GCK (glucokinase / hexokinase-4, P35557) — review notes

Summary of gene function

GCK encodes glucokinase (hexokinase-4 / hexokinase type IV / hexokinase-D), the
high-Km hexose-phosphorylating enzyme (EC 2.7.1.1) expressed mainly in pancreatic
beta cells and hepatocytes. It catalyzes the first, committed step of glucose
utilization: phosphorylation of D-glucose to D-glucose 6-phosphate using ATP
(RHEA:17825). It also phosphorylates D-mannose and D-fructose (and, weakly,
2-deoxyglucose, glucosamine), but these are of minor physiological relevance
[UniProt P35557 CATALYTIC ACTIVITY; PMID:7742312].

The defining property that distinguishes GCK from HK1-3 is its weak affinity for
glucose (KM ~6 mM, sigmoidal/cooperative kinetics, Hill coefficient ~1.7) and lack
of product inhibition by G6P. This makes it a physiological glucose sensor: its
activity varies steeply across the physiological blood-glucose range, so it sets the
threshold for glucose-stimulated insulin secretion in the beta cell and controls
hepatic glucose uptake/glycogen synthesis in the liver
[PMID:7742312 "KM=6.03 mM for glucose"; UniProt "GCK acts as a glucose sensor in the pancreatic beta cell"].

Regulation and localization

• Cytosolic in both beta cells and hepatocytes; the HPA IDA and Reactome/IBA
  place it in cytosol (GO:0005829) [GOA rows 7, 33, 39, 63, 67-72].
• In hepatocytes, GCK is regulated by the glucokinase regulatory protein GCKR:
  at low glucose (and high fructose-6-phosphate) GCK binds GCKR and the inactive
  complex is sequestered in the nucleus; at high glucose GCK is released back to the
  cytosol [PMID:10456334; UniProt ACTIVITY REGULATION/SUBUNIT]. This is the basis of
  the nucleus (GO:0005634) and nucleoplasm (GO:0005654) annotations and the Reactome
  GCK1:GCKR transport reactions.
• Interacts with MIDN (midnolin ubiquitin-like domain), preferentially at low
  glucose, inhibiting activity PMID:24187134; with PFKFB1/PFK-2/FBPase-2
  PMID:11522786; with GCKR [PMID:16173921 Y2H, PMID:32296183 HuRI].

Disease

• MODY2 / GCK-MODY (MIM:125851): heterozygous inactivating mutations → mild,
  stable fasting hyperglycemia (compensated by the WT allele).
• PNDM1 (MIM:606176): homozygous/biallelic loss → permanent neonatal diabetes;
  protein instability is a major severity determinant PMID:25015100.
• HHF3 / GCK-hyperinsulinism (MIM:602485): heterozygous activating (gain-of-function)
  mutations, often in the allosteric activator site → hyperinsulinemic hypoglycemia
  [PMID:12941786, PMID:15277402, PMID:11916951, PMID:17082186, PMID:19146401].
• T2D susceptibility variants (GWAS, e.g. rs1799884) affect fasting glucose /
  insulin secretion PMID:20668700.

Annotation review decisions (high level)

• Core MF: glucokinase activity (GO:0004340) — strongly supported by many EXP/IDA
  annotations and the whole disease literature. ACCEPT the experimental instances.
• Hexokinase activity (GO:0004396), ATP binding (GO:0005524), D-glucose
  binding (GO:0005536) — correct and experimentally supported; ACCEPT.
• Fructokinase (GO:0008865) / mannokinase (GO:0019158) — genuine in-vitro
  activities (PMID:7742312), but of minor/uncertain physiological relevance; the EXP
  instances are real so ACCEPT/KEEP_AS_NON_CORE; the RHEA/IBA electronic ones are the
  same broad substrate promiscuity.
• Glucose/G6P metabolic process, glycolysis, glucose homeostasis, regulation of
  insulin secretion, glucose sensor activity — all well supported; core BP/MF.
• protein binding (GO:0005515) IPI — uninformative MF; MARK_AS_OVER_ANNOTATED
  (per policy, do not REMOVE IPIs). The real interactions (GCKR, MIDN, PFKFB1) are
  captured in notes/description.
• calcium ion import (GO:0070509) — Ensembl-projected IEA from mouse ortholog;
  not a GCK molecular function; over-propagated electronic inference → MARK_AS_OVER_ANNOTATED.
• cytoplasmic side of mitochondrial outer membrane (GO:0032473) / mitochondrion
  (GO:0005739) — these come from the hexokinase family IBA/ISS (HK1-3 are OMM-bound
  via their N-terminal hydrophobic anchor; GCK lacks this anchor and is cytosolic).
  Over-annotation by family inheritance → MARK_AS_OVER_ANNOTATED.
• purine nucleotide metabolic process (GO:0006163), nicotinamide nucleotide
  metabolic process (GO:0046496) — ARBA electronic mappings; too indirect / not the
  gene's role (ATP is a co-substrate, not evidence of purine metabolism) →
  MARK_AS_OVER_ANNOTATED.