D-2-Hydroxyglutaric acid (BioDeep_00000002868)

 

Secondary id: BioDeep_00001868343

human metabolite PANOMIX_OTCML-2023 Endogenous blood metabolite natural product


代谢物信息卡片


alpha-Hydroxyglutarate, disodium salt

化学式: C5H8O5 (148.0372)
中文名称: 2-羟基戊二酸
谱图信息: 最多检出来源 Homo sapiens(plant) 31.69%

分子结构信息

SMILES: C(CC(=O)O)C(C(=O)O)O
InChI: InChI=1S/C5H8O5/c6-3(5(9)10)1-2-4(7)8/h3,6H,1-2H2,(H,7,8)(H,9,10)/t3-/m1/s1

描述信息

In humans, D-2-hydroxyglutaric acid is formed by a hydroxyacid-oxoacid transhydrogenase whereas in bacteria it is formed by a 2-hydroxyglutarate synthase. D-2-Hydroxyglutaric acid is also formed via the normal activity of hydroxyacid-oxoacid transhydrogenase during conversion of 4-hydroxybutyrate to succinate semialdehyde. The compound can be converted to alpha-ketoglutaric acid through the action of a 2-hydroxyglutarate dehydrogenase (EC 1.1.99.2). In humans, there are two such enzymes (D2HGDH and L2HGDH). Both the D and the L stereoisomers of hydroxyglutaric acid are found in body fluids. D-2-Hydroxyglutaric acid is a biochemical hallmark of the inherited neurometabolic disorder D-2-hydroxyglutaric aciduria (OMIM: 600721) and the genetic disorder glutaric aciduria II. D-2-Hydroxyglutaric aciduria (caused by loss of D2HGDH or gain of function of IDH) is rare, with symptoms including cancer, macrocephaly, cardiomyopathy, mental retardation, hypotonia, and cortical blindness. An elevated urine level of D-2-hydroxyglutaric acid has been reported in patients with spondyloenchondrodysplasia (OMIM: 271550). D-2-Hydroxyglutaric acid can be converted to alpha-ketoglutaric acid through the action of 2-hydroxyglutarate dehydrogenase (D2HGDH). Additionally, the enzyme D-3-phosphoglycerate dehydrogenase (PHGDH) can catalyze the NADH-dependent reduction of alpha-ketoglutarate (AKG) to D-2-hydroxyglutarate (D-2HG). Nyhan et al. (1995) described 3 female patients, 2 of them sibs, who were found to have excess accumulation of D-2-hydroxyglutaric acid in the urine. The phenotype was quite variable, even among the sibs, but included mental retardation, macrocephaly with cerebral atrophy, hypotonia, seizures, and involuntary movements. One of the patients developed severe intermittent vomiting and was given a pyloromyotomy. The electroencephalogram demonstrated hypsarrhythmia. There was an increased concentration of protein in cerebrospinal fluid, an unusual finding in inborn errors of metabolism. D-2-Hydroxyglutaric acid can also be produced via gain-of-function mutations in the cytosolic and mitochondrial isoforms of isocitrate dehydrogenase (IDH). IDH is part of the TCA cycle and this compound is generated in high abundance when IDH is mutated. Since D-2-hydroxyglutaric acid is sufficiently similar in structure to 2-oxoglutarate (2OG), it is able to inhibit a range of 2OG-dependent dioxygenases, including histone lysine demethylases (KDMs) and members of the ten-eleven translocation (TET) family of 5-methylcytosine (5mC) hydroxylases. This inhibitory effect leads to alterations in the hypoxia-inducible factor (HIF)-mediated hypoxic response and alterations in gene expression through global epigenetic remodeling. The net effect is that D-2-hydroxyglutaric acid causes a cascading effect that leads genetic perturbations and malignant transformation. Depending on the circumstances, D-2-hydroxyglutaric acid can act as an oncometabolite, a neurotoxin, an acidogen, and a metabotoxin. An oncometabolite is a compound that promotes tumour growth and survival. A neurotoxin is compound that is toxic to neurons or nerual tissue. An acidogen is an acidic compound that induces acidosis, which has multiple adverse effects on many organ systems. A metabotoxin is an endogenously produced metabolite that causes adverse health effects at chronically high levels. As an oncometabolite, D-2-hydroxyglutaric acid is a competitive inhibitor of multiple alpha-ketoglutarate-dependent dioxygenases, including histone demethylases and the TET family of 5mC hydroxylases. As a result, high levels of 2-hydroxyglutarate lead to genome-wide histone and DNA methylation alterations, which in turn lead to mutations that ultimately cause cancer (PMID: 29038145). As a neurotoxin, D-2-hydroxyglutaric acid mediates its neurotoxicity through activation of N-methyl-D-aspartate receptors. D-2-Hydroxyglutaric acid is structurally similar to the excitatory amino acid glutamate and stimul...
Tissue accumulation of high amounts of D 2 hydroxyglutaric acid is the biochemical hallmark of the inherited neurometabolic disorder D 2 hydroxyglutaric aciduria.

