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(-) Description

Title :  RAT DIHYDROOROTATE DEHYDROGENASE (DHOD)IN COMPLEX WITH BREQUINAR
 
Authors :  M. Hansen, J. Le Nours, E. Johansson, T. Antal, A. Ullrich, M. Loffler, S. Larsen
Date :  08 Jan 04  (Deposition) - 01 Apr 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.44
Chains :  Asym./Biol. Unit :  A
Keywords :  Dihydroorotate Dehydrogenase, Brequinar, Atovaquone, Nucleotide Metabolism, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Hansen, J. Le Nours, E. Johansson, T. Antal, A. Ullrich, M. Loffler, S. Larsen
Inhibitor Binding In A Class 2 Dihydroorotate Dehydrogenase Causes Variations In The Membrane-Associated N-Terminal Domain
Protein Sci. V. 13 1031 2004
PubMed-ID: 15044733  |  Reference-DOI: 10.1110/PS.03533004

(-) Compounds

Molecule 1 - DIHYDROOROTATE DEHYDROGENASE
    ChainsA
    EC Number1.3.99.11
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism CommonBLACK RAT, ROOF RAT
    Organism ScientificRATTUS RATTUS
    Organism Taxid10117
    SynonymMITOCHONDRIAL PRECURSOR, DIHYDROOROTATE OXIDASE, DHODEHASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 5)

Asymmetric/Biological Unit (5, 5)
No.NameCountTypeFull Name
1BRF1Ligand/Ion6-FLUORO-2-(2'-FLUORO-1,1'-BIPHENYL-4-YL)-3-METHYLQUINOLINE-4-CARBOXYLIC ACID
2FMN1Ligand/IonFLAVIN MONONUCLEOTIDE
3NA1Ligand/IonSODIUM ION
4NI1Ligand/IonNICKEL (II) ION
5ORO1Ligand/IonOROTIC ACID

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:203 , PRO A:204 , ALA A:206 , THR A:247 , ARG A:248BINDING SITE FOR RESIDUE NI A1400
2AC2SOFTWARELEU A:42 , MET A:43 , GLN A:47 , PRO A:52 , ALA A:55 , HIS A:56 , ALA A:59 , VAL A:134 , ARG A:136 , TYR A:356 , ILE A:360 , PRO A:364BINDING SITE FOR RESIDUE BRF A1397
3AC3SOFTWAREALA A:95 , ALA A:96 , GLY A:97 , LYS A:100 , GLY A:119 , SER A:120 , ASN A:145 , ASN A:181 , ASN A:212 , LYS A:255 , THR A:283 , ASN A:284 , SER A:305 , GLY A:306 , VAL A:333 , GLY A:334 , GLY A:335 , LEU A:355 , TYR A:356 , THR A:357 , ORO A:1399 , HOH A:2025 , HOH A:2034 , HOH A:2041BINDING SITE FOR RESIDUE FMN A1398
4AC4SOFTWARELYS A:100 , ASN A:145 , TYR A:147 , GLY A:148 , PHE A:149 , ASN A:212 , SER A:215 , ASN A:284 , THR A:285 , FMN A:1398BINDING SITE FOR RESIDUE ORO A1399

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1UUO)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Arg A:131 -Pro A:132
2Val A:282 -Thr A:283

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1UUO)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DHODEHASE_1PS00911 Dihydroorotate dehydrogenase signature 1.PYRD_RAT113-132  1A:114-133
2DHODEHASE_2PS00912 Dihydroorotate dehydrogenase signature 2.PYRD_RAT329-349  1A:330-350

(-) Exons   (0, 0)

(no "Exon" information available for 1UUO)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:351
 aligned with PYRD_RAT | Q63707 from UniProtKB/Swiss-Prot  Length:395

