YjjW is a radical S-adenosyl-L-methionine (SAM) enzyme of the glycyl-radical-enzyme activase family, the founding member of its own subfamily (NCBIfam TIGR04041, "YjjW family glycine radical enzyme activase"). It has a radical SAM domain with the CX3CX2C [4Fe-4S] cluster-binding motif and two additional ferredoxin-type domains that may carry further iron-sulfur clusters. yjjW is encoded immediately downstream of, and overlapping, yjjI on the same strand, the standard arrangement of a glycyl radical enzyme and its dedicated activase. YjjI is a glycyl-radical-enzyme-family protein of unknown function, carrying a glycine-loop motif but no assigned reaction. By analogy with the characterised activases PflA and NrdG, YjjW is expected to install the glycyl radical on YjjI by reductive cleavage of SAM to a 5'-deoxyadenosyl radical that abstracts a hydrogen atom from the YjjI glycine. No activity of YjjW has been demonstrated, and the reaction catalysed by its partner YjjI is not known; despite the family's historical name, there is no evidence that YjjW activates pyruvate formate-lyase.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003824 catalytic activity | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO mapping from the radical SAM domain (IPR007197). True but uninformative. The gene already carries the specific activity it implies, glycyl-radical enzyme activating activity (GO:0043364). Reason: Project rule for generic radical SAM rows: MODIFY GO:0003824 to the specific reaction MF the gene carries. YjjW carries GO:0043364 (IBA and ISS). It keeps the radical SAM ligands and is translationally coupled to the GRE gene yjjI (file:ECOLI/pflC/pflC-bioinformatics/RESULTS.md). Proposed replacements: glycyl-radical enzyme activating activity Supporting Evidence: file:ECOLI/yjjW/yjjW-uniprot.txt Belongs to the organic radical-activating enzymes family. file:ECOLI/pflC/pflC-bioinformatics/RESULTS.md yjjW overlaps the 3' end of yjjI by 29 bp |
| GO:0005515 protein binding | IPI PMID:24561554 The binary protein-protein interaction landscape of Escheric... | REMOVE | Summary: Binary interaction with GalE (UDP-glucose 4-epimerase, P09147), from the proteome-scale E. coli Y2H interactome. Reason: Generic protein binding from a high-throughput Y2H screen carries no functional information, and GalE has no link to radical chemistry or to YjjW's predicted activase role. Per the curation guidelines, avoid protein binding where no informative MF can be drawn. Removing it does not assert the interaction is false. Supporting Evidence: file:ECOLI/yjjW/yjjW-uniprot.txt P39409; P09147: galE; NbExp=2 |
| GO:0005515 protein binding | IPI PMID:24561554 The binary protein-protein interaction landscape of Escheric... | REMOVE | Summary: Binary interaction with DpiA (response regulator, P0AEF4), from the proteome-scale E. coli Y2H interactome. Reason: Generic protein binding from a high-throughput Y2H screen, with no functional information and no link to YjjW's predicted activase role. Per the curation guidelines, avoid uninformative protein binding. Removal does not assert the interaction is false. Supporting Evidence: file:ECOLI/yjjW/yjjW-uniprot.txt P39409; P0AEF4: dpiA; NbExp=2 |
| GO:0005515 protein binding | IPI PMID:24561554 The binary protein-protein interaction landscape of Escheric... | REMOVE | Summary: Binary interaction with MinC (cell-division inhibitor, P18196), from the proteome-scale E. coli Y2H interactome. Reason: Generic protein binding from a high-throughput Y2H screen, with no functional information and no link to YjjW's predicted activase role. Per the curation guidelines, avoid uninformative protein binding. Removal does not assert the interaction is false. Supporting Evidence: file:ECOLI/yjjW/yjjW-uniprot.txt P39409; P18196: minC; NbExp=2 |
| GO:0016491 oxidoreductase activity | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO mapping from the radical-activating-enzyme signatures. GO:0043364 is a direct is_a child of oxidoreductase activity (QuickGO), so this is the general parent of the activity the gene already carries. Reason: Correct but general. Per the curation guidelines, MODIFY a correct but general term to the specific descendant the gene carries: GO:0043364. Proposed replacements: glycyl-radical enzyme activating activity Supporting Evidence: file:ECOLI/yjjW/yjjW-uniprot.txt Belongs to the organic radical-activating enzymes family. |
| GO:0043364 glycyl-radical enzyme activating activity | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT IBA from PTN001251485 in PTHR30352, grounded in E. coli PflA (P0A9N4) and NrdG (P0A9N8), both with established activase activity. The node asserts only the general activity (generation of a glycyl radical on a partner GRE), not a particular substrate GRE. Reason: The node placement is sound. Every characterised member of the family is a GRE activase, and YjjW is inside the clade: it keeps the radical SAM cysteine triad and SAM-binding residues. Genome context fits strongly: yjjW overlaps the 3' end of the GRE gene yjjI on the same strand (file:ECOLI/pflC/pflC-bioinformatics/RESULTS.md), and the dedicated NCBIfam family TIGR04041 describes exactly this YjjW-YjjI pair. The term names no substrate, so it is the right level even though YjjI's reaction is unknown. YjjW's activase activity has not been directly shown, but the inference is as strong as sequence and context allow. Supporting Evidence: file:ECOLI/pflC/pflC-bioinformatics/RESULTS.md yjjW overlaps the 3' end of yjjI by 29 bp file:ECOLI/yjjW/yjjW-uniprot.txt /evidence="ECO:0000250|UniProtKB:P0A9N4" PMID:42361324 radical is post-translationally installed by GRE activating enzymes (GRE-AEs), all of which are members of the radical S-adenosyl-L-methionine (RS) superfamily of enzymes. |