同义名列表

32 个代谢物同义名

alpha-Hydroxyglutarate, disodium salt; alpha-Hydroxyglutarate, (DL)-isomer; alpha-Hydroxyglutarate, (L)-isomer; alpha-Hydroxyglutarate, (D)-isomer; delta-alpha-Hydroxyglutaric acid; (2R)-2-hydroxypentanedioic acid; (R)-2-Hydroxy-pentanedioic acid; D-α-Hydroxyglutaric acid; (R)-alpha-Hydroxyglutaric acid; 2-Hydroxy-delta-glutaric acid; delta-alpha-Hydroxyglutarate; delta-2-Hydroxyglutaric acid; (R)-2-Hydroxy-pentanedioate; (R)-a-Hydroxyglutaric acid; (R)-2-Hydroxyglutaric acid; (R)-alpha-Hydroxyglutarate; 2-Hydroxy-delta-glutarate; 2-Hydroxy-D-glutaric acid; D-a-Hydroxyglutaric acid; D-2-Hydroxyglutaric acid; (R)-Hydroxyglutaric acid; delta-2-Hydroxyglutarate; alpha-Hydroxyglutarate; (R)-a-Hydroxyglutarate; (R)-2-Hydroxyglutarate; 2-hydroxyglutaric acid; 2-Hydroxy-D-glutarate; D-2-Hydroxyglutarate; D-a-Hydroxyglutarate; (R)-Hydroxyglutarate; 2-Hydroxyglutarate; D-2-Hydroxyglutaric acid



数据库引用编号

21 个数据库交叉引用编号

分类词条

相关代谢途径

Reactome(6)

BioCyc(0)

PlantCyc(0)

代谢反应

79 个相关的代谢反应过程信息。

Reactome(71)

BioCyc(0)

WikiPathways(0)

Plant Reactome(0)

INOH(0)

PlantCyc(0)

COVID-19 Disease Map(0)

PathBank(8)

PharmGKB(0)

24 个相关的物种来源信息

在这里通过桑基图来展示出与当前的这个代谢物在我们的BioDeep知识库中具有相关联信息的其他代谢物。在这里进行关联的信息来源主要有：

  • PubMed: 来源于PubMed文献库中的文献信息，我们通过自然语言数据挖掘得到的在同一篇文献中被同时提及的相关代谢物列表，这个列表按照代谢物同时出现的文献数量降序排序，取前10个代谢物作为相关研究中关联性很高的代谢物集合展示在桑基图中。
  • NCBI Taxonomy: 通过文献数据挖掘，得到的代谢物物种来源信息关联。这个关联信息同样按照出现的次数降序排序，取前10个代谢物作为高关联度的代谢物集合展示在桑吉图上。
  • Chemical Taxonomy: 在物质分类上处于同一个分类集合中的其他代谢物
  • Chemical Reaction: 在化学反应过程中，存在为当前代谢物相关联的生化反应过程中的反应底物或者反应产物的关联代谢物信息。

