Summary: Dihydroorotate dehydrogenase

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Wikipedia: Dihydroorotate dehydrogenase
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This is the Wikipedia entry entitled "Dihydroorotate dehydrogenase". More...

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Dihydroorotate dehydrogenase Edit Wikipedia article

Dihydroorotate oxidase

Identifiers

Databases

PDB structures

AmiGO / EGO

Search
PMC	articles
PubMed	articles
NCBI	proteins

Dihydroorotate dehydrogenase from E. coli

Identifiers

Symbol

DHO_dh

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

Human dihydroorotate dehydrogenase
Identifiers
Symbol	DHODH
Entrez	1723
HUGO	2867
OMIM	126064
PDB	1D3G
RefSeq	NM_001361
UniProt	Q02127
Other data
EC number	1.3.3.1
Locus	Chr. 16 q22

Dihydroorotate dehydrogenase (EC 1.3.3.1) is an enzyme that catalyzes the fourth step in the de novo biosynthesis of pyrimidine. It converts dihydroorotate to orotate:

(S)-dihydroorotate + O₂ $\rightleftharpoons$ orotate + H₂O₂

4,5-Dihydroorotic acid
Orotic acid. Note the double bond in the ring.

Human dihydroorotate dehydrogenase 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.^[1]

[edit] Human proteins containing this domain

DHODH; DPYD;

[edit] Clinical significance

The anti-inflammatory drug leflunomide has 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.^[2] Leflunomide is being used for treatment of rheumatoid and psoriatic arthritis.

Mutations in this gene have been shown to cause Miller syndrome ^[3] also known as Genee-Wiedemann syndrome, Wildervanck-Smith syndrome or post axial acrofacial dystosis (POADS).

[edit] References

^ Lacroute F, Thomas D, Nagy M (1992). "Divergent evolution of pyrimidine biosynthesis between anaerobic and aerobic yeasts". Proc. Natl. Acad. Sci. U.S.A. 89 (19): 8966–70. doi:10.1073/pnas.89.19.8966. PMC 50045. PMID 1409592. //www.ncbi.nlm.nih.gov/pmc/articles/PMC50045/.
^ Liu S, Neidhardt EA, Grossman TH, Ocain T, Clardy J (January 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.
^ Ng SB, Buckingham KJ,Lee C, Bigham AW, Tabor HK, Dent KM, Huff CD, Shannon PT, Jabs EW, Nickerson DA, Shendure J, Bamshad MJ (December 2009). "Exome Sequencing identifies the cause of a mendelian disorder". Nature Genetics 42 (1): 30–5. doi:10.1038/ng.499. PMC 2847889. PMID 19915526. //www.ncbi.nlm.nih.gov/pmc/articles/PMC2847889/.

[edit] Further reading

Rowland P, Björnberg O, Nielsen FS, Jensen KF, Larsen S (June 1998). "The crystal structure of Lactococcus lactis dihydroorotate dehydrogenase A complexed with the enzyme reaction product throws light on its enzymatic function". Protein Sci. 7 (6): 1269–79. doi:10.1002/pro.5560070601. PMC 2144028. PMID 9655329. http://www.proteinscience.org/cgi/content/abstract/7/6/1269.

[edit] External links

dihydroorotate dehydrogenase at the US National Library of Medicine Medical Subject Headings (MeSH)

Oxidoreductases: CH-CH oxidoreductases (EC 1.3)

1.3.1: NAD/NADP acceptor

1.3.3: Oxygen acceptor

1.3.5: Quinone

Succinate dehydrogenase
- SDHA
- SDHB
- SDHC
- SDHD

1.3.99: Other acceptors

B
enzm
1.1
- 2
- 3
- 4
- 5
- 6
- 7
- 8
- 10
- 11
- 13
- 14
- 15-18
2.1
- 2
- 3
- 4
- 5
- 6
- 7
- 8
2.7.10
2.7.11-12
3.1
- - 3.1.3.48
- 2
- 3
- 4
  - 3.4.21
- 5
- 6
- 7
- 22
- 23
- 24
4.1
- 2
- 3
- 4
- 5
- 6
5.1
- 2
- 3
- 4
- 99
6.1-3
- 4
- 5-6

