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(-) Description

Title :  CRYSTAL STRUCTURE OF DIHYDROOROTATE DEHYDROGENASE FROM LEISHMANIA MAJOR IN COMPLEX WITH 5-AMINOOROTIC ACID
 
Authors :  M. P. Pinheiro, J. R. Rocha, J. Cheleski, C. A. Montanari, M. C. Nonato
Date :  13 Apr 10  (Deposition) - 23 Feb 11  (Release) - 23 Feb 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.96
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Dihydroorotate Dehydrogenase, Pyrd, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Cheleski, J. R. Rocha, M. P. Pinheiro, H. J. Wiggers, A. B. Da Silva, M. C. Nonato, C. A. Montanari
Novel Insights For Dihydroorotate Dehydrogenase Class 1A Inhibitors Discovery.
Eur. J. Med. Chem. V. 45 5899 2010
PubMed-ID: 20965617  |  Reference-DOI: 10.1016/J.EJMECH.2010.09.055

(-) Compounds

Molecule 1 - DIHYDROOROTATE DEHYDROGENASE
    Chains: A, B
    EC Number: 1.3.3.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: LMJF16.0530
    Organism Scientific: LEISHMANIA MAJOR
    Organism Taxid: 5664
    Strain: FRIEDLIN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 10)

Asymmetric/Biological Unit (4, 10)
No.NameCountTypeFull Name
1FMN2Ligand/IonFLAVIN MONONUCLEOTIDE
2GOL5Ligand/IonGLYCEROL
3IJZ2Ligand/Ion5-AMINO-2,6-DIOXO-1,2,3,6-TETRAHYDROPYRIMIDINE-4-CARBOXYLIC ACID
4SO41Ligand/IonSULFATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREALA A:19 , ALA A:20 , GLY A:21 , LYS A:44 , SER A:45 , TYR A:59 , ASN A:68 , MET A:70 , ASN A:128 , LYS A:165 , ILE A:194 , ASN A:195 , GLY A:222 , GLY A:223 , VAL A:226 , CYS A:249 , GLY A:250 , GLY A:251 , GLY A:272 , THR A:273 , IJZ A:314 , HOH A:337 , HOH A:341 , HOH A:393 , HOH A:470BINDING SITE FOR RESIDUE FMN A 313
02AC2SOFTWARELYS A:44 , ASN A:68 , MET A:70 , GLY A:71 , LEU A:72 , ASN A:128 , ASN A:195 , SER A:196 , FMN A:313BINDING SITE FOR RESIDUE IJZ A 314
03AC3SOFTWAREALA B:19 , ALA B:20 , GLY B:21 , LYS B:44 , SER B:45 , TYR B:59 , ASN B:68 , MET B:70 , ASN B:128 , LYS B:165 , ILE B:194 , ASN B:195 , GLY B:222 , GLY B:223 , VAL B:226 , CYS B:249 , GLY B:250 , GLY B:251 , GLY B:272 , THR B:273 , IJZ B:314 , HOH B:348 , HOH B:379 , HOH B:434BINDING SITE FOR RESIDUE FMN B 313
04AC4SOFTWARELYS B:44 , ASN B:68 , MET B:70 , GLY B:71 , LEU B:72 , ASN B:128 , ASN B:195 , SER B:196 , FMN B:313 , HOH B:363 , HOH B:457BINDING SITE FOR RESIDUE IJZ B 314
05AC5SOFTWARELEU A:231 , VAL B:202 , ILE B:203 , HOH B:444 , HOH B:534BINDING SITE FOR RESIDUE GOL B 315
06AC6SOFTWAREVAL A:202 , ILE A:203 , HOH A:438 , HOH A:492 , LEU B:231 , LEU B:260BINDING SITE FOR RESIDUE GOL A 315
07AC7SOFTWAREASP A:171 , PHE A:172 , ALA A:173 , ASN B:199 , LYS B:215BINDING SITE FOR RESIDUE GOL A 316
08AC8SOFTWAREASN A:199 , LYS A:215 , ASP B:171 , PHE B:172 , HOH B:400BINDING SITE FOR RESIDUE GOL B 316
09AC9SOFTWAREGLU A:206 , THR A:207 , GLU A:208 , GLU B:206 , THR B:207 , GLU B:208 , ARG B:310 , HOH B:487 , HOH B:522BINDING SITE FOR RESIDUE GOL A 317
10BC1SOFTWAREHIS A:160 , SER A:161 , HOH A:536 , HOH A:537BINDING SITE FOR RESIDUE SO4 A 318

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Thr A:56 -Pro A:57
2Cys A:193 -Ile A:194
3Thr B:56 -Pro B:57
4Cys B:193 -Ile B:194

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3MJY)

(-) Exons   (0, 0)

(no "Exon" information available for 3MJY)

(-) 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:306
 aligned with Q4QEW7_LEIMA | Q4QEW7 from UniProtKB/TrEMBL  Length:320

