NRAS (P01111) curation notes

Research journal for the GO annotation review of human NRAS (GTPase NRas, HGNC:7989,
UniProt P01111). There was no pre-generated deep-research file, so literature was
assembled from the publications/ cache (PMIDs cited in NRAS-goa.tsv) and the UniProt
record (NRAS-uniprot.txt).

Core identity

NRAS ("Neuroblastoma RAS viral oncogene homolog") is one of the three canonical RAS
small GTPases (HRAS, KRAS, NRAS). It is a 189-aa precursor (mature 1-186 after CAAX
processing) belonging to the small GTPase superfamily, Ras family
[file:human/NRAS/NRAS-uniprot.txt "Belongs to the small GTPase superfamily. Ras family."].

• Molecular function: binds GDP/GTP and possesses intrinsic GTPase activity; cycles
  between an inactive GDP-bound and an active GTP-bound state
  [file:human/NRAS/NRAS-uniprot.txt "Ras proteins bind GDP/GTP and possess intrinsic GTPase activity"]
  [file:human/NRAS/NRAS-uniprot.txt "Alternates between an inactive form bound to GDP and an active form bound to GTP. Activated by a guanine nucleotide-exchange factor (GEF) and inactivated by a GTPase-activating protein (GAP)."].
  EC 3.6.5.2; catalyzes GTP + H2O = GDP + phosphate + H+ [UniProt CATALYTIC ACTIVITY].
• The conserved effector region (residues 32-40) and the P-loop / G-boxes (GxxxxGKS at
  10-18, etc.) mediate nucleotide binding [UniProt FT BINDING 10..18, 29..30, 57..61, 116..119].

Membrane localization and the acylation cycle

NRAS is anchored to membranes via C-terminal lipidation: S-farnesyl at Cys-186 and
S-palmitoyl at Cys-181 [UniProt LIPID 181 (palmitoyl), 186 (farnesyl);
PMID:2661017 "All ras proteins are polyisoprenylated but only some are palmitoylated"].
A constitutive de/re-palmitoylation cycle drives rapid shuttling between the plasma
membrane and the Golgi apparatus:
- PMID:15705808
- PMID:15705808
- Palmitoylated by the ZDHHC9-GOLGA7 complex; depalmitoylated by ABHD17A/B/C
[UniProt PTM; PMID:26701913 "ABHD17 catalytic activity is required for N-Ras depalmitoylation and re-localization to internal cellular membranes"].
- Cys-181-to-Ser mutation abolishes plasma membrane localization
[UniProt MUTAGEN 181 "C->S: Loss of plasma membrane localization." (PMID:26701913)].
- UniProt SUBCELLULAR LOCATION: Cell membrane (lipid-anchor, cytoplasmic side) and
Golgi apparatus membrane; "Shuttles between the plasma membrane and the Golgi apparatus."
Both supported experimentally by PMID:15705808 and PMID:26701913.

So plasma membrane and Golgi membrane are both bona-fide experimentally supported
locations. Endoplasmic reticulum membrane appears in Reactome RAS-processing reactions
(farnesylation/ICMT/RCE1 occur at the ER) — plausible as a transient processing site
but only TAS-supported.

Signaling: RTK -> RAS -> MAPK / PI3K

Active GTP-bound NRAS transduces signals from receptor tyrosine kinases (activated by
GEFs such as SOS1, RasGRP) to downstream effectors:
- RAF kinases (ARAF, BRAF, RAF1) -> MEK -> ERK MAPK cascade. UniProt INTERACTION lists
direct binding to ARAF (Q96II5), BRAF (P15056), RAF1 (P04049).
- PI3K (binds PIK3R1 P27986-2 per UniProt INTERACTION; Reactome R-HSA-9658253 "RAS:GTP binds PI3K").
- RalGDS / RGL3 (Q3MIN7), RIN1 (Q13671) effectors (UniProt INTERACTION; IntAct GOA lines).
- STK19 phosphorylates NRAS at Ser-89 to enhance binding to downstream effectors and
promote oncogenic NRAS-driven melanocyte transformation
PMID:30712867.
PMID:30712867 is the experimental basis (IDA) for both GTPase activity and Ras protein
signal transduction in GOA, and the UniProt FUNCTION statement (ECO:0000269|PubMed:30712867).

