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(-) Description

Title :  PLASMODIUM FALCIPARUM DIHYDROOROTATE DEHYDROGENASE BOUND WITH TRIAZOLOPYRIMIDINE-BASED INHIBITOR DSM1
 
Authors :  X. Deng, M. A. Phillips
Date :  06 Jul 09  (Deposition) - 28 Jul 09  (Release) - 20 Oct 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Plasmodium Falciparum, Dihydroorotate Dehydrogenase, Triazolopyrimidine, Inhibitor, Dsm1, Fad, Flavoprotein, Membrane, Mitochondrion, Mitochondrion Inner Membrane, Oxidoreductase, Pyrimidine Biosynthesis, Transit Peptide (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Deng, R. Gujjar, F. El Mazouni, W. Kaminsky, N. A. Malmquist, E. J. Goldsmith, P. K. Rathod, M. A. Phillips
Structural Plasticity Of Malaria Dihydroorotate Dehydrogenase Allows Selective Binding Of Diverse Chemical Scaffolds.
J. Biol. Chem. V. 284 26999 2009
PubMed-ID: 19640844  |  Reference-DOI: 10.1074/JBC.M109.028589
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DIHYDROOROTATE DEHYDROGENASE HOMOLOG, MITOCHONDRIAL
    Chains: A
    EC Number: 1.3.3.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B
    Expression System Strain: BL21
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 158-569 WITH 384-413 DELETED
    Gene: PFF0160C, PLASMODIUM FALCIPARUM
    Organism Scientific: PLASMODIUM FALCIPARUM 3D7
    Organism Taxid: 36329
    Synonym: DHODEHASE, DIHYDROOROTATE OXIDASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 4)

Asymmetric/Biological Unit (4, 4)
No.NameCountTypeFull Name
1FMN1Ligand/IonFLAVIN MONONUCLEOTIDE
2JZ81Ligand/Ion5-METHYL-7-(NAPHTHALEN-2-YLAMINO)-1H-[1,2,4]TRIAZOLO[1,5-A]PYRIMIDINE-3,8-DIIUM
3LDA1Ligand/IonLAURYL DIMETHYLAMINE-N-OXIDE
4ORO1Ligand/IonOROTIC ACID

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:15 , GLY A:181 , CYS A:184 , HIS A:185 , PHE A:188 , LEU A:189 , LEU A:197 , PHE A:227 , ARG A:265 , LEU A:531 , VAL A:532 , MET A:536BINDING SITE FOR RESIDUE JZ8 A 1001
2AC2SOFTWAREHOH A:11 , HOH A:13 , HOH A:20 , ALA A:224 , ALA A:225 , GLY A:226 , LYS A:229 , THR A:249 , ASN A:274 , ASN A:342 , LYS A:429 , SER A:457 , ASN A:458 , SER A:477 , GLY A:478 , LEU A:481 , SER A:505 , GLY A:506 , GLY A:507 , TYR A:528 , SER A:529 , ORO A:1003BINDING SITE FOR RESIDUE FMN A 1002
3AC3SOFTWARELYS A:229 , ASN A:274 , CYS A:276 , GLY A:277 , PHE A:278 , ASN A:342 , SER A:345 , ASN A:347 , ASN A:458 , THR A:459 , FMN A:1002BINDING SITE FOR RESIDUE ORO A 1003
4AC4SOFTWAREHOH A:2 , HOH A:39 , HOH A:47 , ASP A:180 , PRO A:261 , ILE A:263 , PHE A:264 , ARG A:265 , ASP A:266 , VAL A:267 , GLU A:268 , GLU A:375 , ASN A:381 , ASP A:382BINDING SITE FOR RESIDUE LDA A 1004

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3I65)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Gly A:248 -Thr A:249
2Lys A:260 -Pro A:261
3Ile A:456 -Ser A:457
4Ser A:505 -Gly A:506