Metabolism: amino acid metabolism · nucleotide enzymes

Purine metabolism

Anabolism	R5P->IMP: Ribose-phosphate diphosphokinase · Amidophosphoribosyltransferase · Phosphoribosylglycinamide formyltransferase · AIR synthetase (FGAM cyclase) · Phosphoribosylaminoimidazole carboxylase · Phosphoribosylaminoimidazolesuccinocarboxamide synthase · IMP synthase IMP->AMP: Adenylosuccinate synthase · Adenylosuccinate lyase · reverse (AMP deaminase) IMP->GMP: IMP dehydrogenase · GMP synthase · reverse (GMP reductase)

Nucleotide salvage	Hypoxanthine-guanine phosphoribosyltransferase · Adenine phosphoribosyltransferase

Catabolism	Adenosine deaminase · Purine nucleoside phosphorylase · Guanine deaminase · Xanthine oxidase · Urate oxidase

Pyrimidine metabolism

Anabolism	CAD (Carbamoyl phosphate synthase II, Aspartate carbamoyltransferase, Dihydroorotase) Dihydroorotate dehydrogenase · Orotidine 5'-phosphate decarboxylase/Uridine monophosphate synthetase CTP synthase

Catabolism	Dihydropyrimidine dehydrogenase · Dihydropyrimidinase/DPYS · Beta-ureidopropionase/UPB1

Deoxyribonucleotides

Ribonucleotide reductase · Nucleoside-diphosphate kinase · DCMP deaminase · Thymidylate synthase · Dihydrofolate reductase

M: MET

mt, k, c/g/r/p/y/i, f/h/s/l/o/e, a/u, n, m

k, cgrp/y/i, f/h/s/l/o/e, au, n, m, epon

m (A16/C10), i (k, c/g/r/p/y/i, f/h/s/o/e, a/u, n, m)

v t e Mitochondrial proteins

Outer membrane	fatty acid degradation (Carnitine palmitoyltransferase I, Long fatty acyl CoA synthetase) tryptophan metabolism (Kynureninase) monoamine neurotransmitter metabolism (Monoamine oxidase)

Intermembrane space	Adenylate kinase - Creatine kinase

Inner membrane	oxidative phosphorylation (Coenzyme Q - cytochrome c reductase, Cytochrome c, NADH dehydrogenase, Succinate dehydrogenase) pyrimidine metabolism (Dihydroorotate dehydrogenase) mitochondrial shuttle (Malate-aspartate shuttle, Glycerol phosphate shuttle) other (Glutamate aspartate transporter, Glycerol-3-phosphate dehydrogenase, ATP synthase, Carnitine palmitoyltransferase II, Uncoupling protein)

Matrix	citric acid cycle (Citrate synthase, Aconitase, Isocitrate dehydrogenase, Oxoglutarate dehydrogenase, Succinyl coenzyme A synthetase, Fumarase, Malate dehydrogenase) anaplerotic reactions (Aspartate transaminase, Glutamate dehydrogenase, Pyruvate dehydrogenase complex) urea cycle (Carbamoyl phosphate synthetase I, Ornithine transcarbamylase, N-Acetylglutamate synthase) alcohol metabolism (ALDH2) PMPCB

Other/to be sorted	steroidogenesis (Cholesterol side-chain cleavage enzyme, Steroid 11-beta-hydroxylase, Aldosterone synthase), Frataxin Mitochondrial membrane transport protein (Mitochondrial permeability transition pore, Mitochondrial carrier)

Mitochondrial DNA	Complex I (MT-ND1, MT-ND2, MT-ND3, MT-ND4, MT-ND4L, MT-ND5, MT-ND6) - Complex III (MT-CYB) - Complex IV (MT-CO1, MT-CO2, MT-CO3) ATP synthase (MT-ATP6, MT-ATP8) tRNA (MT-TA, MT-TC, MT-TD, MT-TE, MT-TF, MT-TG, MT-TH, MT-TI, MT-TK, MT-TL1, MT-TL2, MT-TM, MT-TN, MT-TP, MT-TQ, MT-TR, MT-TS1, MT-TS2, MT-TT, MT-TV, MT-TW, MT-TY)

see also mitochondrial diseases B strc: edmb (perx), skel (ctrs), epit, cili, mito, nucl (chro)

This article incorporates text from the public domain Pfam and InterPro IPR001295

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Dihydroorotate dehydrogenase Provide feedback

No Pfam abstract.

