YdeM is a 385-residue radical S-adenosyl-L-methionine (SAM) protein of the anaerobic sulfatase-maturating enzyme (anSME) family and a paralog of AslB. It consists of a radical SAM core, carrying the CxxxCxxC motif that binds the SAM-cleaving [4Fe-4S] cluster, and a C-terminal SPASM domain predicted to hold two auxiliary [4Fe-4S] clusters. Every cluster-ligand cysteine, SAM-contact residue and the catalytic aspartate of the structurally characterised Clostridium perfringens anSME are conserved, so the protein is expected to be catalytically competent. Characterised anSMEs convert the active-site cysteine or serine of sulfatases to C-alpha-formylglycine. The gene lies next to ydeN, which encodes an uncharacterised sulfatase-family protein predicted to carry a serine at the formylglycine position. Deleting ydeM, together with aslB and yidF, does not prevent E. coli K-12 from maturing heterologous cysteine-type sulfatases, so YdeM is not needed for that reaction; whether it matures YdeN or any other serine-type substrate, or acts on something else, is unknown. No activity of the purified protein has been reported.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003824 catalytic activity | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: Root-level catalytic activity from the radical SAM InterPro signature. YdeM keeps all 17 cluster, SAM and catalytic-base features of the C. perfringens anSME (file:ECOLI/aslB/aslB-bioinformatics/RESULTS.md), but no reaction has been shown for it. Reason: Per the RADICAL_SAM project's treatment rule for generic rows: with no reaction known, GO:0003824 is already as precise as the evidence allows. It is not false, but no specific descendant is supported, and the family's Cys-type sulfatase maturation activity was not observed for YdeM in vivo (PMID:17303125). Supporting Evidence: file:ECOLI/aslB/aslB-bioinformatics/RESULTS.md Neither E. coli paralog shows any sign of degeneration of the catalytic machinery file:ECOLI/ydeM/ydeM-uniprot.txt Belongs to the radical SAM superfamily. Anaerobic sulfatase-maturating enzyme family. |
| GO:0006974 DNA damage response | IEP PMID:11967071 Over 1000 genes are involved in the DNA damage response of E... | MARK AS OVER ANNOTATED | Summary: Inferred from expression pattern: ydeM is one of the roughly 30% of E. coli genes whose transcript level changed after mitomycin C treatment in a genome-wide array study (PMID:11967071). No study links YdeM protein activity to DNA repair, damage tolerance or the SOS response. Reason: A change in transcript level within a response that touches nearly a third of the genome shows only that ydeM expression is affected by DNA damage, not that YdeM does any of the work of responding to it. The row is retained as data about expression but marked as over-annotation of the gene's function, consistent with how other E. coli reviews in this repository treat rows from this study. Supporting Evidence: PMID:11967071 a large number of genes (nearly 30% of all genes) displayed significant changes in their expression level |
| GO:0016491 oxidoreductase activity | IEA GO_REF:0000002 | UNDECIDED | Summary: Oxidoreductase activity mapped from the sulfatase-maturase radical SAM signature. Characterised anSMEs oxidise a sulfatase cysteine or serine to formylglycine (PMID:16766528, PMID:14749327), and YdeM keeps their catalytic machinery, but no oxidation by YdeM, and no substrate, has been shown. Reason: A family-level prediction of reaction class. The family function was not observed for YdeM in K-12 deletion mutants with Cys-type substrates (PMID:17303125), and no assay of YdeM itself exists, so the reaction class can be neither confirmed nor excluded. Supporting Evidence: PMID:14749327 AtsB oxidizes serine to FGly by a radical mechanism that is initiated through reductive cleavage of SAM PMID:17303125 these putative anSME are not involved in Cys-type sulfatase maturation |
| GO:0051536 iron-sulfur cluster binding | IEA GO_REF:0000002 | MODIFY | Summary: Generic iron-sulfur cluster binding from the radical SAM signature. The clusters predicted for YdeM are [4Fe-4S] clusters, one in the radical SAM core and two in the SPASM domain, with all cysteine ligands conserved. Reason: Correct but general. Per the RADICAL_SAM project's treatment rule, replace with the descendant GO:0051539 4 iron, 4 sulfur cluster binding, which the gene already carries. Proposed replacements: 4 iron, 4 sulfur cluster binding Supporting Evidence: file:ECOLI/ydeM/ydeM-uniprot.txt Binds 3 [4Fe-4S] clusters (By similarity). |
