gcvP

id: C5AUG0
gene_symbol: gcvP
product_type: PROTEIN
taxon:
  id: NCBITaxon:272630
  label: Methylorubrum extorquens AM1
description: 'gcvP encodes glycine dehydrogenase (decarboxylating) (EC 1.4.4.2), also
  known as glycine cleavage system P protein, which catalyzes the first step of the
  glycine cleavage system. The P protein binds the alpha-amino group of glycine through
  its pyridoxal phosphate cofactor (at Lys-699), cleaves the C-C bond to release CO2,
  and transfers the remaining methylamine moiety to the lipoamide cofactor of the
  H protein (gcvH). This initiates the oxidative decarboxylation of glycine, which
  is then completed by the T and L proteins to produce 5,10-methylene-THF, CO2, and
  ammonia. The enzyme belongs to the GcvP family and functions as a component of the
  four-protein glycine cleavage complex (P, T, L, and H). In methylotrophs, the glycine
  cleavage system connects the serine cycle to the THF one-carbon pool: glycine (produced
  from serine by serA) is oxidatively cleaved by the GCV system, generating 5,10-methylene-THF
  that feeds into C1 metabolism. GcvP is a large protein (948 AA) with three characteristic
  domains: two N-terminal glycine cleavage system P-protein domains (residues 14-438
  and 474-721) and a C-terminal domain (residues 766-887). The enzyme is essential
  for glycine catabolism and for recycling one-carbon units during methylotrophic
  growth.'
existing_annotations:
- term:
    id: GO:0004375
    label: glycine dehydrogenase (decarboxylating) activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: This is the primary and specific catalytic activity of GcvP - the oxidative
      decarboxylation of glycine. The P protein binds glycine through its pyridoxal
      phosphate cofactor, cleaves the C-C bond to release CO2, and transfers the methylamine
      moiety to the H protein. [file:METEA/gcvP/gcvP-uniprot.txt, "Glycine dehydrogenase
      (decarboxylating)"; "EC=1.4.4.2"; "N(6)-[(R)-lipoyl]-L-lysyl-[glycine-cleavage
      complex H protein] + glycine + H(+) = N(6)-[(R)-S(8)-aminomethyldihydrolipoyl]-L-lysyl-[glycine-cleavage
      complex H protein] + CO2"]
    action: ACCEPT
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: IEA
  original_reference_id: GO_REF:0000118
  review:
    summary: 'GcvP functions in the cytosol as part of the glycine cleavage complex.
      While cytosol is more specific than cytoplasm, the primary location annotation
      should be the glycine cleavage complex. [file:METEA/gcvP/gcvP-uniprot.txt, "The
      glycine cleavage system is composed of four proteins: P, T, L and H"]'
    action: ACCEPT
- term:
    id: GO:0005960
    label: glycine cleavage complex
  evidence_type: IEA
  original_reference_id: GO_REF:0000118
  review:
    summary: 'GcvP is a component of the glycine cleavage complex, working together
      with gcvT, gcvH, and gcvL to catalyze the oxidative cleavage of glycine. This
      is the primary cellular location for the enzyme. [file:METEA/gcvP/gcvP-uniprot.txt,
      "Glycine cleavage system P-protein"; "The glycine cleavage system is composed
      of four proteins: P, T, L and H"]'
    action: ACCEPT
- term:
    id: GO:0006544
    label: glycine metabolic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    summary: This is a general parent term for all glycine metabolism. While technically
      correct, the more specific term GO:0019464 (glycine decarboxylation via glycine
      cleavage system) provides better functional annotation.
    action: KEEP_AS_NON_CORE
- term:
    id: GO:0006546
    label: glycine catabolic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    summary: GcvP catalyzes the first step of glycine catabolism via the glycine cleavage
      system, initiating the oxidative decarboxylation of glycine. While correct,
      the more specific term GO:0019464 provides better functional annotation.
    action: KEEP_AS_NON_CORE
- term:
    id: GO:0016491
    label: oxidoreductase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000043
  review:
    summary: This is a very general parent term for all oxidoreductase enzymes. While
      technically correct (GcvP catalyzes an oxidative decarboxylation), the more
      specific term GO:0004375 (glycine dehydrogenase activity) provides much better
      functional annotation.
    action: KEEP_AS_NON_CORE
- term:
    id: GO:0016594
    label: glycine binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000118
  review:
    summary: GcvP binds glycine as its substrate through the pyridoxal phosphate cofactor.
