Dihydroorotate dehydrogenase

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Dihydroorotate oxidase
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Dihydroorotate dehydrogenase monomer + inhibitor, Human
Identifiers
EC no. 1.3.5.2
CAS no. 9029-03-2
Databases
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ExPASy NiceZyme view
KEGG KEGG entry
MetaCyc metabolic pathway
PRIAM profile
PDB structures RCSB PDB PDBe PDBsum
Gene Ontology AmiGO / QuickGO
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PMC articles
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NCBI proteins
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Dihydroorotate dehydrogenase from E. coli
Identifiers
SymbolDHO_dh
Pfam PF01180
InterPro IPR001295
PROSITE PDOC00708
SCOP2 1dor / SCOPe / SUPFAM
OPM superfamily 56
OPM protein 1uum
CDD cd02810
Membranome 250
Available protein structures:
Pfam   structures / ECOD  
PDB RCSB PDB; PDBe; PDBj
PDBsum structure summary
Human dihydroorotate dehydrogenase
Identifiers
SymbolDHODH
NCBI gene 1723
HGNC 2867
OMIM 126064
PDB 1D3G
RefSeq NM_001361
UniProt Q02127
Other data
EC number 1.3.3.1
Locus Chr. 16 q22
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Structures Swiss-model
Domains InterPro

Dihydroorotate dehydrogenase (DHODH) is an enzyme that in humans is encoded by the DHODH gene on chromosome 16. The protein encoded by this gene catalyzes the fourth enzymatic step, the ubiquinone-mediated oxidation of dihydroorotate to orotate, in de novo pyrimidine biosynthesis. This protein is a mitochondrial protein located on the outer surface of the inner mitochondrial membrane (IMM). [1] Inhibitors of this enzyme are used to treat autoimmune diseases such as rheumatoid arthritis. [2]

Contents

Structure

DHODH can vary in cofactor content, oligomeric state, subcellular localization, and membrane association. An overall sequence alignment of these DHODH variants presents two classes of DHODHs: the cytosolic Class 1 and the membrane-bound Class 2. In Class 1 DHODH, a basic cysteine residue catalyzes the oxidation reaction, whereas in Class 2, the serine serves this catalytic function. Structurally, Class 1 DHODHs can also be divided into two subclasses, one of which forms homodimers and uses fumarate as its electron acceptor, and the other which forms heterotetramers and uses NAD+ as its electron acceptor. This second subclass contains an addition subunit (PyrK) containing an iron-sulfur cluster and a flavin adenine dinucleotide (FAD). Meanwhile, Class 2 DHODHs use coenzyme Q/ubiquinones for their oxidant. [2]

In higher eukaryotes, this class of DHODH contains an N-terminal bipartite signal comprising a cationic, amphipathic mitochondrial targeting sequence of about 30 residues and a hydrophobic transmembrane sequence. The targeting sequence is responsible for this protein's localization to the IMM, possibly from recruiting the import apparatus and mediating ΔΨ-driven transport across the inner and outer mitochondrial membranes, while the transmembrane sequence is essential for its insertion into the IMM. [2] [3] This sequence is adjacent to a pair of α-helices, α1 and α2, which are connected by a short loop. Together, this pair forms a hydrophobic funnel that is suggested to serve as the insertion site for ubiquinone, in conjunction with the FMN binding cavity at the C-terminal. [2] The two terminal domains are directly connected by an extended loop. The C-terminal domain is the larger of the two and folds into a conserved α/β-barrel structure with a core of eight parallel β-strands surrounded by eight α helices. [2] [4]

Function

Human DHODH is a ubiquitous FMN flavoprotein. In bacteria (gene pyrD), it is located on the inner side of the cytosolic membrane. In some yeasts, such as in Saccharomyces cerevisiae (gene URA1), it is a cytosolic protein, whereas, in other eukaryotes, it is found in the mitochondria. [5] It is also the only enzyme in the pyrimidine biosynthesis pathway located in the mitochondria rather than the cytosol. [4]

As an enzyme associated with the electron transport chain, DHODH links mitochondrial bioenergetics, cell proliferation, ROS production, and apoptosis in certain cell types. DHODH depletion also resulted in increased ROS production, decreased membrane potential and cell growth retardation. [4] Also, due to its role in DNA synthesis, inhibition of DHODH may provide a means to regulate transcriptional elongation. [6]