| GO:0051539 4 iron, 4 sulfur cluster binding | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: [4Fe-4S] cluster binding from the anSME-type SPASM signature, supported by the intact radical SAM motif (CNLKCDYC, residues 12 to 19) and the eight conserved SPASM cysteines (file:ECOLI/aslB/aslB-bioinformatics/RESULTS.md). Not measured on YdeM itself. Reason: True and as precise as the evidence allows, but per the RADICAL_SAM project's treatment rule it is core only where catalysis is established, which it is not for YdeM. Supporting Evidence: file:ECOLI/aslB/aslB-bioinformatics/RESULTS.md YdeM keeps all 17 reference features: 11 cluster cysteines file:ECOLI/ydeM/ydeM-uniprot.txt Binds 3 [4Fe-4S] clusters (By similarity). |
| GO:0051604 protein maturation | ISS PMID:16766528 A new type of bacterial sulfatase reveals a novel maturation... | UNDECIDED | Summary: Sequence-similarity transfer of protein maturation from the C. perfringens Cys-type anSME that founded the family (PMID:16766528). In E. coli K-12, deleting ydeM, aslB and yidF did not impair maturation of heterologous Cys-type sulfatases (PMID:17303125), and UniProt records that YdeM is not involved in Cys-type sulfatase maturation in vivo. Ser-type maturation was not tested, and ydeM sits next to ydeN, whose product is a predicted Ser-type sulfatase (UniProt P77318), so a maturation role for that kind of substrate remains possible. Reason: The cited paper does not assay YdeM. The in vivo test in K-12 refutes the specific transferred activity (Cys-type sulfatase maturation) but not maturation of a Ser-type sulfatase such as the neighbouring YdeN, and the catalytic machinery is fully intact. The term is therefore neither supported nor excluded; the same judgement is made for the paralog aslB. Supporting Evidence: PMID:17303125 knocking-out of aslB, ydeM and yidF does not impair Cys-type sulfatase maturation file:ECOLI/ydeM/ydeM-uniprot.txt it is not involved in Cys-type sulfatase maturation in vivo file:ECOLI/aslB/aslB-bioinformatics/RESULTS.md YdeM is likewise encoded next to a predicted Ser-type sulfatase, YdeN |
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Download this section (compressed HTML)Q: Is YdeN, the predicted Ser-type sulfatase encoded next to ydeM, a substrate of YdeM, and are AslB and YdeM each dedicated to their neighbouring sulfatase or redundant?
Suggested experts: Olivier Berteau, Thomas Dierks
Q: Under which conditions is ydeM expressed, and is it co-regulated with ydeN?
Suggested experts: Olivier Berteau
Experiment: Express YdeN (wild type and S132A) in wild-type, ydeM-deleted and aslB ydeM double-deleted E. coli K-12 under anaerobic conditions; detect formylglycine at position 132 by mass spectrometry and measure sulfatase activity on aryl sulfate substrates. In vitro, assay reconstituted YdeM with a YdeN motif peptide for SAM-dependent formylglycine and 5'-deoxyadenosine formation.
Hypothesis: YdeM is a serine-type anaerobic sulfatase-maturating enzyme for YdeN.
Type: genetic and in vitro enzymology
What is not known — curated, literature-grounded statements of the open unknowns (the inverse of core functions).
Gap: The substrate and reaction of YdeM are unknown: it is not established whether it converts the active-site serine of the neighbouring YdeN, or of any other protein, to formylglycine, or acts on a different substrate.
OPEN BIOLOGY MF_DARK
What is known: Established: YdeM keeps every cluster-ligand cysteine, SAM-contact residue and the catalytic aspartate of the C. perfringens anSME. Deleting ydeM, aslB and yidF does not block maturation of heterologous Cys-type sulfatases in E. coli K-12. Ser-type maturation and the activity of purified YdeM have not been tested.
Significance: Together with AslB, YdeM is one of two intact anSME-family enzymes in a bacterium with no detectable sulfatase activity; identifying their substrates would show whether these are latent sulfatase maturases or enzymes repurposed for another modification.
What would resolve it: Assay anaerobically reconstituted YdeM for SAM-dependent formylglycine formation on YdeN peptides spanning Ser132, and test formylglycine in YdeN expressed in wild-type and ydeM-deleted cells under anaerobic, sulfate-limited growth.
Provenance (the field's own admissions):
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