Literature references

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

Similarity to PfamA using HHSearch:

NMO Dus

External database links

HOMSTRAD:	DHOdehase
PANDIT:	PF01180
PROSITE:	PDOC00708
Pseudofam:	PF01180
SCOP:	1dor
SYSTERS:	DHO_dh

This tab holds annotation information from the InterPro database.

InterPro entry IPR012135

Dihydroorotate dehydrogenase (DHOD), also known as dihydroorotate oxidase, catalyses the fourth step in de novo pyrimidine biosynthesis, the stereospecific oxidation of (S)-dihydroorotate to orotate, which is the only redox reaction in this pathway. DHODs can be divided into two mains classes: class 1 cytosolic enzymes found primarily in Gram-positive bacteria, and class 2 membrane-associated enzymes found primarily in eukaryotic mitochondria and Gram-negative bacteria [PUBMED:9405053].

The class 1 DHODs can be further divided into subclasses 1A and 1B, which differ in their structural organisation and use of electron acceptors. The 1A enzyme is a homodimer of two PyrD subunits where each subunit forms a TIM barrel fold with a bound FMN cofactor located near the top of the barrel [PUBMED:9655329]. Fumarate is the natural electron acceptor for this enzyme. The 1B enzyme, in contrast is a heterotetramer composed of a central, FMN-containing, PyrD homodimer resembling the 1A homodimer, and two additional PyrK subunits which contain FAD and a 2Fe-2S cluster [PUBMED:11188687]. These additional groups allow the enzyme to use NAD(+) as its natural electron acceptor.

The class 2 membrane-associated enzymes are monomers which have the FMN-containing TIM barrel domain found in the class 1 PyrD subunit, and an additional N-terminal alpha helical domain [PUBMED:10673429, PUBMED:12220493]. These enzymes use respiratory quinones as the physiological electron acceptor.

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Molecular function	dihydroorotate dehydrogenase activity (GO:0004152)
Biological process	UMP biosynthetic process (GO:0006222)
Biological process	oxidation-reduction process (GO:0055114)

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan TIM_barrel (CL0036), which contains the following 57 members:

Ala_racemase_N ALAD Aldolase AP_endonuc_2 BtpA CdhD CutC DAHP_synth_1 DAHP_synth_2 DeoC DHDPS DHO_dh DHquinase_I DUF1341 DUF2090 DUF556 DUF561 DUF692 DUF993 Dus F_bP_aldolase FMN_dh G3P_antiterm Glu_syn_central Glu_synthase His_biosynth HMGL-like IGPS IMPDH iPGM_N MtrH NanE NAPRTase NeuB NMO OMPdecase Orn_Arg_deC_N Oxidored_FMN PcrB PdxJ PhosphMutase PRAI Pterin_bind QRPTase_C Racemase_4 RhaA Ribul_P_3_epim SOR_SNZ Tagatose_6_P_K ThiG TIM TIM-br_sig_trns TMP-TENI Transaldolase Trp_syntA UvdE UxuA

Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

There are various ways to view or download the sequence alignments that we store. We provide several sequence viewers and a plain-text Stockholm-format file for download.

Alignment types

We make a range of alignments for each Pfam-A family:

seed: the curated alignment from which the HMM for the family is built
full: the alignment generated by searching the sequence database using the HMM
RP15/RP35/RP55/RP75: Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
NCBI: alignment generated by searching the NCBI sequence database using the family HMM
meta: alignment generated by searching the metagenomics sequence database using the family HMM

Viewing

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Pfam viewer: an HTML-based viewer that uses DAS to retrieve alignment fragments on request

Reformatting

You can download (or view in your browser) a text representation of a Pfam alignment in various formats:

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You can also change the order in which sequences are listed in the alignment, change how insertions are represented, alter the characters that are used to represent gaps in sequences and, finally, choose whether to download the alignment or to view it in your browser directly.

