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Protein

Dihydroorotate dehydrogenase (fumarate)

Gene

pyr4

Organism
Trypanosoma cruzi (strain CL Brener)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the conversion of dihydroorotate to orotate with fumarate as the electron acceptor. Molecular oxygen can replace fumarate in vitro.

Catalytic activityi

(S)-dihydroorotate + fumarate = orotate + succinate.

Cofactori

FMN1 PublicationNote: Binds 1 FMN per subunit.1 Publication

Kineticsi

  1. KM=57.3 µM for dihydroorotate1 Publication
  2. KM=62.2 µM for fumarate1 Publication

    pH dependencei

    Optimum pH is 7.1 Publication

    Temperature dependencei

    Optimum temperature is 37 degrees Celsius.1 Publication

    Pathwayi: UMP biosynthesis via de novo pathway

    This protein is involved in the pathway UMP biosynthesis via de novo pathway, which is part of Pyrimidine metabolism.
    View all proteins of this organism that are known to be involved in the pathway UMP biosynthesis via de novo pathway and in Pyrimidine metabolism.

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Binding sitei21FMN; via carbonyl oxygen1 Publication1
    Binding sitei45Substrate1
    Binding sitei129FMN1 Publication1
    Binding sitei129Substrate1
    Active sitei132NucleophileBy similarity1
    Binding sitei134Substrate1
    Binding sitei166FMN1 Publication1
    Binding sitei195FMN; via carbonyl oxygen1 Publication1
    Binding sitei224FMN; via amide nitrogen1 Publication1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Nucleotide bindingi45 – 46FMN1 Publication2
    Nucleotide bindingi251 – 252FMN1 Publication2
    Nucleotide bindingi273 – 274FMN1 Publication2

    GO - Molecular functioni

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Biological processi

    Pyrimidine biosynthesis

    Keywords - Ligandi

    Flavoprotein, FMN

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-14470.
    BRENDAi1.3.5.2. 6524.
    1.3.98.1. 6524.
    UniPathwayiUPA00070.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Dihydroorotate dehydrogenase (fumarate) (EC:1.3.98.1)
    Short name:
    DHOD
    Short name:
    DHODase
    Short name:
    DHOdehase
    Alternative name(s):
    Dihydroorotate oxidase
    Gene namesi
    Name:pyr4
    Synonyms:tcdhod2
    ORF Names:Tc00.1047053508375.50
    OrganismiTrypanosoma cruzi (strain CL Brener)
    Taxonomic identifieri353153 [NCBI]
    Taxonomic lineageiEukaryotaEuglenozoaKinetoplastidaTrypanosomatidaeTrypanosomaSchizotrypanum
    Proteomesi
    • UP000002296 Componenti: Unassembled WGS sequence

    Subcellular locationi

    GO - Cellular componenti

    Complete GO annotation...

    Keywords - Cellular componenti

    Cytoplasm

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00004095581 – 314Dihydroorotate dehydrogenase (fumarate)Add BLAST314

    Proteomic databases

    PaxDbiQ4D3W2.

    Interactioni

    Subunit structurei

    Homodimer.1 Publication

    Protein-protein interaction databases

    STRINGi353153.XP_809064.1.

    Structurei

    Secondary structure

    1314
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi6 – 8Combined sources3
    Beta strandi11 – 19Combined sources9
    Helixi28 – 36Combined sources9
    Beta strandi40 – 43Combined sources4
    Beta strandi60 – 63Combined sources4
    Beta strandi66 – 69Combined sources4
    Helixi78 – 87Combined sources10
    Turni91 – 93Combined sources3
    Beta strandi96 – 100Combined sources5
    Helixi105 – 122Combined sources18
    Beta strandi125 – 129Combined sources5
    Helixi141 – 143Combined sources3
    Helixi145 – 159Combined sources15
    Beta strandi163 – 167Combined sources5
    Helixi173 – 184Combined sources12
    Beta strandi189 – 194Combined sources6
    Beta strandi198 – 202Combined sources5
    Turni206 – 209Combined sources4
    Beta strandi210 – 212Combined sources3
    Helixi215 – 218Combined sources4
    Beta strandi219 – 224Combined sources6
    Helixi225 – 227Combined sources3
    Helixi228 – 241Combined sources14
    Beta strandi245 – 252Combined sources8
    Helixi256 – 265Combined sources10
    Beta strandi268 – 272Combined sources5
    Helixi274 – 279Combined sources6
    Helixi283 – 298Combined sources16
    Turni304 – 308Combined sources5