Mechanism

In mammalian species, DHODH catalyzes the fourth step in de novo pyrimidine biosynthesis, which involves the ubiquinone-mediated oxidation of dihydroorotate to orotate and the reduction of FMN to dihydroflavin mononucleotide (FMNH2):

(S)-dihydroorotate + O2 orotate + H2O2

The particular mechanism for the dehydrogenation of dihydroorotic acid by DHODH differs between the two classes of DHODH. Class 1 DHODHs follow a concerted mechanism, in which the two C–H bonds of dihydroorotic acid break in concert. Class 2 DHODHs follow a stepwise mechanism, in which the breaking of the C–H bonds precedes the equilibration of iminium into orotic acid. [2]

Inhibitors

Clinical significance

The immunomodulatory drugs teriflunomide and leflunomide have been shown to inhibit DHODH. Human DHODH has two domains: an alpha/beta-barrel domain containing the active site and an alpha-helical domain that forms the opening of a tunnel leading to the active site. Leflunomide has been shown to bind in this tunnel. [7] Leflunomide is being used for treatment of rheumatoid and psoriatic arthritis, as well as multiple sclerosis. [2] [7] Its immunosuppressive effects have been attributed to the depletion of the pyrimidine supply for T cells or to more complex interferon or interleukin-mediated pathways, but nonetheless require further research. [2]

Additionally, DHODH may play a role in retinoid N-(4-hydroxyphenyl)retinamide (4HPR)-mediated cancer suppression. Inhibition of DHODH activity with teriflunomide or expression with RNA interference resulted in reduced ROS generation in, and thus apoptosis of, transformed skin and prostate epithelial cells. [8]

Mutations in this gene have been shown to cause Miller syndrome, also known as Genee-Wiedemann syndrome, Wildervanck-Smith syndrome or post-axial acrofacial dystosis. [9] [10]

Interactions

DHODH binds to its FMN cofactor in conjunction with ubiquinone to catalyze the oxidation of dihydroorotate to orotate. [2]

Related Research Articles

<span class="mw-page-title-main">Oxidative phosphorylation</span> Metabolic pathway

Oxidative phosphorylation or electron transport-linked phosphorylation or terminal oxidation is the metabolic pathway in which cells use enzymes to oxidize nutrients, thereby releasing chemical energy in order to produce adenosine triphosphate (ATP). In eukaryotes, this takes place inside mitochondria. Almost all aerobic organisms carry out oxidative phosphorylation. This pathway is so pervasive because it releases more energy than alternative fermentation processes such as anaerobic glycolysis.

<span class="mw-page-title-main">Respiratory complex I</span> Protein complex involved in cellular respiration

Respiratory complex I, EC 7.1.1.2 is the first large protein complex of the respiratory chains of many organisms from bacteria to humans. It catalyzes the transfer of electrons from NADH to coenzyme Q10 (CoQ10) and translocates protons across the inner mitochondrial membrane in eukaryotes or the plasma membrane of bacteria.

<span class="mw-page-title-main">Flavin adenine dinucleotide</span> Redox-active coenzyme

In biochemistry, flavin adenine dinucleotide (FAD) is a redox-active coenzyme associated with various proteins, which is involved with several enzymatic reactions in metabolism. A flavoprotein is a protein that contains a flavin group, which may be in the form of FAD or flavin mononucleotide (FMN). Many flavoproteins are known: components of the succinate dehydrogenase complex, α-ketoglutarate dehydrogenase, and a component of the pyruvate dehydrogenase complex.

<span class="mw-page-title-main">Orotic acid</span> Chemical compound synthesized in the body via a mitochondrial enzyme

Orotic acid is a pyrimidinedione and a carboxylic acid. Historically, it was believed to be part of the vitamin B complex and was called vitamin B13, but it is now known that it is not a vitamin.

<span class="mw-page-title-main">Inner mitochondrial membrane</span>

The inner mitochondrial membrane (IMM) is the mitochondrial membrane which separates the mitochondrial matrix from the intermembrane space.

Pyrimidine biosynthesis occurs both in the body and through organic synthesis.

<span class="mw-page-title-main">Electron-transferring-flavoprotein dehydrogenase</span> Protein family

Electron-transferring-flavoprotein dehydrogenase is an enzyme that transfers electrons from electron-transferring flavoprotein in the mitochondrial matrix, to the ubiquinone pool in the inner mitochondrial membrane. It is part of the electron transport chain. The enzyme is found in both prokaryotes and eukaryotes and contains a flavin and FE-S cluster. In humans, it is encoded by the ETFDH gene. Deficiency in ETF dehydrogenase causes the human genetic disease multiple acyl-CoA dehydrogenase deficiency.