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3I65)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DHODEHASE_1PS00911 Dihydroorotate dehydrogenase signature 1.PYRD_PLAF7243-262  1A:243-262
2DHODEHASE_2PS00912 Dihydroorotate dehydrogenase signature 2.PYRD_PLAF7502-522  1A:502-522

(-) Exons   (0, 0)

(no "Exon" information available for 3I65)

(-) 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:370
 aligned with PYRD_PLAF7 | Q08210 from UniProtKB/Swiss-Prot  Length:569

    Alignment length:408
                                   169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559        
           PYRD_PLAF7   160 SYNPEFFLYDIFLKFCLKYIDGEICHDLFLLLGKYNILPYDTSNDSIYACTNIKHLDFINPFGVAAGFDKNGVCIDSILKLGFSFIEIGTITPRGQTGNAKPRIFRDVESRSIINSCGFNNMGCDKVTENLILFRKRQEEDKLLSKHIVGVSIGKNKDTVNIVDDLKYCINKIGRYADYIAINVSSPNTPGLRDNQEAGKLKNIILSVKEEIDNLEKNNIMNDESTYNEDNKIVEKKNNFNKNNSHMMKDAKDNFLWFNTTKKKPLVFVKLAPDLNQEQKKEIADVLLETNIDGMIISNTTTQINDIKSFENKKGGVSGAKLKDISTKFICEMYNYTNKQIPIIASGGIFSGLDALEKIEAGASVCQLYSCLVFNGMKSAVQIKRELNHLLYQRGYYNLKEAIGRKHS 567
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 3i65A00 A:160-567 Aldolase class I                                                                                                                                                                                                                                                                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhheee..eee...eee.........hhhhhhh....eeeeeee............eeee....eeee.......hhhhhhhhhhhhhhhhh.hhhhh..eeeeee.......hhhhhhhhhhhhhhhhh.eeeee.....--------.hhhhhhhhhhhhhhhhhhhhhh..hhh------------------------------hhh........eeeeee....hhhhhhhhhhhhhhhh..eeee.........hhhhh....eeee..hhhhhhhhhhhhhhhh.....eee.....hhhhhhhhhhhheeeeeehhhhhhhh.hhhhhhhhhhhhhhhhh....hhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------DHODEHASE_1         -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DHODEHASE_2          --------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3i65 A 160 SYNPEFFLYDIFLKFCLKYIDGEICHDLFLLLGKYNILPYDTSNDSIYACTNIKHLDFINPFGVAAGFDKNGVCIDSILKLGFSFIEIGTITPRGQTGNAKPRIFRDVESRSIINSCGFNNMGCDKVTENLILFRKRQEEDKLLSKHIVGVSIGKNKDTVNIVDDLKYCINKIGRYADYIAINVSSPN--------EAGKLKNIILSVKEEIDNLEKNNIMNDE------------------------------FLWFNTTKKKPLVFVKLAPDLNQEQKKEIADVLLETNIDGMIISNTTTQINDIKSFENKKGGVSGAKLKDISTKFICEMYNYTNKQIPIIASGGIFSGLDALEKIEAGASVCQLYSCLVFNGMKSAVQIKRELNHLLYQRGYYNLKEAIGRKHS 567
                                   169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       | -      |359       369       379   |     -         -         -    |  419       429       439       449       459       469       479       489       499       509       519       529       539       549       559        
                                                                                                                                                                                                                     347      356                        383                            414
   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  (0, 0)

(no "SCOP Domain" information available for 3I65)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3I65)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PYRD_PLAF7 | Q08210)
molecular function
    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: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.
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: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: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: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.
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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PYRD_PLAF7 | Q08210: 1tv5 3i68 3i6r 3o8a 3sfk 4cq8 4cq9 4cqa 4orm 4rx0 5boo 5del 5fi8 5tbo

(-) Related Entries Specified in the PDB File

3i68 3i6r