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    2DJLX-ray1.38A/B1-314[»]
    2DJXX-ray1.58A/B1-314[»]
    2E68X-ray1.38A/B1-314[»]
    2E6AX-ray1.64A/B1-314[»]
    2E6DX-ray1.94A/B1-314[»]
    2E6FX-ray1.26A/B1-314[»]
    3C3NX-ray2.20A/B/C/D3-314[»]
    3W1AX-ray1.42A/B2-314[»]
    3W1LX-ray1.70A/B2-314[»]
    3W1MX-ray1.90A/B2-314[»]
    3W1NX-ray2.40A/B2-314[»]
    3W1PX-ray2.00A/B2-314[»]
    3W1QX-ray1.85A/B2-314[»]
    3W1RX-ray1.58A/B2-314[»]
    3W1TX-ray1.68A/B2-314[»]
    3W1UX-ray1.85A/B2-314[»]
    3W1XX-ray1.45A/B2-314[»]
    3W22X-ray1.98A/B2-314[»]
    3W23X-ray1.48A/B2-314[»]
    3W2JX-ray1.42A/B2-314[»]
    3W2KX-ray1.54A/B2-314[»]
    3W2LX-ray1.64A/B2-314[»]
    3W2MX-ray1.58A/B2-314[»]
    3W2NX-ray1.96A/B2-314[»]
    3W2UX-ray2.25A/B2-314[»]
    3W3OX-ray1.96A/B2-314[»]
    3W6YX-ray2.68A/B2-314[»]
    3W70X-ray2.60A/B2-314[»]
    3W71X-ray1.68A/B2-314[»]
    3W72X-ray1.55A/B2-314[»]
    3W73X-ray1.78A/B2-314[»]
    3W74X-ray1.90A/B2-314[»]
    3W75X-ray1.47A/B2-314[»]
    3W76X-ray1.58A/B2-314[»]
    3W7CX-ray1.75A/B2-314[»]
    3W7DX-ray1.52A/B2-314[»]
    3W7EX-ray1.56A/B2-314[»]
    3W7GX-ray1.55A/B2-314[»]
    3W7HX-ray1.67A/B2-314[»]
    3W7IX-ray1.69A/B2-314[»]
    3W7JX-ray1.58A/B2-314[»]
    3W7KX-ray1.61A/B2-314[»]
    3W7LX-ray1.88A/B2-314[»]
    3W7MX-ray2.40A/B2-314[»]
    3W7NX-ray2.39A/B2-314[»]
    3W7OX-ray1.68A/B2-314[»]
    3W7PX-ray1.70A/B2-314[»]
    3W7QX-ray1.83A/B2-314[»]
    3W83X-ray2.80A/B2-314[»]
    3W84X-ray1.93A/B2-314[»]
    3W85X-ray2.00A/B2-314[»]
    3W86X-ray1.50A/B2-314[»]
    3W87X-ray1.43A/B2-314[»]
    3W88X-ray1.40A/B2-314[»]
    4JD4X-ray1.51A/B2-314[»]
    4JDBX-ray1.82A/B2-314[»]
    5E93X-ray1.41A/B2-314[»]
    5EA9X-ray1.71A/B2-314[»]
    ProteinModelPortaliQ4D3W2.
    SMRiQ4D3W2.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ4D3W2.

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni69 – 73Substrate binding5
    Regioni196 – 197Substrate binding2

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiKOG1436. Eukaryota.
    COG0167. LUCA.
    KOiK00226.