| GO:0043364 glycyl-radical enzyme activating activity | IEA GO_REF:0000116 | ACCEPT | Summary: Rhea-to-GO mapping from the UniProt catalytic-activity line, RHEA:61976, the generic glycyl-[protein] activation reaction. Unlike PflC and YbiY, this entry uses the generic reaction and EC 1.97.1.-, not the PFL-specific EC 1.97.1.4. Reason: The GO term asserted is the general activase activity, which is the correct level for an activase whose substrate GRE (YjjI) has no assigned reaction. The generic RHEA:61976 mapping is appropriate; there is no PFL-specific over-annotation to correct here. Supporting Evidence: file:ECOLI/yjjW/yjjW-uniprot.txt Xref=Rhea:RHEA:61976 |
| GO:0043364 glycyl-radical enzyme activating activity | ISS GO_REF:0000024 | ACCEPT | Summary: Manual ISS transfer from E. coli PflA (P0A9N4), which has experimentally established glycyl-radical activase activity. A curator judged YjjW similar enough to PflA to carry the general activase activity. Reason: Consistent with the IBA and the generic Rhea row, and with genome context. The transfer is of the general activase activity, not a specific substrate, which is the right level given that YjjI's reaction is unknown. This reinforces the IBA rather than duplicating it, and is kept. Supporting Evidence: file:ECOLI/yjjW/yjjW-uniprot.txt /evidence="ECO:0000250|UniProtKB:P0A9N4" file:ECOLI/pflC/pflC-bioinformatics/RESULTS.md Members of this family may be misannotated as pyruvate formate lyase activating enzyme. |
| GO:0051536 iron-sulfur cluster binding | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO mapping from the radical SAM domain. YjjW keeps the CX3CX2C triad (C31, C35, C38) that binds the radical SAM [4Fe-4S] cluster, and is modelled to bind up to three [4Fe-4S] clusters in total. Reason: Project rule for generic radical SAM rows: MODIFY GO:0051536 to its descendant GO:0051539, which the gene already carries. The clusters bound are [4Fe-4S] clusters. Proposed replacements: 4 iron, 4 sulfur cluster binding Supporting Evidence: file:ECOLI/yjjW/yjjW-uniprot.txt May bind up to 3 [4Fe-4S] clusters. One cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine. |
| GO:0051539 4 iron, 4 sulfur cluster binding | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: InterPro2GO mapping from the radical-activating-enzyme signature. YjjW keeps the radical SAM cysteine triad and has two ferredoxin-type domains that may hold additional [4Fe-4S] clusters. Reason: Project rule: GO:0051539 is ACCEPT for radical SAM enzymes with established catalysis and KEEP_AS_NON_CORE where catalysis is not established. No activity or cluster content has been measured for YjjW, and its substrate GRE's reaction is unknown. Cluster binding is well supported by the conserved ligands, but is kept as non-core. Supporting Evidence: file:ECOLI/yjjW/yjjW-uniprot.txt /ligand_note="4Fe-4S-S-AdoMet" PMID:42361324 with eight additional conserved cysteine residues that could ligate up to two additional [4Fe-4S] clusters for a total of three [4Fe-4S] clusters. |
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Download this section (compressed HTML)Q: What reaction does YjjI catalyse, and is YjjW its dedicated and sole activase?
Q: Are yjjW and yjjI co-transcribed and co-regulated, and under what growth conditions is the pair expressed?
Experiment: Reconstitute YjjW and YjjI anaerobically and test SAM-dependent glycyl-radical installation on YjjI by EPR, with reduced flavodoxin and a reductant.
Hypothesis: YjjW installs a glycyl radical on YjjI.
Type: in vitro enzymology
Experiment: Screen activated YjjI against candidate substrate classes by LC-MS and NMR, informed by homology modelling of its active site, to identify the reaction whose activase is YjjW.
Hypothesis: YjjI catalyses a specific, identifiable radical reaction.
Type: substrate screening
What is not known — curated, literature-grounded statements of the open unknowns (the inverse of core functions).
Gap: The reaction catalysed by the YjjW-activated glycyl radical enzyme YjjI is unknown, so the physiological process that YjjW's activase activity serves cannot be named.
OPEN BIOLOGY BP_DARK
What is known: YjjW is a radical SAM protein of the dedicated YjjW activase family (TIGR04041), coupled to yjjI. YjjI is a glycyl-radical-enzyme-family protein with an internal Gly-loop motif and no assigned substrate or reaction. Neither protein has been purified or assayed, and no deletion phenotype has been reported.
Significance: Identifying the YjjI reaction would reveal a new anaerobic glycyl-radical metabolic capability of E. coli and its relatives, and would let YjjW's activase role be placed in a pathway.
What would resolve it: Purify YjjI and YjjW anaerobically, reconstitute clusters, and use YjjW to install the YjjI glycyl radical (EPR). Screen candidate substrates (e.g. amino acids, sugars, sugar phosphates) for YjjI turnover by LC-MS, guided by its active-site residues, and test yjjIW deletion phenotypes under anaerobic conditions.
Provenance (the field's own admissions):
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