Page last updated: 2024-10-24

peptidyl-histidine dioxygenase activity

Definition

Target type: molecularfunction

Catalysis of the reaction: L-histidyl-[protein] + 2-oxoglutarate + O2 = (3S)-3-hydroxy-L-histidyl-[protein] + succinate + CO2. [PMID:21251231, RHEA:54256]

Peptidyl-histidine dioxygenase (PHD) activity is a crucial enzymatic process involved in the post-translational modification of proteins. This activity catalyzes the hydroxylation of histidine residues within proteins, specifically at the C2 position of the imidazole ring. This hydroxylation reaction introduces a hydroxyl group to the histidine residue, leading to the formation of 2-hydroxyhistidine.

The PHD enzyme utilizes molecular oxygen (O2) and a reducing agent, such as α-ketoglutarate, as essential cofactors for its catalytic activity. The reaction mechanism involves a series of steps that begin with the binding of the substrate protein and α-ketoglutarate to the enzyme's active site.

1. **Oxygen Activation:** The enzyme utilizes iron ions in its active site to bind and activate molecular oxygen. The activated oxygen molecule then reacts with α-ketoglutarate, leading to the formation of a reactive intermediate, succinate.

2. **Hydroxylation:** The activated oxygen atom is then transferred to the histidine residue in the substrate protein, resulting in the formation of 2-hydroxyhistidine. This hydroxylation reaction is highly specific for the C2 position of the histidine ring.

3. **Product Release:** After hydroxylation, the enzyme releases the modified protein, succinate, and carbon dioxide.

PHD activity plays a critical role in diverse cellular processes, including:

* **Hypoxia Sensing:** PHD enzymes are key regulators of the cellular response to low oxygen levels (hypoxia). Hydroxylation of specific histidine residues in proteins involved in oxygen homeostasis, such as hypoxia-inducible factor (HIF), alters their stability and activity, ultimately influencing gene expression and cellular adaptation to oxygen deprivation.
* **Transcriptional Regulation:** PHD enzymes regulate the activity of various transcription factors, including HIF, by modulating their stability and interactions with other proteins. This, in turn, influences gene expression and cellular responses.
* **Protein Stability:** Hydroxylation by PHD enzymes can affect the stability and degradation of target proteins. This can influence a wide range of cellular functions, including protein folding, assembly, and turnover.
* **Cellular Signaling:** PHD activity contributes to various signaling pathways by modulating the activity of signaling molecules, including kinases and phosphatases.

Overall, peptidyl-histidine dioxygenase activity is a critical enzymatic process that regulates a diverse range of cellular functions by modifying the histidine residues in proteins. Its role in hypoxia sensing, transcriptional regulation, protein stability, and cellular signaling highlights its significance in maintaining cellular homeostasis and responding to environmental changes.'
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Proteins (1)

ProteinDefinitionTaxonomy
Hypoxia-inducible factor 1-alpha inhibitorA hypoxia-inducible factor 1-alpha inhibitor that is encoded in the genome of human. [PRO:DNx, UniProtKB:Q9NWT6]Homo sapiens (human)

Compounds (12)

CompoundDefinitionClassesRoles
alpha-ketoglutaric acid2-oxoglutaric acid : An oxo dicarboxylic acid that consists of glutaric acid bearing an oxo substituent at position 2. It is an intermediate metabolite in Krebs cycle.oxo dicarboxylic acidfundamental metabolite
succinylacetone4,6-dioxoheptanoic acid : A dioxo monocarboxylic acid that is heptanoic acid in which oxo groups replace the hydrogens at positions 4 and 6. It is an abnormal metabolite of the tyrosine metabolic pathway and a marker for type 1 tyrosinaemia.

succinylacetone: inhibitor of heme biosynthesis
beta-diketone;
dioxo monocarboxylic acid
human metabolite
2,4-pyridinedicarboxylic acidlutidinic acid : A pyridinedicarboxylic acid carrying carboxy groups at positions 2 and 4.pyridinedicarboxylic acid
daminozidedaminozide: induces tumorsstraight-chain fatty acid
d-2-hydroxyglutarate(R)-2-hydroxyglutaric acid : The (R)-enantiomer of 2-hydroxyglutaric acid.2-hydroxyglutaric acidalgal metabolite
alpha-hydroxyglutarate, (l)-isomer2-hydroxyglutaric acid
oxalylglycineN-oxalylglycine : An amino dicarboxylic acid that is iminodiacetic acid with an oxo substituent. It is used as an inhibitor of alpha-ketoglutarate dependent (EC 1.14.11.*) enzymes.

oxalylglycine: structure given in first source
amino dicarboxylic acid;
N-acylglycine
EC 1.14.11.* (oxidoreductase acting on paired donors, 2-oxoglutarate as one donor, incorporating 1 atom each of oxygen into both donors) inhibitor
quercetin7-hydroxyflavonol;
pentahydroxyflavone
antibacterial agent;
antineoplastic agent;
antioxidant;
Aurora kinase inhibitor;
chelator;
EC 1.10.99.2 [ribosyldihydronicotinamide dehydrogenase (quinone)] inhibitor;
geroprotector;
phytoestrogen;
plant metabolite;
protein kinase inhibitor;
radical scavenger
fg-4592roxadustat : An N-acylglycine resulting from the formal condensation of the amino group of glycine with the carboxy group of 4-hydroxy-1-methyl-7-phenoxyisoquinoline-3-carboxylic acid. It is an inhibitor of hypoxia inducible factor prolyl hydroxylase (HIF-PH).

roxadustat: structure in first source
aromatic ether;
isoquinolines;
N-acylglycine
EC 1.14.11.2 (procollagen-proline dioxygenase) inhibitor;
EC 1.14.11.29 (hypoxia-inducible factor-proline dioxygenase) inhibitor
ascorbic acidAscorbic Acid: A six carbon compound related to glucose. It is found naturally in citrus fruits and many vegetables. Ascorbic acid is an essential nutrient in human diets, and necessary to maintain connective tissue and bone. Its biologically active form, vitamin C, functions as a reducing agent and coenzyme in several metabolic pathways. Vitamin C is considered an antioxidant.

L-ascorbate : The L-enantiomer of ascorbate and conjugate base of L-ascorbic acid, arising from selective deprotonation of the 3-hydroxy group. Required for a range of essential metabolic reactions in all animals and plants.

L-ascorbic acid : The L-enantiomer of ascorbic acid and conjugate acid of L-ascorbate.

vitamin C : Any member of a group of vitamers that belong to the chemical structural class called butenolides that exhibit biological activity against vitamin C deficiency in animals. The vitamers include L-ascorbic acid and its salt, ionized and oxidized forms.
ascorbic acid;
vitamin C
coenzyme;
cofactor;
flour treatment agent;
food antioxidant;
food colour retention agent;
geroprotector;
plant metabolite;
skin lightening agent
bay 85-3934
gsk1278863daprodustat : A member of the class of barbiturates that is barbituric acid substituted by cyclohexyl groups at positions 1 and 3, and by a (carboxymethyl)aminocarbonyl group at position 5. It is an inhibitor of hypoxia-inducible factor prolyl hydroxylase developed by GlaxoSmithKline for the treatment of anaemia in patients with chronic kidney disease.

GSK1278863: a HIF prolyl hydroxylase inhibitor