ARAF (human, UniProt P10398) - curation notes

Identity

UniProt P10398 (ARAF_HUMAN), 606 aa, "Serine/threonine-protein kinase A-Raf", EC 2.7.11.1;
synonyms ARAF1, PKS, PKS2 [file:human/ARAF/ARAF-uniprot.txt].
PANTHER PTHR44329 (official name "SERINE/THREONINE-PROTEIN KINASE TNNI3K-RELATED"), subfamily
PTHR44329:SF55 "SERINE_THREONINE-PROTEIN KINASE A-RAF" [file:human/ARAF/ARAF-uniprot.txt].
Isoform 2 (DA-Raf1) lacks the kinase domain and acts as a dominant-negative RAS antagonist
[file:human/ARAF/ARAF-uniprot.txt "Has a wider tissue distribution than isoform 1, and acts as
a dominant-negative antagonist"].
No GO-CAM model in gocams/index.tsv contains P10398.

RAF-family MAP3K: RAS-GTP recruits ARAF to the membrane; ARAF homo/heterodimerises with BRAF/CRAF and
phosphorylates MEK1/MEK2 [file:human/ARAF/ARAF-deep-research-falcon.md "ARAF can form homodimers and
heterodimers with BRAF or CRAF."; "Wild-type ARAF immunoprecipitates generated phosphorylated MEK1"].
Weakest RAF paralog under most conditions (BRAF > CRAF > ARAF), but not a pseudokinase
[file:human/ARAF/ARAF-deep-research-falcon.md].
Direct MEK2 binding via the ARAF kinase domain [PMID:11909642 "A-Raf was identified as a novel partner
that interacts with MEK2"; "regions critical for this interaction were located between residues 255 and
606 that represent the kinase domain of A-Raf"].
Other reported direct substrates are secondary: BAD (RAF kinases generally) PMID:19667065, PFKFB2 in vitro PMID:36402789.

Inactive RAFs bound by 14-3-3 at S214/S582 in ARAF [Reactome:R-HSA-5672951 "S214 and S582 in ARAF"].
S214 dephosphorylated by PP2A/PP1 and by the SHOC2-MRAS-PP1C complex [Reactome:R-HSA-5672961;
PMID:35768504 "NTpS from ARAF, BRAF and CRAF ... were dephosphorylated with a significantly higher
catalytic efficiency by the complex"].
RAS binding: the N-terminal regulatory region (RBD + CRD) binds HRAS / RRAS2 in Y2H
PMID:12620389; RAS-GTP effector PMID:24441586.
HSP90/CDC37 client kinase PMID:22939624.

Cytosol (inactive, 14-3-3-bound) and plasma membrane (active, RAS-bound); mitochondria (MST2
sequestration; TOM/TIM partners in Y2H) [file:human/ARAF/ARAF-deep-research-falcon.md "ARAF also has
important non-catalytic functions, particularly sequestration of the pro-apoptotic kinase MST2 at
mitochondria."].

MAPK (ERK1/2) cascade: core.
Galpha12-ARAF-MEK-ERK axis upregulates RFFL, which ubiquitinates PRR5L, promoting mTORC2-dependent
PKCdelta HM phosphorylation PMID:22609986.
This is an indirect downstream output of ARAF MAP3K activity -> non-core.
Anti-apoptotic (BAD phosphorylation, MST2 sequestration) -> non-core.

Kinase MF rows (IEA/TAS/IDA/IBA) accepted; GO:0004709 is the core MF.
59 GO:0005515 protein binding rows split by partner class (per BRAF conventions):
MEK2 -> GO:0031434; 14-3-3 (SFN, YWHAE, YWHAZ) -> GO:0071889; BRAF -> GO:0046982;
HRAS/RRAS2 -> GO:0031267; HSP90AB1 -> GO:0051879. Partners without informative function
(Y2H preys such as TIMM44, TIMM50, PRPF6, NUDT14, ASS1, CPS1, RABGGTB, EFEMP1, NELFCD, PBK, COPS3;
innate immune AP-MS TIRAP/IRAK2/IRF7; SMAD4; HERC2) -> REMOVE (uninformative; interaction not
asserted false).
GO:0033138 positive regulation of peptidyl-serine phosphorylation (BAD) -> MODIFY to GO:0018105
(ARAF performs, not regulates, the phosphorylation), consistent with BRAF review.
GO:0036211 protein modification process (TAS) -> MODIFY to GO:0006468 protein phosphorylation.
PMID:19593445 (known batch miscitation) is not present in the ARAF GOA set.

Rows: GO:0005739 IBA (PTN000584576) and IEA (GO_REF:0000107, Ensembl projection from mouse Araf P04627). Both stay KEEP_AS_NON_CORE; reasons now record the check.
IBA: interpro/panther/PTHR44329/PTHR44329-paint.tsv seeds PTN000584576 → GO:0005739 with MGI:88065 and MGI:88190 (taxon 33511, 2017). In QuickGO, mouse Araf has a mitochondrion IDA (MGI, PMID:12931191, the liver mitochondrial BAD/glucokinase complex study; abstract-only in cache) and mouse Braf an IDA (MGI, PMID:16116448). So the node rests on experimental rows.
IEA (GO_REF:0000107): the source ortholog is mouse Araf, whose row is that MGI IDA. It is not circular.
Independent support for A-RAF: fetched PMID:10848612 (Yuryev et al. 2000, full text). Rat liver mitochondria were purified with markers PMID:10848612. A-RAF was protease-protected PMID:10848612. A review also notes it PMID:21779496. No ER marker was reported, but immunogold over mitochondria plus protease protection goes beyond a crude fraction. The organelle claim stands.
Rule 4: stays at the root, because the lines disagree. Yuryev place a pool in the IMS and maybe the matrix PMID:10848612, but they hedge PMID:10848612. The better-supported MST2 sequestration and BAD-related roles need the cytosolic face. ARAF has no recognised presequence or anchor. PMID:10848612 and PMID:21779496 were added to references and as supported_by on both rows.
Outcome: root.