EryCIV is a pyridoxal-5'-phosphate (PLP)-dependent sugar aminotransferase of the DegT/DnrJ/EryC1 family that acts in TDP-D-desosamine biosynthesis for erythromycin in Saccharopolyspora erythraea; eryCIV mutants accumulate the desosamine-deficient intermediate 3-alpha-mycarosyl erythronolide B. EryCIV is about 60% identical to DesI of Streptomyces venezuelae, the structurally characterized PLP-dependent aminotransferase of the desosamine pathway that forms dTDP-4-amino-4,6-dideoxy-D-glucose, and it retains the catalytic PLP Schiff-base lysine that the related PLP-dependent sugar dehydratases (ColD, AscC) replace with histidine. It is therefore inferred to catalyse C-4 transamination of dTDP-4-dehydro-6-deoxy-D-glucose, although the reaction has not been assayed for EryCIV itself. Its database name, NDP-6-deoxyhexose 3,4-dehydratase, derives from early sequence similarity to the AscC 3,4-dehydratase.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000271 polysaccharide biosynthetic process | IEA GO_REF:0000118 | MODIFY | Summary: Incorrect biological process. EryCIV acts in biosynthesis of the aminodeoxysugar D-desosamine (a monosaccharide moiety of erythromycin), not a polysaccharide. Reason: Wrong process class; replace with GO:1901115 (erythromycin biosynthetic process), to which desosamine biosynthesis contributes. Proposed replacements: erythromycin biosynthetic process |
| GO:0008483 transaminase activity | IEA GO_REF:0000118 | MODIFY | Summary: EryCIV is a PLP-dependent sugar aminotransferase, so transaminase activity is correct but too general; the specific activity inferred from its DesI ortholog is the C-4 transamination of dTDP-4-dehydro-6-deoxy-D-glucose (GO:0019179, EC:2.6.1.33). Reason: Re-reviewed after a blinded OpenScientist control run (file:SACEN/eryCIV/eryCIV-hypotheses/function-hypothesis-go-0008483/openscientist.md). The earlier UNDECIDED rested on a conflict between the dehydratase name and the transaminase term. That conflict is resolved in favour of transamination: EryCIV retains the catalytic PLP Schiff-base lysine (K200) that the DegT/DnrJ/EryC1-family dehydratases replace with histidine, and it is about 61% identical to DesI (Q9ZGH0), the desosamine-pathway enzyme that Burgie and Holden (PMID:17630700) describe as a PLP-dependent aminotransferase crystallized with its product dTDP-4-amino-4,6-dideoxyglucose. The dehydratase name derives from the 1997 sequence similarity to AscC (PMID:9353926, abstract). Both the sequence identity and the active-site residue were reproduced locally. GO:0019179 (dTDP-4-amino-4,6-dideoxy-D-glucose:2-oxoglutarate transaminase activity; EC:2.6.1.33, RHEA:19085) is the existing child of GO:0008483 whose product matches DesI, so no new term is needed. Caveats: the amino donor (glutamate/2-oxoglutarate in the GO definition) and the sugar substrate have not been assayed for EryCIV itself, and the inference is orthology-based. Proposed replacements: dTDP-4-amino-4,6-dideoxy-D-glucose:2-oxoglutarate transaminase activity Supporting Evidence: PMID:17630700 The focus of this x-ray crystallographic analysis is the third enzyme in the pathway, a PLP-dependent aminotransferase referred to as DesI. PMID:17630700 The structure of DesI was solved in complex with its product, dTDP-4-amino-4,6-dideoxyglucose file:SACEN/eryCIV/eryCIV-hypotheses/function-hypothesis-go-0008483/openscientist.md EryCIV has Lys, not His file:SACEN/eryCIV/eryCIV-hypotheses/function-hypothesis-go-0008483/openscientist.md DesI is an X-ray-characterized PLP-dependent aminotransferase that converts file:SACEN/eryCIV/eryCIV-hypotheses/function-hypothesis-go-0008483/openscientist.md The legacy "3,4-dehydratase" database name that still clings to eryCIV is a pre-structural mis-label, contradicted by the active-site analysis file:SACEN/eryCIV/eryCIV-hypotheses/function-hypothesis-go-0008483/openscientist.md No direct enzymatic assay for EryCIV itself. |
| GO:0030170 pyridoxal phosphate binding | IEA GO_REF:0000118 | ACCEPT | Summary: PLP binding; consistent across the family assignment and UniProt keyword. Reason: Correct cofactor for this PLP-dependent DegT/DnrJ/EryC1-family enzyme. Supporting Evidence: file:SACEN/eryCIV/eryCIV-uniprot.txt EryCIV NDP-6-deoxyhexose 3,4-dehydratase |
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Download this section (compressed HTML)Q: Does EryCIV catalyse C-4 transamination of dTDP-4-dehydro-6-deoxy-D-glucose like its ortholog DesI, and which amino donor does it use? Sequence and active-site evidence (conserved catalytic lysine, about 60% identity to DesI) favour transamination over the 3,4-dehydration implied by its database name, but no EryCIV assay exists. Tracked in projects/FUNCTION_KNOWLEDGE_GAPS.md.
Experiment: Purify EryCIV, reconstitute with PLP and assay transamination of dTDP-4-dehydro-6-deoxy-D-glucose with L-glutamate (and other amino donors), detecting dTDP-4-amino-4,6-dideoxy-D-glucose by LC-MS, with a K200A mutant as a loss-of-function control; test cross-complementation of an S. venezuelae desI mutant.
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