    Alignment length:363
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392   
             PYRD_RAT    33 DDHFYAEYLMPGLQRLLDPESAHRLAVRVTSLGLLPRATFQDSDMLEVKVLGHKFRNPVGIAAGFDKNGEAVDGLYKLGFGFVEVGSVTPQPQEGNPRPRVFRLPEDQAVINRYGFNSHGLSVVEHRLRARQQKQAQLTADGLPLGINLGKNKTSEDAAADYAEGVRTLGPLADYLVVNVSSPNTAGLRSLQGKTELRHLLSKVLQERDALKGTRKPAVLVKIAPDLTAQDKEDIASVARELGIDGLIVTNTTVSRPVGLQGALRSETGGLSGKPLRDLSTQTIREMYALTQGRIPIIGVGGVSSGQDALEKIQAGASLVQLYTALIFLGPPVVVRVKRELEALLKERGFTTVTDAIGADHRR 395
               SCOP domains d1uuoa_ A: Dihydroorotate dehydrogen    ase                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 1uuoA00 A:34-396 Aldolase class I                                                                                                                                                                                                                                                                                                                                           CATH domains
               Pfam domains ------------------------------------    ----DHO_dh-1uuoA01 A:78-378                                                                                                                                                                                                                                                                                      ------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....----.......eee..eee...eee.........hhhhhhhh...eeeeeee............eeeehhh.eeee.......hhhhhhhhhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhhh.eeeee....--------.hhhhhhhhhhhhhhhhhh.......eeeee.....hhhhhhhhhhhhhhhh..eeee....................eeee..hhhhhhhhhhhhhhhh.....eeee....hhhhhhhhhhhh..eeeehhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------DHODEHASE_1         ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DHODEHASE_2          ---------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1uuo A  34 DDHFYAEYLMPGLQRLLDPESAHRLAVRVTSLGLLP----QDSDMLEVKVLGHKFRNPVGIAAGFDKNGEAVDGLYKLGFGFVEVGSVTPQPQEGNPRPRVFRLPEDQAVINRYGFNSHGLSVVEHRLRARQQKQAQLTADGLPLGINLGKNKTSEDAAADYAEGVRTLGPLADYLVVNVSSP--------QGKTELRHLLSKVLQERDALKGTRKPAVLVKIAPDLTAQDKEDIASVARELGIDGLIVTNTTVSRPVGLQGALRSETGGLSGKPLRDLSTQTIREMYALTQGRIPIIGVGGVSSGQDALEKIQAGASLVQLYTALIFLGPPVVVRVKRELEALLKERGFTTVTDAIGADHRR 396
                                    43        53        63     |   -|       83        93       103       113       123       133       143       153       163       173       183       193       203       213  |      - |     233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393   
                                                              69   74                                                                                                                                           216      225                                                                                                                                                                           

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (27, 27)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PYRD_RAT | Q63707)
molecular function
    GO:0010181    FMN binding    Interacting selectively and non-covalently with flavin mono nucleotide. Flavin mono nucleotide (FMN) is the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0004152    dihydroorotate dehydrogenase activity    Catalysis of the reaction: (S)-dihydroorotate + A = AH(2) + orotate.
    GO:0008144    drug binding    Interacting selectively and non-covalently with a drug, any naturally occurring or synthetic substance, other than a nutrient, that, when administered or applied to an organism, affects the structure or functioning of the organism; in particular, any such substance used in the diagnosis, prevention, or treatment of disease.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0016627    oxidoreductase activity, acting on the CH-CH group of donors    Catalysis of an oxidation-reduction (redox) reaction in which a CH-CH group acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
    GO:0048039    ubiquinone binding    Interacting selectively and non-covalently with ubiquinone, a quinone derivative with a tail of isoprene units.
biological process
    GO:0044205    'de novo' UMP biosynthetic process    The chemical reactions and pathways resulting in the formation of UMP, uridine monophosphate, starting with the synthesis of (S)-dihydroorotate from bicarbonate; UMP biosynthesis may either occur via reduction by quinone, NAD(+) or oxygen.
    GO:0006207    'de novo' pyrimidine nucleobase biosynthetic process    The chemical reactions and pathways resulting in the formation of pyrimidine nucleobases, 1,3-diazine, organic nitrogenous bases, beginning with the synthesis of a pyrimidine ring from simpler precursors.
    GO:0007565    female pregnancy    The set of physiological processes that allow an embryo or foetus to develop within the body of a female animal. It covers the time from fertilization of a female ovum by a male spermatozoon until birth.
    GO:0007595    lactation    The regulated release of milk from the mammary glands and the period of time that a mother lactates to feed her young.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0043065    positive regulation of apoptotic process    Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
    GO:0006221    pyrimidine nucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of a pyrimidine nucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
    GO:0090140    regulation of mitochondrial fission    Any process that modulates the rate, frequency or extent of mitochondrial fission. Mitochondrial fission is the division of a mitochondrion within a cell to form two or more separate mitochondrial compartments.
    GO:1903576    response to L-arginine    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a L-arginine stimulus.
    GO:0031000    response to caffeine    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a caffeine stimulus. Caffeine is an alkaloid found in numerous plant species, where it acts as a natural pesticide that paralyzes and kills certain insects feeding upon them.
    GO:0042493    response to drug    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
    GO:0014070    response to organic cyclic compound    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic cyclic compound stimulus.
    GO:0042594    response to starvation    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a starvation stimulus, deprivation of nourishment.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005743    mitochondrial inner membrane    The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    GO:0043025    neuronal cell body    The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        PYRD_RAT | Q637071uum 4ori

(-) Related Entries Specified in the PDB File

1uum RAT DIHYDROOROTATE DEHYDROGENASE (DHOD)IN COMPLEX WITH ATOVAQUONE