pflA (P0A9N4) notes

Part of the RADICAL_SAM project (projects/RADICAL_SAM.md), Phase 2 E. coli K-12.

Literature sources

No deep-research file is available for this gene: the falcon provider fails authentication
(403) and asta returned nothing useful in Phase 1, so deep research was not run. These notes are
built from cached publications (publications/PMID_*.md), the UniProt record, PubMed and
QuickGO. The Knappe-lab papers are abstract-only in the cache; PMID:19711960, PMID:24016774 and
PMID:28768413 (Broderick lab) have full text.

Identity and family

• Pyruvate formate-lyase 1-activating enzyme (PFL-AE, PFL activase, PflA; 246 aa, Met1
  removed), EC 1.97.1.4. Founding member of the organic radical-activating enzyme family of
  the radical SAM superfamily; paralogs NrdG, PflC, YbiY, YjjW.
  [file:ECOLI/pflA/pflA-uniprot.txt "Activation of pyruvate formate-lyase 1 under anaerobic conditions by generation of an organic free radical, using S-adenosylmethionine and reduced flavodoxin as cosubstrates to produce 5'-deoxy-adenosine."]

Activity

• Active PFL (Ea) is formed from inactive PFL (Ei) post-translationally by a distinct
  activating enzyme, coupled to SAM cleavage to methionine and 5'-deoxyadenosine.
  PMID:6364987
• Radical is on PflB Gly734. PMID:1310545
• Mechanism: 5'-dAdo radical abstracts the pro-S H of Gly734; dihydroflavodoxin is the
  physiological reductant; heptapeptide RVSGYAV (PflB 731-737) is a substrate.
  PMID:8175649
• Flavodoxin (FldA) binds PFL-AE only in its FMN-bound holo form.
  PMID:24016774
• Structure (Vey 2008): substrate-free and peptide-bound PFL-AE, first activase structures.
  PMID:18852451

Cofactors

• [4Fe-4S] cluster; Cys29/33/36 (mature numbering; Cys30/34/37 in UniProt) essential;
  cluster required for SAM binding.
  PMID:9478932
  PMID:9478932
• Cluster interconverts in vivo with O2 status; only [4Fe-4S]+ is active.
  PMID:19711960
• Catalytically essential monovalent cation site, liganded by a SAM carboxylate oxygen;
  activity maximal with K+.
  PMID:28768413

Location

• Cytosol by fractionation proteomics (PMID:15911532; abstract-only).

Processes

• GO has no glycyl radical formation term; PAINT places GO:0018201 peptidyl-glycine
  modification and GO:0051604 protein maturation on the PflA node, and PflA has both by IDA.
  PflA performs the modification, so these pass the participation test.
• GOA carries no pyruvate fermentation / mixed-acid fermentation term for PflA, consistent with
  the activase being upstream of PflB's catalysis. No NEW downstream process is proposed.
• DNA damage response (IEP, PMID:11967071): genome-wide mitomycin C microarray; the abstract
  does not mention pflA. Expression change, not participation.

Decisions

• Core MF: GO:0043365 (ACCEPT), GO:0051539 (ACCEPT), NEW GO:1904047 (IDA PMID:9478932).
• Core BP: GO:0018201 + GO:0051604 (ACCEPT).
• Generic rows per RADICAL_SAM rule (GO:0003824, GO:0016491, GO:0043364 → MODIFY to
  GO:0043365; GO:0051536 → GO:0051539).