3O8A - JenaLib

Title :   CRYSTAL STRUCTURE OF PLASMODIUM FALCIPARUM DIHYDROOROTATE DEHYDROGENASE BOUND WITH NOVEL INHIBITOR GENZ667348

Authors :   X. Deng, M. L. Booker, M. A. Phillips

Date :   02 Aug 10 (Deposition) - 18 Aug 10 (Release) - 12 Jan 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym./Biol. Unit : A

Keywords :   Alpha Beta Fold, Dihydroorotate Dehydrogenase, Oxidoreductase, Pyrimidine Biosynthesis, Genz667348, Fad, Flavoprotein, Mitochondrion Inner Membrane (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. L. Booker, C. M. Bastos, M. L. Kramer, R. H. Barker, R. Skerlj, A. B. Sidhu, X. Deng, C. Celatka, J. F. Cortese, J. E. Guerrero Bravo, K. N. Crespo Llado, A. E. Serrano, I. Angulo-Barturen, M. B. Jimenez-Diaz, S. Viera, H. Garuti, S. Wittlin, P. Papastogiannidis, J. W. Lin, C. J. Janse, S. M. Khan, M. Duraisingh, B. Coleman, E. J. Goldsmith, M. A. Phillips, B. Munoz, D. F. Wirth, J. D. Klinger, R. Wiegand, E. Sybertz
Novel Inhibitors Of Plasmodium Falciparum Dihydroorotate Dehydrogenase With Anti-Malarial Activity In The Mouse Model.
J. Biol. Chem. V. 285 33054 2010
PubMed-ID: 20702404 | Reference-DOI: 10.1074/JBC.M110.162081

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (5, 5)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 2)

Exons (0, 0)

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:375
 aligned with PYRD_PLAF7 | Q08210 from UniProtKB/Swiss-Prot  Length:569

    Alignment length:405
                                   170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560     
           PYRD_PLAF7   161 YNPEFFLYDIFLKFCLKYIDGEICHDLFLLLGKYNILPYDTSNDSIYACTNIKHLDFINPFGVAAGFDKNGVCIDSILKLGFSFIEIGTITPRGQTGNAKPRIFRDVESRSIINSCGFNNMGCDKVTENLILFRKRQEEDKLLSKHIVGVSIGKNKDTVNIVDDLKYCINKIGRYADYIAINVSSPNTPGLRDNQEAGKLKNIILSVKEEIDNLEKNNIMNDESTYNEDNKIVEKKNNFNKNNSHMMKDAKDNFLWFNTTKKKPLVFVKLAPDLNQEQKKEIADVLLETNIDGMIISNTTTQINDIKSFENKKGGVSGAKLKDISTKFICEMYNYTNKQIPIIASGGIFSGLDALEKIEAGASVCQLYSCLVFNGMKSAVQIKRELNHLLYQRGYYNLKEAIGRK 565
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------DHO_dh-3o8aA01 A:207-550                                                                                                                                                                                                                                                                                                                                --------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...............eee..eee...eee.........hhhhhhh....eeeeeee............eeee....eeee.......hhhhhhhhhhhhhhhhhhh......eeeeee.......hhhhhhhhhhhhhhhhh.eeeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhh..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
                 3o8a A 161 YNPEFFLYDIFLKFCLKYIDGEICHDLFLLLGKYNILPYDTSNDSIYACTNIKHLDFINPFGVAAGFDKNGVCIDSILKLGFSFIEIGTITPRGQTGNAKPRIFRDVESRSIINSCGFNNMGCDKVTENLILFRKRQEEDKLLSKHIVGVSIGKNKDTVNIVDDLKYCINKIGRYADYIAINVSSPNTPGLRDNQEAGKLKNIILSVKEEIDNLEKNNIMNDE------------------------------FLWFNTTKKKPLVFVKLAPDLNQEQKKEIADVLLETNIDGMIISNTTTQINDIKSFENKKGGVSGAKLKDISTKFICEMYNYTNKQIPIIASGGIFSGLDALEKIEAGASVCQLYSCLVFNGMKSAVQIKRELNHLLYQRGYYNLKEAIGRK 565
                                   170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380  |      -         -         -   |   420       430       440       450       460       470       480       490       500       510       520       530       540       550       560     
                                                                                                                                                                                                                                                        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)

CATH Domains (0, 0)

Pfam Domains (1, 1)

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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	Cis Peptide Bonds
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		Ile A:456 - Ser A:457	[ RasMol ]
		Lys A:260 - Pro A:261	[ RasMol ]
		Pro A:349 - Gly A:350	[ RasMol ]
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