CBR1 review notes

2026-10-10

Setup and literature search

• Seeded genes/yeast/CBR1/CBR1-ai-review.yaml with just fetch-gene yeast CBR1
  and then cached all GOA PMIDs with just fetch-gene-pmids yeast CBR1.
• Tried to run automated deep research with
  just deep-research-falcon yeast CBR1 --fallback perplexity-lite; the local
  agentapi executable and provider API keys were unavailable, so this review
  is based on manual PubMed/web search, cached publications, UniProt, and the
  local PAINT cache.
• Manual web/PubMed search for newer Saccharomyces Cbr1/Dph3/diphthamide
  papers found the expected Cbr1/Dph3 discovery paper from 2016, follow-up
  Dph1-Dph2 mechanism papers from 2019 and 2021, and no newer primary paper
  that changes the core assignment.

Core activity synthesis

• Cbr1 is the CBR1-like, membrane-anchored NADH-cytochrome b5 reductase in
  PANTHER family PTHR19370, subfamily PTHR19370:SF184. The old
  microsomal purification paper directly characterized NADH-specific
  ferricytochrome-b5 reduction in yeast: "The presence of NADH-cytochrome b5
  reductase [EC 1.6.2.2] in microsomes from anaerobically grown yeast was
  confirmed by its isolation and purification" and "The reductase required NADH
  as a specific electron donor, and could reduce some redox dyes as well as
  cytochrom b5." PMID:14930
• Lin et al. identified Cbr1 as the major yeast Dph3 reductase by a Dph3 SILAC
  interactome, in vitro Dph3 reduction, reconstitution of Dph1-Dph2 activity
  with Cbr1/Dph3/NADH, and reductase deletion phenotypes. Useful exact snippets:
  "Here, using a proteomic approach, we identified Saccharomyces cerevisiae
  cytochrome b5 reductase (Cbr1) as a NADH-dependent reductase for Dph3";
  "Upon addition of NADH to initiate the reaction, Dph3 was rapidly reduced by
  Cbr1"; "formation of tRNA modifications was partially impaired"; and "In
  summary, we identified Cbr1 as the major physiological reductase of Dph3".
  PMID:27694803
• Dong et al. 2014 established the Dph1-Dph2/Dph3 radical-SAM system but did
  not identify Cbr1; the Cbr1 assignment comes from the later Lin et al.
  reductase paper. The paper's own summary is that "yeast Dph3 (also known as
  KTI11), a CSL-type zinc finger protein, can bind iron and in the reduced state
  can serve as an electron donor to reduce the Fe-S cluster in Dph1-Dph2".
  PMID:24422557
• Zhang et al. 2019 refined the Dph1-Dph2 heterodimer mechanism using Cbr1,
  Dph3, and NADH as the natural reducing system. The key distinction for GO is
  that Dph1-Dph2 performs ACP transfer, while Cbr1 reduces Dph3 upstream:
  "Dph1-Dph2 heterodimer is a non-canonical radical SAM enzyme that transfers
  the ACP group from SAM to EF2" and "the Dph1 Fe-S cluster serves a catalytic
  role while the Dph2 Fe-S cluster facilitates the reduction of Dph1 cluster by
  the Dph3/Cbr1/NADH system." PMID:31463593
• Zhang et al. 2021 showed that Dph3 can donate the fourth iron to oxygen-
  damaged Dph1-Dph2, with the Cbr1/Dph3/NADH system both supplying electrons
  and enabling Fe-S cluster repair during aerobic diphthamide biosynthesis. The
  abstract states that "the small iron-containing protein Dph3 donates one Fe
  atom to convert the [3Fe-4S] cluster in Dph1-Dph2 to a functional [4Fe-4S]
  cluster during the radical-SAM enzyme catalytic cycle." PMID:34154323

PAINT and IBA notes

• PANTHER:PTN001064671 is the Saccharomycetales CBR1-like node. It carries
  GO:0004128 from SGD:S000001305 and GO:0005886 from
  CGD:CAL0000182794. Yeast CBR1 is inside this node, and the SGD CBR1 self
  seed for cytochrome-b5 reductase activity is expected because PAINT used the
  experimental yeast annotation to place the ancestral IBD.
• PANTHER:PTN001064672 records a fungal-branch negative for the broad
  eukaryotic mitochondrial IBD and a positive plasma-membrane IBD seeded by SGD
  MCR1. Treat that as a PAINT-localization split, not as evidence that
  Cbr1 has lost mitochondrial-outer-membrane localization in yeast: yeast Cbr1
  has direct mitochondrial outer-membrane proteomics evidence and literature
  describes Cbr1 on the ER and mitochondrial outer membrane with a cytosolic
  catalytic domain [PMID:16407407; PMID:27694803].
• PANTHER:PTN001833551 puts the very broad GO:0016491 oxidoreductase activity at the family root. For Cbr1 this is true but far less informative
  than the exact NADH:ferricytochrome-b5 and NADH:Dph3 reductase activities.

Annotation calls to watch

• The GO:0090560 rows should not be accepted literally as Cbr1 itself enabling
  2-(3-amino-3-carboxypropyl)histidine synthase activity. That reaction is
  catalyzed by Dph1-Dph2; Cbr1 reduces Dph3 upstream and should be captured as
  NADH-dependent Dph3 reductase activity, plus a contributes_to relationship
  to the Dph1-Dph2 complex function if the model treats Cbr1 as a component of
  the reducing system.
• GO:0003954 NADH dehydrogenase activity and GO:0016491 oxidoreductase activity are broad ancestors. Prefer the Rhea-backed
  GO:0090524 cytochrome-b5 reductase activity, acting on NADH and a proposed
  NADH-dependent Dph3 reductase term for the two known electron acceptors.
• Mitochondrion and mitochondrial outer-membrane rows are high-throughput or
  subcellular-location mappings but match the expected Cbr1 membrane topology.
  The nucleus row comes from an N-terminal GFP SWAp-Tag library whose tag sits
  directly upstream of Cbr1's only transmembrane helix at residues 7-27, so it
  is best treated as over-annotated.