4 sulfur cluster binding | IEA GO_REF:0000002 | ACCEPT | Summary: [4Fe-4S] cluster binding - the hallmark cofactor of a radical-SAM enzyme; supported by the UniProt iron/iron-sulfur/SAM keywords. Reason: Correct and specific cofactor binding. Supporting Evidence: file:SACEN/eryCV/eryCV-uniprot.txt EryCV NDP-4,6-dideoxyhexose 3,4-enoyl reductase |
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Download this section (compressed HTML)Q: EVIDENCE GAP: what radical-SAM reaction does EryCV catalyze? It binds a [4Fe-4S] cluster and SAM (radical-SAM/DesII-type), but its UniProt/EMBL name ("3,4-enoyl reductase") and the GOA term ("ammonia-lyase activity") are conflicting electronic (IEA) assignments, with no experimental annotation. Tracked in projects/FUNCTION_KNOWLEDGE_GAPS.md.
Experiment: Reconstitute EryCV with its [4Fe-4S] cluster and SAM to determine the actual radical-SAM reaction on the TDP-deoxysugar intermediate (e.g. dehydration/deamination vs reduction), resolving the ammonia-lyase-vs-reductase annotation conflict.
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