Downloading

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

	Seed (12)	Full (6787)	Representative proteomes				NCBI (6540)	Meta (4232)
	Seed (12)	Full (6787)	RP15 (544)	RP35 (1054)	RP55 (1421)	RP75 (1697)	NCBI (6540)	Meta (4232)
Jalview	View	View	View	View	View	View	View	View
HTML	View		View	View	View	View
PP/heatmap	₁		View	View	View	View
Pfam viewer	View	View

¹Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: available, not generated, — not available.

Format an alignment

	Seed (12)	Full (6787)	Representative proteomes				NCBI (6540)	Meta (4232)
	Seed (12)	Full (6787)	RP15 (544)	RP35 (1054)	RP55 (1421)	RP75 (1697)	NCBI (6540)	Meta (4232)
Alignment:
Format:
Order:	Tree Alphabetical
Sequence:	Inserts lower case All upper case
Gaps:
Download/view:	Download View

Download options

We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

	Seed (12)	Full (6787)	Representative proteomes				NCBI (6540)	Meta (4232)
	Seed (12)	Full (6787)	RP15 (544)	RP35 (1054)	RP55 (1421)	RP75 (1697)	NCBI (6540)	Meta (4232)
Raw Stockholm	Download	Download	Download	Download	Download	Download	Download	Download
Gzipped	Download	Download	Download	Download	Download	Download	Download	Download

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

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Trees

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.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation

Seed source:

Prosite

Previous IDs:

DHOdehase;

Type:

Domain

Author:

Finn RD, Bateman A, Griffiths-Jones SR

Number in seed:

12

Number in full:

6787

Average length of the domain:

282.50 aa

Average identity of full alignment:

29 %

Average coverage of the sequence by the domain:

80.42 %

HMM information

HMM build commands:

build method: hmmbuild -o /dev/null HMM SEED

search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq

Model details:

Parameter	Sequence	Domain
Gathering cut-off	20.3	20.3
Trusted cut-off	20.3	20.3
Noise cut-off	20.2	20.2

Model length:

295

Family (HMM) version:

16

Download:

download the raw HMM for this family

Species distribution

Sunburst
Tree

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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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How the sunburst is generated

The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.

In order to reduce the complexity of the representation, we reduce the number of taxonomic levels that we show. We consider only the following eight major taxonomic levels:

superkingdom
kingdom
phylum
class
order
family
genus
species

Colouring and labels

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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.

So that these nodes are not simply omitted from the sunburst tree, we group them together in a separate branch (or segment of the sunburst tree). Since we cannot determine the lineage for these unmapped species, we show all levels between the superkingdom and the species as "uncategorised".

Sub-species

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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Unfortunately we have found that there are problems viewing the interactive tree when the it becomes larger than a certain limit. Furthermore, we have found that Internet Explorer can become unresponsive when viewing some trees, regardless of their size. We therefore show a text representation of the species tree when the size is above a certain limit or if you are using Internet Explorer to view the site.

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Interactive tree

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.

We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.

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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Interactions

There are 6 interactions for this family. More...

DHO_dh Fer4 Pyr_redox Pyr_redox_2 DHODB_Fe-S_bind FAD_binding_6

Structures

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 118 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 seqence.

Loading structure mapping...

Archea	Eukaryota
Bacteria	Other sequences
Viruses	Unclassified
Viroids	Unclassified sequence

Family: DHO_dh (PF01180)

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Summary: Dihydroorotate dehydrogenase

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Dihydroorotate dehydrogenase Edit Wikipedia article

Contents

[edit] Human proteins containing this domain

[edit] Clinical significance

[edit] References

[edit] Further reading

[edit] External links

Dihydroorotate dehydrogenase Provide feedback

Literature references

Internal database links

External database links

InterPro entry IPR012135

Gene Ontology

Domain organisation

Pfam Clan

Alignments

Alignment types

Viewing

Reformatting

Downloading

View options

Format an alignment

Download options

External links

HMM logo

Trees

Curation and family details

Curation

HMM information

Species distribution

Sunburst controls

Weight segments by...

Change the size of the sunburst

Colour assignments

Selections

Currently selected:

How the sunburst is generated

Colouring and labels

Anomalies in the taxonomy tree

Missing taxonomic levels

Unmapped species names

Sub-species

Too many species/sequences

Tree controls

Annotation

Download tree

Selected sequences

Species trees

Interactive tree

Interactions

Structures