Summary: Dihydroorotate dehydrogenase
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Dihydroorotate dehydrogenase Edit Wikipedia article
Dihydroorotate dehydrogenase monomer + inhibitor, Human
|PDB structures||RCSB PDB PDBe PDBsum|
|Gene Ontology||AmiGO / QuickGO|
Dihydroorotate dehydrogenase from E. coli
|SCOPe||1dor / SUPFAM|
|Human dihydroorotate dehydrogenase|
|Locus||Chr. 16 q22|
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). Inhibitors of this enzyme are used to treat autoimmune diseases such as rheumatoid arthritis.
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.
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 proteinâ€™s localization to the IMM, possibly from recruiting the import apparatus and mediating Î”Î¨-driven transport across the inner and outer mitochondrial membranes, while the transmembrane sequence is essential for its insertion into the IMM. This sequence is adjacent to a pair of Î±-helices, Î±1 and Î±2, 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. 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 Î±/Î²-barrel structure with a core of eight parallel Î²-strands surrounded by eight Î± helices.
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. It is also the only enzyme in the pyrimidine biosynthesis pathway located in the mitochondria rather than the cytosol.
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. Also, due to its role in DNA synthesis, inhibition of DHODH may provide a means to regulate transcriptional elongation.
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
Orotic acid. Note the double bond in the ring.
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 Câ€“H bonds of dihydroorotic acid break in concert. Class 2 DHODHs follow a stepwise mechanism, in which the breaking of the Câ€“H bonds precedes the equilibration of iminium into orotic acid.
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. Leflunomide is being used for treatment of rheumatoid and psoriatic arthritis, as well as multiple sclerosis. 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.
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.
DHODH binds to its FMN cofactor in conjunction with ubiquinone to catalyze the oxidation of dihydroorotate to orotate.
Model organisms have been used in the study of DHODH function. A conditional knockout mouse line called Dhodhtm1b(EUCOMM)Wtsi was generated at the Wellcome Trust Sanger Institute. Male and female animals underwent a standardized phenotypic screen to determine the effects of deletion. Additional screens performed: - In-depth immunological phenotyping
|All data available at.|
|Peripheral blood leukocytes 6 Weeks||Normal|
|Haematology 6 Weeks||Normal|
|Homozygous viability at P14||Abnormal|
|Recessive lethal study||Abnormal|
|Glucose tolerance test||Normal|
|Auditory brainstem response||Normal|
|Haematology 16 Weeks||Normal|
|Peripheral blood leukocytes 16 Weeks||Normal|
|Cytotoxic T Cell Function||Normal|
|Mesenteric Lymph Node Immunophenotyping||Normal|
|Bone Marrow Immunophenotyping||Normal|
- "Entrez Gene: DHODH dihydroorotate dehydrogenase (quinone)".
- 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): 3148â€“67. doi:10.1021/jm301848w. PMID 23452331.
- Rawls J, Knecht W, Diekert K, Lill R, LÃ¶ffler M (Apr 2000). "Requirements for the mitochondrial import and localization of dihydroorotate dehydrogenase". European Journal of Biochemistry / FEBS. 267 (7): 2079â€“87. doi:10.1046/j.1432-1327.2000.01213.x. PMID 10727948.
- Fang J, Uchiumi T, Yagi M, Matsumoto S, Amamoto R, Takazaki S, Yamaza H, Nonaka K, Kang D (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.
- 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): 8966â€“70. doi:10.1073/pnas.89.19.8966. PMC 50045. PMID 1409592.
- 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): 518â€“22. doi:10.1038/nature09882. PMC 3759979. PMID 21430780.
- 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): 25â€“33. doi:10.1016/S0969-2126(00)00077-0. PMID 10673429.
- 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): 109â€“16. doi:10.1016/j.freeradbiomed.2010.04.006. PMC 2875309. PMID 20399851.
- Ng SB, Buckingham KJ, Lee C, Bigham AW, Tabor HK, Dent KM, Huff CD, Shannon PT, Jabs EW, Nickerson DA, Shendure J, Bamshad MJ (Jan 2010). "Exome sequencing identifies the cause of a mendelian disorder". Nature Genetics. 42 (1): 30â€“5. doi:10.1038/ng.499. PMC 2847889. PMID 19915526.
- Fang J, Uchiumi T, Yagi M, Matsumoto S, Amamoto R, Saito T, Takazaki S, Kanki T, Yamaza H, Nonaka K, Kang D (Dec 2012). "Protein instability and functional defects caused by mutations of dihydro-orotate dehydrogenase in Miller syndrome patients". Bioscience Reports. 32 (6): 631â€“9. doi:10.1042/BSR20120046. PMC 3497730. PMID 22967083.
- Gerdin AK (2010). "The Sanger Mouse Genetics Programme: high throughput characterisation of knockout mice". Acta Ophthalmologica. 88: 925â€“7. doi:10.1111/j.1755-3768.2010.4142.x.
- "International Mouse Phenotyping Consortium".
