GLUD2 (P49448) review notes

Human GLUD2, glutamate dehydrogenase 2, mitochondrial (EC 1.4.1.3). HGNC:4336, GeneID 2747,
X-linked, intronless. UniProt entry name DHE4_HUMAN. Sources below are the local files in
genes/human/GLUD2/ and cached publications in publications/.

Identity, gene origin, expression

• GLUD2 is a hominoid-specific retrogene that arose by retroposition (reverse transcription of
  a GLUD1 mRNA) in the common hominoid ancestor ~18-25 Mya; it is intronless and X-linked
  PMID:18688271.
• Originally described as a "novel human glutamate dehydrogenase expressed in neural and testicular
  tissues and encoded by an X-linked intronless gene"; RT-PCR showed expression in retina, testis,
  and, at lower levels, brain PMID:8207021.
• UniProt TISSUE SPECIFICITY: "Expressed in retina, testis and, at a lower level, brain."
  [file:human/GLUD2/GLUD2-uniprot.txt]. In brain, GDH is predominantly astrocytic
  PMID:12742085.
• Note: a later observation cited in PMID:18688271 says GLUD2 is transcribed in many/most human
  tissues, in contrast to the earlier brain/retina/testis-restricted picture
  PMID:18688271.
  HPA (UniProt DR) lists it as "Group enriched (liver, testis)".

Molecular function (catalysis)

• Reversible oxidative deamination of L-glutamate, using either NAD+ or NADP+ as cofactor
  (EC 1.4.1.3). UniProt records both catalytic activities
  [file:human/GLUD2/GLUD2-uniprot.txt "Reaction=L-glutamate + NAD(+) + H2O = 2-oxoglutarate + NH4(+) + NADH +"]
  and
  [file:human/GLUD2/GLUD2-uniprot.txt "Reaction=L-glutamate + NADP(+) + H2O = 2-oxoglutarate + NH4(+) + NADPH"].
• The recombinant retinal (GLUD2) enzyme catalyzed the oxidative deamination of glutamate with
  catalytic properties similar to native brain GDH
  PMID:8207021.
• The reaction links glutamate/amino-acid/nitrogen metabolism to the TCA cycle by producing
  2-oxoglutarate (alpha-ketoglutarate) and ammonia
  PMID:18688271.
• Because the deamination/reductive-amination reaction is reversible, GDH can also run in the
  glutamate-synthesizing (reductive amination) direction; GOA carries an IDA for
  L-glutamate biosynthetic process (GO:0097054) from PMID:11032875.

Allosteric regulation (the adaptive, GLUD2-distinguishing properties)

• Unlike housekeeping GLUD1, GLUD2 is essentially insensitive to GTP inhibition in its basal
  state, has low basal activity, and is strongly activated by ADP and by L-leucine
  PMID:11032875
  PMID:11032875
  PMID:11032875.
• Two positively selected substitutions (Arg443Ser and Gly456Ala relative to GLUD1) account for the
  GTP resistance and ADP dependence, adapting GLUD2 to a high ADP:ATP ratio and intracellular
  acidification, as in synaptic astrocytes during glutamatergic transmission
  PMID:12742085
  PMID:15578726.
• So GO terms "GTP binding" (GO:0005525), "ADP binding" (GO:0043531) and "L-leucine binding"
  (GO:0070728) reflect experimentally documented allosteric-effector binding, not the catalytic
  active site. ADP is an activator (physiologically the salient one for GLUD2); GTP binds but does
  not inhibit basal GLUD2; L-leucine is an activator.

Subcellular localization

• UniProt: Mitochondrion matrix (SUBCELLULAR LOCATION, evidence PubMed:22709669)
  [file:human/GLUD2/GLUD2-uniprot.txt "SUBCELLULAR LOCATION: Mitochondrion matrix"]; N-terminal
  transit peptide residues 1-53 [file:human/GLUD2/GLUD2-uniprot.txt "TRANSIT 1..53"].
• GLUD2 is specifically targeted to mitochondria (in contrast to GLUD1, which is mitochondrial
  AND cytoplasmic), because of a positively selected E7K substitution in its mitochondrial targeting
  sequence PMID:18688271.
• This is the experimental basis for the NOT located_in cytosol annotation (GO:0005829, IDA,
  PMID:18688271): GLUD2 is restricted to mitochondria and, unlike GLUD1, is not appreciably
  cytosolic. GOA also has an IDA "located_in mitochondrion" (GO:0005739) from the same paper.
• Confirmed as a mitochondrial protein by the high-confidence human mitochondrial proteome
  (HTP, PMID:34800366) and by HPA immunofluorescence (IDA, GO_REF:0000052).

Interactions

• UniProt INTERACTION line: P49448 (GLUD2) with P00367 (GLUD1)
  [file:human/GLUD2/GLUD2-uniprot.txt "P49448; P00367: GLUD1; NbExp=2"]. GDH assembles as a
  homohexamer [file:human/GLUD2/GLUD2-uniprot.txt "SUBUNIT: Homohexamer"]; GLUD1 and GLUD2 are near-
  identical paralogs that can co-assemble.
• The two IPI "protein binding" (GO:0005515) annotations (PMID:28514442, PMID:33961781) are
  high-throughput AP-MS interactome screens; both cite WITH = UniProtKB:P00367 (GLUD1). These are
  uninformative bare protein-binding annotations (over-annotation), consistent with the documented
  GLUD1-GLUD2 association but not adding specific functional insight.

Family / structure

• Belongs to the Glu/Leu/Phe/Val dehydrogenases family [file:human/GLUD2/GLUD2-uniprot.txt
  "SIMILARITY: Belongs to the Glu/Leu/Phe/Val dehydrogenases family"]; NAD(P)-binding Rossmann fold;
  PANTHER PTHR11606:SF15 GLUTAMATE DEHYDROGENASE 2, MITOCHONDRIAL. X-ray structure 6G2U.

Curation decisions summary

Core functions:
- MF: GO:0004353 L-glutamate dehydrogenase [NAD(P)+] activity — best single term for the
dual-cofactor (NAD+ and NADP+) EC 1.4.1.3 reaction that UniProt documents. GO:0004352 (NAD+) and
GO:0004354 (NADP+) are the cofactor-specific children, both experimentally/IEA supported.
- MF: GO:0043531 ADP binding — physiologically salient allosteric activator (IDA, PMID:12742085).
- BP: GO:0006538 L-glutamate catabolic process (deamination direction) and
GO:0006536 glutamate metabolic process.
- CC: GO:0005759 mitochondrial matrix.

Actions: experimental MF/BP/CC annotations describing catalysis, effector binding, and mitochondrial
matrix localization are ACCEPTed (or KEEP_AS_NON_CORE where they are supporting biology). The two
bare "protein binding" IPI annotations are MARK_AS_OVER_ANNOTATED (never REMOVE experimental IPI).
Generic IEA parents (oxidoreductase activity, amino acid metabolic process) are KEEP_AS_NON_CORE as
correct-but-general; the EC/InterPro/RHEA IEA catalytic terms are ACCEPT/MODIFY toward the specific
dual-cofactor term. The NOT located_in cytosol IDA is ACCEPTed (well-supported negative).