In enzymology, an orotate reductase (NADH) (EC 1.3.1.14) is an enzyme that catalyzes the chemical reaction

In enzymology, an orotate reductase (NADPH) (EC 1.3.1.15) is an enzyme that catalyzes the chemical reaction

<span class="mw-page-title-main">NDUFA13</span> Protein-coding gene in the species Homo sapiens

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 is an enzyme that in humans is encoded by the NDUFA13 gene. The NDUFA13 protein is a subunit of NADH dehydrogenase (ubiquinone), which is located in the mitochondrial inner membrane and is the largest of the five complexes of the electron transport chain.

<span class="mw-page-title-main">NDUFA5</span> Protein-coding gene in the species Homo sapiens

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 is an enzyme that in humans is encoded by the NDUFA5 gene. The NDUFA5 protein is a subunit of NADH dehydrogenase (ubiquinone), which is located in the mitochondrial inner membrane and is the largest of the five complexes of the electron transport chain.

<span class="mw-page-title-main">NDUFB9</span> Protein-coding gene in the species Homo sapiens

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 is an enzyme that in humans is encoded by the NDUFB9 gene. NADH dehydrogenase (ubiquinone) 1 beta subcomplex subunit 9 is an accessory subunit of the NADH dehydrogenase (ubiquinone) complex, located in the mitochondrial inner membrane. It is also known as Complex I and is the largest of the five complexes of the electron transport chain.

<span class="mw-page-title-main">NDUFA8</span> Protein-coding gene in the species Homo sapiens

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8 is an enzyme that in humans is encoded by the NDUFA8 gene. The NDUFA8 protein is a subunit of NADH dehydrogenase (ubiquinone), which is located in the mitochondrial inner membrane and is the largest of the five complexes of the electron transport chain.

<span class="mw-page-title-main">NDUFA12</span> Protein-coding gene in the species Homo sapiens

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 is an enzyme that in humans is encoded by the NDUFA12 gene. The NDUFA12 protein is a subunit of NADH dehydrogenase (ubiquinone), which is located in the mitochondrial inner membrane and is the largest of the five complexes of the electron transport chain. Mutations in subunits of NADH dehydrogenase (ubiquinone), also known as Complex I, frequently lead to complex neurodegenerative diseases such as Leigh's syndrome that result from mitochondrial complex I deficiency.

<span class="mw-page-title-main">NDUFB10</span> Protein-coding gene in the species Homo sapiens

NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 is an enzyme that in humans is encoded by the NDUFB10 gene. NADH dehydrogenase (ubiquinone) 1 beta subcomplex subunit 10 is an accessory subunit of the NADH dehydrogenase (ubiquinone) complex, located in the mitochondrial inner membrane. It is also known as Complex I and is the largest of the five complexes of the electron transport chain.

<span class="mw-page-title-main">Miller syndrome</span> Medical condition

Miller syndrome, also known as Genée–Wiedemann syndrome, Wildervanck–Smith syndrome or postaxial acrofacial dysostosis, is an extremely rare genetic condition that manifests as craniofacial, limb and eye deformities. It is caused by a mutation in the DHODH gene. The incidence of the condition is not known, and nothing is known about its pathogenesis.

<span class="mw-page-title-main">Dihydroorotate dehydrogenase (quinone)</span> Class of enzymes

Class 2 dihydroorotate dehydrogenases is an enzyme with systematic name (S)-dihydroorotate:quinone oxidoreductase. This enzyme catalyses the electron transfer from dihydroorotate to a quinone :

<span class="mw-page-title-main">NDUFB3</span> Protein-coding gene in the species Homo sapiens

NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 3, 12kDa is a protein that in humans is encoded by the NDUFB3 gene. NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 3, 12kDa is an accessory subunit of the NADH dehydrogenase (ubiquinone) complex, located in the mitochondrial inner membrane. It is also known as Complex I and is the largest of the five complexes of the electron transport chain. Mutations in this gene contribute to mitochondrial complex I deficiency.

