METAP2

METAP2 is a divalent-metal-dependent methionine aminopeptidase that co-translationally removes the initiator methionine from nascent polypeptides (N-terminal methionine excision, NME), a processing step that controls the maturation, stability, and signaling competence of its substrates (PMID:22035799, PMID:27542228, PMID:33661300). It acts in concert with MetAP1 on M[VT]X-type N-termini, and the two enzymes are jointly required for processing of these substrates in vivo, with cellular sensitivity to METAP2 inhibition tracking MetAP1 levels and glutathione homeostasis (PMID:27542228). Characterized substrates include the small G protein Rab37, whose NME is required for Wnt planar cell polarity signaling (PMID:22035799), and both α-globin and βS-globin, where loss of methionine excision retains the iMet, raises hemoglobin S oxygen affinity, and delays HbS polymerization — with βS-globin a fivefold better substrate than α-globin (PMID:33661300). Beyond simple maturation, METAP2-mediated methionine removal exposes position-3 Arg/Lys residues that constitute Arg/N-degrons recognized specifically by the E3 ligase UBR4 (not UBR1 or UBR2), coupling NME to regulated protein degradation [PMID:bio_10.1101_2024.10.03.616566]. METAP2 is the covalent target of fumagillin-class inhibitors, which alkylate active-site His231; this inhibition arrests endothelial cells in G1 with accumulation of p21, suppresses angiogenesis and tumor growth in proportion to the degree of enzyme inhibition, and at higher doses induces apoptosis (PMID:9177176, PMID:26686773, PMID:16525646, PMID:15523682). Inhibitor potency is cofactor-dependent, differing markedly between cobalt- and manganese-activated enzyme (PMID:15516829). Independent of its peptidase role, METAP2 (p67) directly binds and inhibits ERK1/2 MAP kinases, and its loss activates ERK signaling and de-represses K-Ras-driven transformation (PMID:21033716).

1. 1997 High

   Establishing the molecular target of the anti-angiogenic natural product fumagillin answered why this compound blocks endothelial growth: it identified METAP2 as a covalently inhibited, selectively targeted metalloprotease distinct from MetAP1.

   Evidence Affinity purification of the fumagillin-binding protein from mammalian cells and in vivo yeast selectivity genetics

   PMID:9177176

   Open questions at the time

   • Did not define the physiological substrates whose processing matters for the anti-angiogenic phenotype
   • Active-site residue alkylated not yet mapped
2. 2005 Medium

   Defining the cell-cycle consequence of METAP2 inhibition explained the anti-proliferative mechanism: fumagillin-class compounds drive G1 arrest with p21 accumulation and apoptosis at higher doses.

   Evidence FACS cell-cycle analysis, p21 western blot, and apoptosis assays in HUVEC and SNU-398 cells across multiple inhibitors

   PMID:15523682

   Open questions at the time

   • Link between enzymatic NME activity and p21 induction not mechanistically resolved
   • Direct substrate driving G1 arrest unidentified
3. 2006 Medium

   Pharmacodynamic correlation tied antitumor efficacy directly to enzyme inhibition, confirming METAP2 catalytic activity as the relevant target in vivo.

   Evidence Tumor-tissue measurement of uninhibited METAP2 with dose-response xenograft correlation using irreversible inhibitor PPI-2458

   PMID:16525646

   Open questions at the time

   • Does not identify the substrate(s) mediating tumor growth inhibition
   • Endothelial vs tumor-cell-intrinsic contribution not separated
4. 2004 Medium

   Showing inhibitor potency depends on the bound divalent metal clarified that METAP2 enzymatic activity is cofactor-conditioned and that reversible active-site engagement is insufficient for cellular efficacy.

   Evidence Biochemical assay with cobalt vs manganese cofactor swap plus HUVEC proliferation and aortic ring angiogenesis assays

   PMID:15516829

   Open questions at the time

   • Physiological metal cofactor in cells not established
   • Why reversible inhibitors fail in cells while covalent ones succeed not fully explained
5. 2010 Medium

   Identifying a direct METAP2-ERK1/2 interaction revealed a non-catalytic signaling function: METAP2 restrains MAP kinase activity and suppresses oncogenic Ras transformation.