      This is an essential substrate binding function that precedes the catalytic
      decarboxylation step. [file:METEA/gcvP/gcvP-uniprot.txt, "The P protein binds
      the alpha-amino group of glycine through its pyridoxal phosphate cofactor"]
    action: ACCEPT
- term:
    id: GO:0019464
    label: glycine decarboxylation via glycine cleavage system
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: GcvP catalyzes the first step of glycine decarboxylation via the glycine
      cleavage system, initiating the oxidative cleavage of glycine by releasing CO2
      and transferring the methylamine moiety to the H protein. This is the specific
      biological process that GcvP participates in. [file:METEA/gcvP/gcvP-uniprot.txt,
      "The glycine cleavage system catalyzes the degradation of glycine"]
    action: ACCEPT
- term:
    id: GO:0030170
    label: pyridoxal phosphate binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000118
  review:
    summary: 'GcvP requires pyridoxal phosphate (PLP) as a cofactor, which is covalently
      bound at Lys-699. The PLP cofactor is essential for binding the alpha-amino
      group of glycine and facilitating the decarboxylation reaction. [file:METEA/gcvP/gcvP-uniprot.txt,
      "COFACTOR: Name=pyridoxal 5''-phosphate"; "N6-(pyridoxal phosphate)lysine" at
      position 699; "The P protein binds the alpha-amino group of glycine through
      its pyridoxal phosphate cofactor"]'
    action: ACCEPT
core_functions:
- description: 'GcvP catalyzes the first and rate-limiting step of the glycine cleavage
    system: the oxidative decarboxylation of glycine via a pyridoxal phosphate-dependent
    mechanism. The P protein binds the alpha-amino group of glycine through its PLP
    cofactor (covalently attached at Lys-699), cleaves the C-C bond to release CO2,
    and transfers the resulting methylamine moiety to the lipoamide cofactor of the
    H protein carrier. This initiates the four-step glycine cleavage process that
    ultimately produces 5,10-methylene-THF, CO2, and ammonia. In methylotrophic bacteria
    like M. extorquens AM1, the glycine cleavage system connects the serine cycle
    to the THF one-carbon pool: glycine (produced from serine via serA) is oxidatively
    cleaved by the GCV system, generating 5,10-methylene-THF for downstream C1 metabolism.
    GcvP is a large, multi-domain protein (948 AA) that functions as part of the four-protein
    complex (P, T, L, H) in the cytosol. The enzyme is essential for glycine catabolism
    and for recycling one-carbon units during growth on C1 compounds.'
  molecular_function:
    id: GO:0004375
    label: glycine dehydrogenase (decarboxylating) activity
  directly_involved_in:
  - id: GO:0019464
    label: glycine decarboxylation via glycine cleavage system
  locations:
  - id: GO:0005960
    label: glycine cleavage complex
  - id: GO:0005829
    label: cytosol
  supported_by:
  - reference_id: file:METEA/gcvP/gcvP-uniprot.txt
    supporting_text: The P protein binds the alpha-amino group of glycine through
      its pyridoxal phosphate cofactor; CO2 is released and the remaining methylamine
      moiety is then transferred to the lipoamide cofactor of the H protein. The glycine
      cleavage system catalyzes the degradation of glycine.
references:
- id: GO_REF:0000002
  title: Gene Ontology annotation through association of InterPro records with GO
    terms.
  findings: []
- id: GO_REF:0000043
  title: Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping
  findings: []
- id: GO_REF:0000118
  title: TreeGrafter-generated GO annotations
  findings: []
- id: GO_REF:0000120
  title: Combined Automated Annotation using Multiple IEA Methods.
  findings: []
- id: file:METEA/gcvP/gcvP-uniprot.txt
  title: UniProt record for gcvP (C5AUG0)
  findings: []
status: COMPLETE