- Skarnes WC, Rosen B, West AP, Koutsourakis M, Bushell W, Iyer V, Mujica AO, Thomas M, Harrow J, Cox T, Jackson D, Severin J, Biggs P, Fu J, Nefedov M, de Jong PJ, Stewart AF, Bradley A (Jun 2011). "A conditional knockout resource for the genome-wide study of mouse gene function". Nature. 474 (7351): 337â€“42. doi:10.1038/nature10163. PMC 3572410. PMID 21677750.
- Dolgin E (Jun 2011). "Mouse library set to be knockout". Nature. 474 (7351): 262â€“3. doi:10.1038/474262a. PMID 21677718.
- Collins FS, Rossant J, Wurst W (Jan 2007). "A mouse for all reasons". Cell. 128 (1): 9â€“13. doi:10.1016/j.cell.2006.12.018. PMID 17218247.
- White JK, Gerdin AK, Karp NA, Ryder E, Buljan M, Bussell JN, et al. (Jul 2013). "Genome-wide generation and systematic phenotyping of knockout mice reveals new roles for many genes". Cell. 154 (2): 452â€“64. doi:10.1016/j.cell.2013.06.022. PMC 3717207. PMID 23870131.
- "Infection and Immunity Immunophenotyping (3i) Consortium".
- Rowland P, BjÃ¶rnberg O, Nielsen FS, Jensen KF, Larsen S (Jun 1998). "The crystal structure of Lactococcus lactis dihydroorotate dehydrogenase A complexed with the enzyme reaction product throws light on its enzymatic function". Protein Science. 7 (6): 1269â€“79. doi:10.1002/pro.5560070601. PMC 2144028. PMID 9655329. Archived from the original on 2008-12-01.
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Dihydroorotate dehydrogenase Provide feedback
No Pfam abstract.
Rowland P, Bjornberg O, Nielsen FS, Jensen KF, Larsen S; , Protein Sci 1998;7:1269-1279.: The crystal structure of Lactococcus lactis dihydroorotate dehydrogenase A complexed with the enzyme reaction product throws light on its enzymatic function. PUBMED:9655329 EPMC:9655329
Internal database links
|SCOOP:||DeoC DUF561 Dus FMN_dh G3P_antiterm Glu_synthase His_biosynth HMGL-like IMPDH NanE NMO Oxidored_FMN PcrB ThiG TMP-TENI Trp_syntA|
|Similarity to PfamA using HHSearch:||FMN_dh Dus NMO|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR005720
Dihydroorotate dehydrogenase ( EC ) (DHOdehase) catalyzes the fourth step in the de novo biosynthesis of pyrimidine, the conversion of dihydroorotate into orotate. DHOdehase is a ubiquitous FAD flavoprotein. In bacteria (gene pyrD), DHOdease is located on the inner side of the cytosolic membrane. In some yeasts, such as in Saccharomyces cerevisiae (gene URA1, subfamily 2), it is a cytosolic protein while in other eukaryotes it is found in the mitochondria [ PUBMED:1409592 ].
This entry represents a domain found in the type I dihydroorotate dehydrogenases and dihydropyrimidine dehydrogenase.
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Cellular component||cytoplasm (GO:0005737)|
|Molecular function||oxidoreductase activity, acting on the CH-CH group of donors (GO:0016627)|
|Biological process||oxidation-reduction process (GO:0055114)|
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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This large superfamily of TIM barrel enzymes all contain a common phosphate binding site. The phosphate is found in a variety of cofactors and ligands such as FMN [1,2].
The clan contains the following 61 members:4HFCP_synth Ala_racemase_N ALAD Aldolase AP_endonuc_2 BtpA CdhD ComA CutC DAHP_synth_1 DAHP_synth_2 DeoC DHDPS DHO_dh DHquinase_I DUF2090 DUF4862 DUF561 DUF692 DUF993 Dus F_bP_aldolase FMN_dh G3P_antiterm GatZ_KbaZ-like Glu_syn_central Glu_synthase His_biosynth HMGL-like IGPS IMPDH KDGP_aldolase Lys-AminoMut_A MtrH NanE NAPRTase NeuB NMO OAM_alpha OMPdecase Orn_Arg_deC_N Oxidored_FMN PcrB PdxJ PRAI PRMT5_TIM Pterin_bind QRPTase_C Radical_SAM Radical_SAM_2 RhaA Ribul_P_3_epim SOR_SNZ TAL_FSA ThiC_Rad_SAM ThiG TIM TMP-TENI Trp_syntA UvdE UxuA
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
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This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.
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|Author:||Finn RD , Bateman A , Griffiths-Jones SR|
|Number in seed:||11|
|Number in full:||13604|
|Average length of the domain:||278.20 aa|
|Average identity of full alignment:||28 %|
|Average coverage of the sequence by the domain:||73.49 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||23|
|Download:||download the raw HMM for this family|
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Unmapped species names
The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.
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Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.
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The tree shows the occurrence of this domain across different species. More...
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For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.
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Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.
We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.
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For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the DHO_dh domain has been found. There are 343 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.
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