    Family and domain databases

    CDDicd04741. DHOD_1A_like. 1 hit.
    Gene3Di3.20.20.70. 1 hit.
    InterProiIPR013785. Aldolase_TIM.
    IPR033886. DHOD_1A.
    IPR005720. Dihydroorotate_DH.
    IPR012135. Dihydroorotate_DH_1_2.
    [Graphical view]
    PfamiPF01180. DHO_dh. 1 hit.
    [Graphical view]
    PIRSFiPIRSF000164. DHO_oxidase. 1 hit.
    TIGRFAMsiTIGR01037. pyrD_sub1_fam. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    Q4D3W2-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MMCLKLNLLD HVFANPFMNA AGVLCSTEED LRCMTASSSG ALVSKSCTSA
    60 70 80 90 100
    PRDGNPEPRY MAFPLGSINS MGLPNLGFDF YLKYASDLHD YSKKPLFLSI
    110 120 130 140 150
    SGLSVEENVA MVRRLAPVAQ EKGVLLELNL SCPNVPGKPQ VAYDFEAMRT
    160 170 180 190 200
    YLQQVSLAYG LPFGVKMPPY FDIAHFDTAA AVLNEFPLVK FVTCVNSVGN
    210 220 230 240 250
    GLVIDAESES VVIKPKQGFG GLGGKYILPT ALANVNAFYR RCPDKLVFGC
    260 270 280 290 300
    GGVYSGEDAF LHILAGASMV QVGTALQEEG PGIFTRLEDE LLEIMARKGY
    310
    RTLEEFRGRV KTIE
    Length:314
    Mass (Da):34,167
    Last modified:September 13, 2005 - v1
    Checksum:i86917A54E3CD11FD
    GO

    Experimental Info

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Sequence conflicti121E → G in BAA74526 (PubMed:16020725).Curated1
    Sequence conflicti121E → G in BAA31360 (PubMed:16020725).Curated1
    Sequence conflicti141V → G in BAA74526 (PubMed:16020725).Curated1
    Sequence conflicti141V → G in BAA31360 (PubMed:16020725).Curated1

    Natural variant

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Natural varianti2M → T in allele DHOD3. 1
    Natural varianti3C → R in alleles DHOD2 and DHOD3. 1
    Natural varianti63F → V in allele DHOD2. 1
    Natural varianti86S → I in alleles DHOD2 and DHOD3. 1
    Natural varianti98L → V in allele DHOD3. 1
    Natural varianti222L → I in alleles DHOD2 and DHOD3. 1
    Natural varianti285T → R in allele DHOD3. 1
    Natural varianti301R → K in allele DHOD2. 1

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AAHK01001070 Genomic DNA. Translation: EAN87213.1.
    AB010286 Genomic DNA. Translation: BAA31360.1.
    AB017765 Genomic DNA. Translation: BAA74526.1.
    AB212956 Genomic DNA. Translation: BAE48283.1.
    PIRiT30523.
    RefSeqiXP_809064.1. XM_803971.1.

    Genome annotation databases

    EnsemblProtistsiEAN87213; EAN87213; Tc00.1047053508375.50.
    GeneIDi3539620.
    KEGGitcr:508375.50.