   Evidence Co-IP and in vitro kinase assays with ectopic expression, siRNA knockdown, and xenografts in K-RasV12-transformed fibroblasts

   PMID:21033716

   Open questions at the time

   • Whether ERK inhibition requires peptidase activity unresolved
   • Structural basis of the METAP2-ERK interaction unknown
6. 2011 High

   Identifying Rab37 as an NME substrate connected METAP2 catalysis to a defined downstream pathway, showing methionine excision is required for Wnt planar cell polarity signaling.

   Evidence N-terminus proteomic profiling, an NME-resistant Rab37 mutant phenocopy, and TNP-470 inhibition in endothelial cells

   PMID:22035799

   Open questions at the time

   • Generality of NME substrate dependence for other phenotypes not addressed
   • How retained Met disrupts Rab37 function biochemically not detailed
7. 2016 High

   Global N-terminome profiling defined the substrate sequence rules and the cooperative requirement for MetAP1, and linked fumagillin sensitivity to MetAP1 levels and glutathione status.

   Evidence N-terminomics across fumagillin-sensitive/insensitive cell lines, proteo-transcriptomics, and glutathione measurement

   PMID:27542228

   Open questions at the time

   • Mechanistic basis of the glutathione-sensitivity correlation unresolved
   • Division of labor between MetAP1 and MetAP2 per substrate incomplete
8. 2016 High

   Crystallographic mapping of the covalent adduct to His231 explained inhibitor selectivity and stereochemistry, and added 14-3-3-γ as a processing target.

   Evidence X-ray crystallography of inhibitor-METAP2 complex, enzymatic assays across three MetAP isoforms, and a 14-3-3-γ N-terminal processing assay

   PMID:26686773

   Open questions at the time

   • Functional consequence of altered 14-3-3-γ processing not established
9. 2021 High

   Demonstrating METAP2 processes α- and βS-globin connected NME to hemoglobin biophysics, showing retained iMet raises HbS oxygen affinity and delays sickling polymerization.

   Evidence In vitro kinetics, erythroid progenitor knockdown, Townes SCD mouse inhibitor treatment, modified HbS crystal structures, and blood rheology

   PMID:33661300

   Open questions at the time

   • Therapeutic window for selective globin modification in vivo not defined
   • Whether MetAP1 contributes to globin processing not tested
10. 2024 Medium

    Coupling METAP2 NME to the UBR4 N-recognin established that methionine excision generates Arg/Lys position-3 degrons, defining a new branch of the Arg/N-degron pathway.

    Evidence N-degron reporter assays, CRISPR knockout of UBR4/UBR1/UBR2, METAP2 inhibitor treatment, and bioinformatic substrate prediction (preprint)

    PMID:bio_10.1101_2024.10.03.616566

    Open questions at the time

    • Not yet peer-reviewed
    • Endogenous substrates degraded via this route require biochemical validation
    • Why UBR4 alone recognizes these degrons unexplained
11. 2026 Low

    Cellular studies linked METAP2 inhibition to ATF4-mediated integrated stress responses via non-canonical mTORC1 signaling, implicating its protein processing in nutrient sensing.

    Evidence In vitro enzymatic inhibition, ATF4 reporter, and mTORC1 pathway analysis with nitroxoline analogs

    PMID:41912098

    Open questions at the time

    • Pathway placement is partially inferential
    • Specific substrate connecting METAP2 to mTORC1 not identified

• It remains unresolved how METAP2's catalytic NME function and its non-catalytic ERK-binding activity are integrated, and which endogenous substrates mediate its angiogenic, metabolic, and degron-generating roles.
• No structure of METAP2 bound to a physiological protein substrate
• Catalytic vs scaffolding contributions to phenotypes not dissected
• In vivo substrate repertoire incomplete