EIF2D (Ligatin, eIF2D) — research notes

UniProt P41214. Single-polypeptide non-canonical translation factor. Contains SUI1 + PUA + SWIB domains; it is the full-length protein of which MCTS1 (N-half) + DENR (C-half) are the split equivalent.

Core function

• PMID:20566627
• UniProt FUNCTION: "Translation initiation factor that is able to deliver tRNA to the P-site of the eukaryotic ribosome in a GTP-independent manner ... can promote release of deacylated tRNA and mRNA from recycled 40S subunits following ABCE1-mediated dissociation of post-termination ribosomal complexes."
• PMID:20713520 Ligatin (= eIF2D) individually promotes eIF2-independent Met-tRNA recruitment and 40S recycling (release of deacylated tRNA/mRNA after ABCE1 splitting).

So core MF: translation initiation factor activity (GTP-independent P-site tRNA delivery); BP: ribosome recycling (40S recovery / ribosome disassembly), reinitiation, IRES init.

Historical "Ligatin = trafficking receptor" conflation

• PMID:2482295 — this 1989 paper named "ligatin" as a phosphoglycoprotein trafficking receptor. The annotations GO:0038023 signaling receptor activity, GO:0006886 intracellular protein transport, and GO:0005737 cytoplasm (TAS PMID:2482295) derive from this. The modern molecular identity of EIF2D/Ligatin as a translation factor (Dmitriev 2010, Skabkin 2010) makes the receptor/transport functions over-annotations / mis-assignments — REMOVE or MARK_AS_OVER_ANNOTATED.

Decisions

• translation initiation factor activity (IBA, IEA, IDA 20566627) — ACCEPT (core).
• formation of translation preinitiation complex (IBA, IEA, IDA 20713520) — ACCEPT.
• ribosome disassembly (IDA 20713520) — ACCEPT (recycling).
• IRES-dependent viral translational initiation (IDA 20713520) — KEEP_AS_NON_CORE.
• RNA binding (IEA) — KEEP_AS_NON_CORE.
• translational initiation (IEA) / protein-containing complex organization (IEA) — KEEP_AS_NON_CORE.
• cytosol/cytoplasm (IDA) — ACCEPT.
• signaling receptor activity (TAS 2482295) — REMOVE (wrong "ligatin" identity).
• intracellular protein transport (TAS 2482295) — REMOVE.
• cytoplasm TAS 2482295 — KEEP_AS_NON_CORE (localization happens to be right but provenance is the receptor paper).