nrdG (P0A9N8) 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, all abstract-only for the NrdG
biochemistry papers), the UniProt record, PubMed and QuickGO.

Identity and family

• Anaerobic ribonucleoside-triphosphate reductase-activating protein (NrdG, 154 aa), the small
  ("beta", "activase", formerly "dA1") component of the class III anaerobic ribonucleotide
  reductase system. EC 1.97.1.-. Organic radical-activating enzyme family of the radical SAM
  superfamily (IPR034457, IPR012837 NrdG, TIGR02491, PTHR30352:SF2, SFLDF00299).
  [file:ECOLI/nrdG/nrdG-uniprot.txt "Activation of anaerobic ribonucleoside-triphosphate reductase under anaerobic conditions by generation of an organic free radical, using S-adenosylmethionine and reduced flavodoxin as cosubstrates to produce 5'-deoxy-adenosine."]
• Paralogs in E. coli K-12: PflA (PFL-AE, activates PflB), PflC/YbiY/YjjW (activases of
  the other glycyl radical enzymes). These are reviewed separately.

Activity (the activase reaction)

• Discovery: the ORF downstream of nrdD encodes a protein needed for, and tightly bound to,
  the glycyl radical of the anaerobic reductase.
  PMID:7852304
• Early fractionation: NrdD (dA3) is the reductase, NrdG (dA1) auxiliary.
  PMID:1460049
• NrdG binds SAM (Kd 10 uM, 1:1) and its Fe-S centre reductively cleaves it, giving methionine
  and the NrdD glycyl radical.
  PMID:9305874
  PMID:9305874
• NrdG is catalytic: one NrdG can activate several NrdD.
  PMID:10531327
• Electron donor is reduced flavodoxin.
  PMID:10821845
• Radical site on NrdD is Gly681. PMID:8621608

Cofactor

• One [4Fe-4S] per polypeptide, with 2+ and 1+ states; O2-labile, decays to [2Fe-2S].
  PMID:10531327
• Three cysteines of the CXXXCXXC motif ligate the cluster; the fourth site is SAM.
  PMID:10821845
• The Fe-S signal first attributed to the reductase (PMID:8381402) came from co-purifying NrdG.
  PMID:8621608

Complex

• NrdD and NrdG form a tight 1:1 complex (alpha2beta2).
  PMID:8621608
• Tamarit 1999 argues NrdG is a catalytic activase rather than an obligate subunit (above).
  ComplexPortal CPX-3821 names the assembly the "nrdDG class III anaerobic ribonucleotide
  reductase activation complex".

Physiology

• nrdG knockouts cannot grow under strict anaerobiosis.
  PMID:8954104
  This is necessity evidence: NrdD performs the ribonucleotide reduction; NrdG installs the
  glycyl radical cofactor on NrdD and does no step of the NTP to dNTP conversion itself.

GO term landscape (QuickGO, checked 2026-10-19)

• GO:0043364 glycyl-radical enzyme activating activity has only two children: GO:0043365
  [formate-C-acetyltransferase]-activating enzyme activity (PflA, EC 1.97.1.4) and GO:0140111
  [choline trimethylamine-lyase]-activating enzyme activity. No NrdG-specific term exists.
• GO has no "glycyl radical formation" process term. The modification is captured by
  GO:0018201 peptidyl-glycine modification and GO:0051604 protein maturation, both of which
  PAINT places on the PflA node (PTN002018048) and which PflA carries by IDA.
• GO:0004748 (ribonucleoside-diphosphate reductase, thioredoxin) is the class I/II RNR
  activity; the class III enzyme is a ribonucleoside-triphosphate reductase.
  PMID:1460049
• IPR012837 (NrdG) InterPro2GO maps to GO:0043365 (PFL activase): wrong substrate for NrdG.

Decisions

• MF core: GO:0043364 (ACCEPT; most specific available) + GO:0051539 + NEW GO:1904047.
• BP: NEW GO:0018201 and GO:0051604 (the activase catalyses the modification; matches PflA).
• Downstream deoxyribonucleotide processes: upstream necessity, not participation;
  MARK_AS_OVER_ANNOTATED. Same pattern to apply to PflA (no fermentation terms) and paralogs.