    Keywords - Coding sequence diversityi

    Polymorphism

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AAHK01001070 Genomic DNA. Translation: EAN87213.1.
    AB010286 Genomic DNA. Translation: BAA31360.1.
    AB017765 Genomic DNA. Translation: BAA74526.1.
    AB212956 Genomic DNA. Translation: BAE48283.1.
    PIRiT30523.
    RefSeqiXP_809064.1. XM_803971.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    2DJLX-ray1.38A/B1-314[»]
    2DJXX-ray1.58A/B1-314[»]
    2E68X-ray1.38A/B1-314[»]
    2E6AX-ray1.64A/B1-314[»]
    2E6DX-ray1.94A/B1-314[»]
    2E6FX-ray1.26A/B1-314[»]
    3C3NX-ray2.20A/B/C/D3-314[»]
    3W1AX-ray1.42A/B2-314[»]
    3W1LX-ray1.70A/B2-314[»]
    3W1MX-ray1.90A/B2-314[»]
    3W1NX-ray2.40A/B2-314[»]
    3W1PX-ray2.00A/B2-314[»]
    3W1QX-ray1.85A/B2-314[»]
    3W1RX-ray1.58A/B2-314[»]
    3W1TX-ray1.68A/B2-314[»]
    3W1UX-ray1.85A/B2-314[»]
    3W1XX-ray1.45A/B2-314[»]
    3W22X-ray1.98A/B2-314[»]
    3W23X-ray1.48A/B2-314[»]
    3W2JX-ray1.42A/B2-314[»]
    3W2KX-ray1.54A/B2-314[»]
    3W2LX-ray1.64A/B2-314[»]
    3W2MX-ray1.58A/B2-314[»]
    3W2NX-ray1.96A/B2-314[»]
    3W2UX-ray2.25A/B2-314[»]
    3W3OX-ray1.96A/B2-314[»]
    3W6YX-ray2.68A/B2-314[»]
    3W70X-ray2.60A/B2-314[»]
    3W71X-ray1.68A/B2-314[»]
    3W72X-ray1.55A/B2-314[»]
    3W73X-ray1.78A/B2-314[»]
    3W74X-ray1.90A/B2-314[»]
    3W75X-ray1.47A/B2-314[»]
    3W76X-ray1.58A/B2-314[»]
    3W7CX-ray1.75A/B2-314[»]
    3W7DX-ray1.52A/B2-314[»]
    3W7EX-ray1.56A/B2-314[»]
    3W7GX-ray1.55A/B2-314[»]
    3W7HX-ray1.67A/B2-314[»]
    3W7IX-ray1.69A/B2-314[»]
    3W7JX-ray1.58A/B2-314[»]
    3W7KX-ray1.61A/B2-314[»]
    3W7LX-ray1.88A/B2-314[»]
    3W7MX-ray2.40A/B2-314[»]
    3W7NX-ray2.39A/B2-314[»]
    3W7OX-ray1.68A/B2-314[»]
    3W7PX-ray1.70A/B2-314[»]
    3W7QX-ray1.83A/B2-314[»]
    3W83X-ray2.80A/B2-314[»]
    3W84X-ray1.93A/B2-314[»]
    3W85X-ray2.00A/B2-314[»]
    3W86X-ray1.50A/B2-314[»]
    3W87X-ray1.43A/B2-314[»]
    3W88X-ray1.40A/B2-314[»]
    4JD4X-ray1.51A/B2-314[»]
    4JDBX-ray1.82A/B2-314[»]
    5E93X-ray1.41A/B2-314[»]
    5EA9X-ray1.71A/B2-314[»]
    ProteinModelPortaliQ4D3W2.
    SMRiQ4D3W2.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi353153.XP_809064.1.

    Proteomic databases

    PaxDbiQ4D3W2.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblProtistsiEAN87213; EAN87213; Tc00.1047053508375.50.
    GeneIDi3539620.
    KEGGitcr:508375.50.

    Phylogenomic databases

    eggNOGiKOG1436. Eukaryota.
    COG0167. LUCA.
    KOiK00226.

    Enzyme and pathway databases

    UniPathwayiUPA00070.
    BioCyciMetaCyc:MONOMER-14470.
    BRENDAi1.3.5.2. 6524.
    1.3.98.1. 6524.

    Miscellaneous databases

    EvolutionaryTraceiQ4D3W2.

    Family and domain databases

    CDDicd04741. DHOD_1A_like. 1 hit.
    Gene3Di3.20.20.70. 1 hit.
    InterProiIPR013785. Aldolase_TIM.
    IPR033886. DHOD_1A.
    IPR005720. Dihydroorotate_DH.
    IPR012135. Dihydroorotate_DH_1_2.
    [Graphical view]
    PfamiPF01180. DHO_dh. 1 hit.
    [Graphical view]
    PIRSFiPIRSF000164. DHO_oxidase. 1 hit.
    TIGRFAMsiTIGR01037. pyrD_sub1_fam. 1 hit.
    ProtoNetiSearch...

    Entry informationi

    Entry nameiPYRD_TRYCC
    AccessioniPrimary (citable) accession number: Q4D3W2
    Secondary accession number(s): O76140
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: May 31, 2011
    Last sequence update: September 13, 2005
    Last modified: November 30, 2016
    This is version 82 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. SIMILARITY comments
      Index of protein domains and families

    Similar proteinsi

    Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
    100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
    90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
    50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.