<span class="mw-page-title-main">NDUFA11</span> Protein and coding gene in humans

NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 is an enzyme that in humans is encoded by the NDUFA11 gene. The NDUFA11 protein is a subunit of NADH dehydrogenase (ubiquinone), which is located in the mitochondrial inner membrane and is the largest of the five complexes of the electron transport chain Mutations in subunits of NADH dehydrogenase (ubiquinone), also known as Complex I, frequently lead to complex neurodegenerative diseases such as Leigh's syndrome. Mutations in this gene are associated with severe mitochondrial complex I deficiency.

<span class="mw-page-title-main">S416</span> Chemical compound

S416 (GTPL-11164) is a drug which acts as a selective inhibitor of the enzyme dihydroorotate dehydrogenase (DHODH). This enzyme is involved in the synthesis of pyrimidine nucleosides in the body, which are required for the synthesis of DNA and RNA. This is an important rate-limiting step in the replication of viruses, and so DHODH inhibitors may have applications as broad-spectrum antiviral drugs. In tests in vitro, S416 was found to have antiviral activity against a range of pathogenic RNA viruses including influenza, Zika virus, Ebola virus and SARS-CoV-2.

References

  1. ↑ "Entrez Gene: DHODH dihydroorotate dehydrogenase (quinone)".
  2. 1 2 3 4 5 6 7 8 9 Munier-Lehmann H, Vidalain PO, Tangy F, Janin YL (Apr 2013). "On dihydroorotate dehydrogenases and their inhibitors and uses". Journal of Medicinal Chemistry. 56 (8): 3148–67. doi:10.1021/jm301848w. PMID   23452331.
  3. ↑ Rawls J, Knecht W, Diekert K, Lill R, Löffler M (Apr 2000). "Requirements for the mitochondrial import and localization of dihydroorotate dehydrogenase". European Journal of Biochemistry. 267 (7): 2079–87. doi: 10.1046/j.1432-1327.2000.01213.x . PMID   10727948.
  4. 1 2 3 Fang J, Uchiumi T, Yagi M, Matsumoto S, Amamoto R, Takazaki S, et al. (5 February 2013). "Dihydro-orotate dehydrogenase is physically associated with the respiratory complex and its loss leads to mitochondrial dysfunction". Bioscience Reports. 33 (2): e00021. doi:10.1042/BSR20120097. PMC   3564035 . PMID   23216091.
  5. ↑ Nagy M, Lacroute F, Thomas D (Oct 1992). "Divergent evolution of pyrimidine biosynthesis between anaerobic and aerobic yeasts". Proceedings of the National Academy of Sciences of the United States of America. 89 (19): 8966–70. Bibcode:1992PNAS...89.8966N. doi: 10.1073/pnas.89.19.8966 . PMC   50045 . PMID   1409592.
  6. ↑ White RM, Cech J, Ratanasirintrawoot S, Lin CY, Rahl PB, Burke CJ, et al. (Mar 2011). "DHODH modulates transcriptional elongation in the neural crest and melanoma". Nature. 471 (7339): 518–22. Bibcode:2011Natur.471..518W. doi:10.1038/nature09882. PMC   3759979 . PMID   21430780.
  7. 1 2 Liu S, Neidhardt EA, Grossman TH, Ocain T, Clardy J (Jan 2000). "Structures of human dihydroorotate dehydrogenase in complex with antiproliferative agents". Structure. 8 (1): 25–33. doi: 10.1016/S0969-2126(00)00077-0 . PMID   10673429.
  8. ↑ Hail N, Chen P, Kepa JJ, Bushman LR, Shearn C (Jul 2010). "Dihydroorotate dehydrogenase is required for N-(4-hydroxyphenyl)retinamide-induced reactive oxygen species production and apoptosis". Free Radical Biology & Medicine. 49 (1): 109–16. doi:10.1016/j.freeradbiomed.2010.04.006. PMC   2875309 . PMID   20399851.
  9. ↑ Ng SB, Buckingham KJ, Lee C, Bigham AW, Tabor HK, Dent KM, et al. (Jan 2010). "Exome sequencing identifies the cause of a mendelian disorder". Nature Genetics. 42 (1): 30–5. doi:10.1038/ng.499. PMC   2847889 . PMID   19915526.
  10. ↑ Fang J, Uchiumi T, Yagi M, Matsumoto S, Amamoto R, Saito T, et al. (Dec 2012). "Protein instability and functional defects caused by mutations of dihydro-orotate dehydrogenase in Miller syndrome patients". Bioscience Reports. 32 (6): 631–9. doi:10.1042/BSR20120046. PMC   3497730 . PMID   22967083.

Further reading

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