SHOC2-PP1C holophosphatase

NRAS (GTP-bound) binds the SHOC2-PP1C (PPP1CA/B/C) holophosphatase complex, a RAF
activator; this complex dephosphorylates the inhibitory S259 site on RAF.
- [file:human/NRAS/NRAS-uniprot.txt "Interacts (active GTP-bound form) with both SHOC2 and PP1c (all isoforms) to form a tertiary complex; SHOC2 and PP1c preferably bind M-Ras/MRAS, but they also bind K-Ras/KRAS, N-Ras/NRAS and H-Ras/HRAS"]
- ComplexPortal CPX-26354 "SHOC2-NRAS-PPP1CA complex"; GOA NAS line GO:0046579
(positive regulation of Ras protein signal transduction, PMID:35831509) reflects this.

Golgi-localized Ras signaling

• PAQR10/PAQR11 are Golgi-resident proteins that elevate Golgi localization and activation
  of HRas, NRas, KRas4A and promote ERK signaling
  PMID:21968647. Basis for the IDA Golgi apparatus (part_of) annotation.
• eNOS regulates N-Ras activation on the Golgi of antigen-stimulated T cells
  [PMID:18641128 title]; this is the IntAct/UniProt protein-binding (RAF1) source line.

Proliferation / disease

• Oncogenic activating mutations at codons 12, 13 and 61 lock NRAS in the GTP-bound state
  and transform cells [UniProt MISCELLANEOUS "Mutations which change AA 12, 13 or 61 activate
  the potential of Ras to transform cultured cells and are implicated in a variety of human tumors"].
  Q61R impairs GTP hydrolysis, trapping NRAS active, and promotes melanomagenesis
  [UniProt VARIANT 61 "impaired GTP hydrolysis activity, trapping NRAS in a constitutive GTP-bound active conformation; promotes melanomagenesis"].
• Disease associations: juvenile myelomonocytic leukemia (JMML), Noonan syndrome 6,
  RAS-associated autoimmune leukoproliferative disorder (RALD), congenital melanocytic
  nevus syndrome (CMNS), neurocutaneous melanosis, keratinocytic nevus, non-medullary
  thyroid cancer 2 (all UniProt DISEASE).
• Positive regulation of cell population proliferation: supported by IBA across the RAS
  family and the canonical RTK->RAS->MAPK->proliferation paradigm.
• Positive regulation of endothelial cell proliferation (IMP, PMID:23619365): miR-146a
  attenuates angiogenesis through downregulation of NRAS in endothelial cells
  PMID:23619365;
  supports a role of NRAS in EC proliferation/angiogenesis (peripheral, non-core).