点击图上的相关代谢物的名称，可以跳转到相关代谢物的信息页面。

亚细胞结构定位 关联基因列表
Cytoplasm 10 AKT1, DNMT3A, FH, FTO, HIF1A, IDH1, LDHA, MTOR, MYC, TP53
Peripheral membrane protein 1 MTOR
Endoplasmic reticulum membrane 1 MTOR
Mitochondrion membrane 1 SLC25A1
Nucleus 12 AKT1, DNMT3A, FH, FTO, HIF1A, LDHA, MTOR, MYC, SIRT3, SLC25A1, TET2, TP53
cytosol 10 AKT1, FH, FTO, GLS, HIF1A, IDH1, IDH2, LDHA, MTOR, TP53
dendrite 1 MTOR
nuclear body 1 HIF1A
phagocytic vesicle 1 MTOR
centrosome 1 TP53
nucleoplasm 9 AKT1, DNMT3A, FTO, HIF1A, MTOR, MYC, SIRT3, TET2, TP53
RNA polymerase II transcription regulator complex 1 HIF1A
Cell membrane 2 AKT1, CD8A
Cytoplasmic side 1 MTOR
lamellipodium 1 AKT1
Multi-pass membrane protein 1 SLC25A1
Golgi apparatus membrane 1 MTOR
Synapse 1 GLS
cell cortex 1 AKT1
glutamatergic synapse 1 AKT1
Golgi membrane 1 MTOR
lysosomal membrane 1 MTOR
mitochondrial inner membrane 4 ATP5ME, L2HGDH, LDHD, SLC25A1
postsynapse 1 AKT1
Cytoplasm, cytosol 2 GLS, IDH1
Lysosome 1 MTOR
plasma membrane 3 AKT1, CD8A, FTO
Membrane 7 AKT1, L2HGDH, LDHA, MTOR, MYC, SLC25A1, TP53
extracellular exosome 5 FH, IDH1, IDH2, LDHA, SLC25A1
Lysosome membrane 1 MTOR
endoplasmic reticulum 1 TP53
mitochondrion 12 ADHFE1, ATP5ME, FH, GLS, IDH1, IDH2, L2HGDH, LDHA, LDHD, SIRT3, SLC25A1, TP53
protein-containing complex 5 AKT1, HIF1A, MYC, SIRT3, TP53
intracellular membrane-bounded organelle 1 FTO
Microsome membrane 1 MTOR
TORC1 complex 1 MTOR
TORC2 complex 1 MTOR
Single-pass type I membrane protein 1 CD8A
extracellular region 2 CD8A, IDH1
Mitochondrion outer membrane 1 MTOR
mitochondrial outer membrane 1 MTOR
[Isoform 2]: Secreted 1 CD8A
Mitochondrion matrix 2 SIRT3, TP53
mitochondrial matrix 6 ADHFE1, FH, GLS, IDH2, SIRT3, TP53
transcription regulator complex 1 TP53
motile cilium 1 HIF1A
Cytoplasm, cytoskeleton, microtubule organizing center, centrosome 1 TP53
external side of plasma membrane 1 CD8A
microtubule cytoskeleton 1 AKT1
nucleolus 2 MYC, TP53
axon cytoplasm 1 HIF1A
cell-cell junction 1 AKT1
vesicle 1 AKT1
Mitochondrion inner membrane 1 SLC25A1
heterochromatin 1 DNMT3A
Cytoplasm, cytoskeleton 1 TP53
spindle 1 AKT1
Peroxisome 2 IDH1, IDH2
peroxisomal matrix 1 IDH1
Nucleus, PML body 2 MTOR, TP53
PML body 2 MTOR, TP53
Mitochondrion intermembrane space 1 AKT1
mitochondrial intermembrane space 1 AKT1
nuclear speck 2 FTO, HIF1A
receptor complex 1 CD8A
ciliary basal body 1 AKT1
chromatin 3 HIF1A, MYC, TP53
Chromosome 3 DNMT3A, FH, TET2
[Isoform 1]: Mitochondrion 1 GLS
Nucleus, nucleolus 1 MYC
site of double-strand break 2 FH, TP53
nuclear envelope 2 MTOR, MYC
Endomembrane system 1 MTOR
Nucleus, nucleoplasm 1 MYC
Nucleus speckle 2 FTO, HIF1A
euchromatin 2 DNMT3A, HIF1A
germ cell nucleus 1 TP53
replication fork 1 TP53
plasma membrane raft 1 CD8A
ficolin-1-rich granule lumen 1 IDH1
secretory granule lumen 1 IDH1
nuclear matrix 2 DNMT3A, TP53
transcription repressor complex 1 TP53
tertiary granule lumen 1 IDH1
XY body 1 DNMT3A
RNA polymerase II transcription repressor complex 1 MYC
chromosome, centromeric region 1 DNMT3A
[Isoform 1]: Nucleus 1 TP53
[Isoform 1]: Cell membrane 1 CD8A
Rough endoplasmic reticulum 1 MYC
[Isoform 3]: Mitochondrion 1 GLS
Cytoplasmic vesicle, phagosome 1 MTOR
proton-transporting ATP synthase complex 1 ATP5ME
[Glutaminase kidney isoform, mitochondrial 68 kDa chain]: Mitochondrion matrix 1 GLS
[Glutaminase kidney isoform, mitochondrial 65 kDa chain]: Mitochondrion matrix 1 GLS
oxidoreductase complex 1 LDHA
proton-transporting ATP synthase complex, coupling factor F(o) 1 ATP5ME
Myc-Max complex 1 MYC
T cell receptor complex 1 CD8A
catalytic complex 1 DNMT3A
[Isoform Mitochondrial]: Mitochondrion 1 FH
[Isoform Cytoplasmic]: Cytoplasm, cytosol 1 FH
nucleoplasmic reticulum 1 MYC


文献列表

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