Annotation-set observations

• GOA has ~178 lines but is heavily inflated by Reactome TAS "plasma membrane" annotations
  (one per reaction, ~120 lines all GO:0005886, located_in, TAS Reactome). These are all the
  same CC term; plasma membrane is well supported (IBA + IDA HPA + EXP). Treat the Reactome PM
  block as ACCEPT (location correct) — no need to favor one over another (duplicates are fine).
• ER membrane (GO:0005789) TAS Reactome: RAS processing occurs at the ER; KEEP_AS_NON_CORE /
  ACCEPT as a processing-transit location, TAS only.
• cytosol (GO:0005829) TAS Reactome R-HSA-9647978 (pro-RAS farnesylated): newly synthesized
  pre-processed RAS is cytosolic; acceptable but peripheral.
• tertiary granule membrane (GO:0070821) and extracellular exosome (GO:0070062), membrane
  (GO:0016020 HDA): high-throughput proteomic localizations; keep as non-core / over-annotation.
• protein binding (GO:0005515, many IPI lines): bare protein binding — uninformative. Per
  curation guidelines, do not endorse; MODIFY toward informative MF where the partner defines
  a function (e.g. RAF1/BRAF/ARAF binding = Ras GTPase binding / signaling) or
  MARK_AS_OVER_ANNOTATED for generic interactome-screen partners. Several IPI lines are from
  large interactome maps (PMID:32296183, 28514442, 33961781, 40205054, 32814053) — over-annotation.
• protein-containing complex binding (GO:0044877 IDA, PMID:23209302): the cited paper is about
  KIF14/Rap1a-Radil, NRAS is not its focus; UNDECIDED / over-annotation.
• G protein activity (GO:0003925, IEA EC mapping): EC 3.6.5.2 maps here; this is the small
  monomeric GTPase enzyme activity = GTPase activity. GO:0003925 is acceptable as an
  EC-mapped enzyme term but GTPase activity (GO:0003924) is the more standard RAS MF.

Core functions (synthesis)

1. GTP/GDP-binding molecular switch with intrinsic GTPase activity (GO:0003924, GO:0005525).
2. Plasma-membrane- and Golgi-membrane-anchored signal transducer relaying RTK input to the
   RAF-MEK-ERK MAPK cascade and PI3K (GO:0007265, GO:0000165; GO:0005886, GO:0000139).
3. Promotion of cell proliferation downstream of this signaling (GO:0008284) — pleiotropic /
   peripheral relative to the switch function.

Final review action plan (applied to YAML 2026-06)

• GTPase activity (GO:0003924) IBA/IEA/ISS/IDA/TAS, GTP binding (GO:0005525) IEA: ACCEPT (core MF).
• G protein activity (GO:0003925) IEA EC-map: KEEP_AS_NON_CORE (less standard than GTPase activity for RAS).
• Ras protein signal transduction (GO:0007265) IBA + IDA: ACCEPT (core BP); MAPK cascade (GO:0000165) IEA + TAS: ACCEPT (core BP).
• signal transduction (GO:0007165) IEA InterPro: KEEP_AS_NON_CORE (broad parent of GO:0007265/GO:0000165).
• plasma membrane (GO:0005886) IBA/IDA/EXP/TAS-Reactome(many): ACCEPT (core CC; Reactome block redundant but location correct).
• Golgi membrane (GO:0000139) EXP/IEA/TAS and Golgi apparatus (GO:0005794) IDA: ACCEPT (core CC; shuttling site).
• ER membrane (GO:0005789) TAS-Reactome: KEEP_AS_NON_CORE (RAS-processing transit site).
• cytosol (GO:0005829) TAS-Reactome (pre-processed RAS): KEEP_AS_NON_CORE.
• membrane (GO:0016020) IEA/HDA, tertiary granule membrane (GO:0070821) TAS, extracellular exosome (GO:0070062) HDA: MARK_AS_OVER_ANNOTATED (generic/HT, loses PM/Golgi specificity).
• positive regulation of cell population proliferation (GO:0008284) IBA: KEEP_AS_NON_CORE (downstream).
• positive regulation of endothelial cell proliferation (GO:0001938) IMP PMID:23619365: KEEP_AS_NON_CORE (peripheral; NRAS as miR-146a target).
• positive regulation of Ras protein signal transduction (GO:0046579) NAS PMID:35831509: KEEP_AS_NON_CORE (complex-level / SHOC2-PP1C).
• protein binding (GO:0005515) IPI x many: bare term — MARK_AS_OVER_ANNOTATED (high-throughput interactome) or note effector partners; not endorsed as informative MF.
• protein-containing complex binding (GO:0044877) IDA PMID:23209302: MARK_AS_OVER_ANNOTATED (paper not focused on NRAS).