    Alignment length:314
                              1                                                                                                                                                                                                                                                                                                                       
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308    
         Q4QEW7_LEIMA     - --MSLQVNLLNNTFANPFMNAAGVMCTTTEELVAMTESASGSLVSKSCTPALREGNPTPRYQALPLGSINSMGLPNNGFDFYLAYAAEQHDYGKKPLFLSMSGLSMRENVEMCKRLAAVATEKGVILELNLSCPNVPGKPQVAYDFDAMRQCLTAVSEVYPHSFGVKMPPYFDFAHFDAAAEILNEFPKVQFITCINSIGNGLVIDAETESVVIKPKQGFGGLGGRYVLPTALANINAFYRRCPGKLIFGCGGVYTGEDAFLHVLAGASMVQVGTALQEEGPSIFERLTSELLGVMAKKRYQTLDEFRGKVRTL 312
               SCOP domains d3mjya_ A: automated matches                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee..eee...eee.......hhhhhhhhhhh....eeeeee............eeee..eeee.......hhhhhhhhhhhh.......eeeee...hhhhhhhhhhhhhhhhhhhh.eeeee..--------hhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhh...eeeeee...eeeee.ee....ee..hhhh.eeeeehhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhheeeeeehhhhhhhh.hhhhhhhhhhhhhhhhhh..hhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mjy A  -1 GSMSLQVNLLNNTFANPFMNAAGVMCTTTEELVAMTESASGSLVSKSCTPALREGNPTPRYQALPLGSINSMGLPNNGFDFYLAYAAEQHDYGKKPLFLSMSGLSMRENVEMCKRLAAVATEKGVILELNLS--------QVAYDFDAMRQCLTAVSEVYPHSFGVKMPPYFDFAHFDAAAEILNEFPKVQFITCINSIGNGLVIDAETESVVIKPKQGFGGLGGRYVLPTALANINAFYRRCPGKLIFGCGGVYTGEDAFLHVLAGASMVQVGTALQEEGPSIFERLTSELLGVMAKKRYQTLDEFRGKVRTL 312
                                     8        18        28        38        48        58        68        78        88        98       108       118       128 |       -|      148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308    
                                                                                                                                                             130      139                                                                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:306
 aligned with Q4QEW7_LEIMA | Q4QEW7 from UniProtKB/TrEMBL  Length:320

    Alignment length:314
                              1                                                                                                                                                                                                                                                                                                                       
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308    
         Q4QEW7_LEIMA     - --MSLQVNLLNNTFANPFMNAAGVMCTTTEELVAMTESASGSLVSKSCTPALREGNPTPRYQALPLGSINSMGLPNNGFDFYLAYAAEQHDYGKKPLFLSMSGLSMRENVEMCKRLAAVATEKGVILELNLSCPNVPGKPQVAYDFDAMRQCLTAVSEVYPHSFGVKMPPYFDFAHFDAAAEILNEFPKVQFITCINSIGNGLVIDAETESVVIKPKQGFGGLGGRYVLPTALANINAFYRRCPGKLIFGCGGVYTGEDAFLHVLAGASMVQVGTALQEEGPSIFERLTSELLGVMAKKRYQTLDEFRGKVRTL 312
               SCOP domains d3mjyb_ B: automated matches                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---DHO_dh-3mjyB01 B:2-294                                                                                                                                                                                                                                                                               ------------------ Pfam domains (1)
           Pfam domains (2) ---DHO_dh-3mjyB02 B:2-294                                                                                                                                                                                                                                                                               ------------------ Pfam domains (2)
         Sec.struct. author ......eee..eee...eee.......hhhhhhhhhhh....eeeeee............eeee..eeee.......hhhhhhhhhhhh.......eeeee...hhhhhhhhhhhhhhhhhhhh.eeeee..--------hhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhh....eeeeee...eeeee.ee....ee..hhhh.eeeeehhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhheeeeeehhhhhhhh.hhhhhhhhhhhhhhhhhh..hhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mjy B  -1 GSMSLQVNLLNNTFANPFMNAAGVMCTTTEELVAMTESASGSLVSKSCTPALREGNPTPRYQALPLGSINSMGLPNNGFDFYLAYAAEQHDYGKKPLFLSMSGLSMRENVEMCKRLAAVATEKGVILELNLS--------QVAYDFDAMRQCLTAVSEVYPHSFGVKMPPYFDFAHFDAAAEILNEFPKVQFITCINSIGNGLVIDAETESVVIKPKQGFGGLGGRYVLPTALANINAFYRRCPGKLIFGCGGVYTGEDAFLHVLAGASMVQVGTALQEEGPSIFERLTSELLGVMAKKRYQTLDEFRGKVRTL 312
                                     8        18        28        38        48        58        68        78        88        98       108       118       128 |       -|      148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308    
                                                                                                                                                             130      139
   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, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3MJY)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: TIM_barrel (694)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q4QEW7_LEIMA | Q4QEW7)
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:0004158    dihydroorotate oxidase activity    Catalysis of the reaction: (S)-dihydroorotate + O(2) = H(2)O(2) + orotate.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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: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:0006222    UMP biosynthetic process    The chemical reactions and pathways resulting in the formation of UMP, uridine monophosphate.
    GO:0006106    fumarate metabolic process    The chemical reactions and pathways involving fumarate, the anion of trans-1,2-ethenedicarboxylic acid, the diastereoisomer of maleate. It is a key intermediate in metabolism and is formed in the TCA cycle from succinate and converted into malate.
    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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0020015    glycosome    A membrane-bounded organelle found in organisms from the order Kinetoplastida that houses the enzymes of glycolysis.

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  1.3.3.1
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 Related Entries

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

UniProtKB/TrEMBL
        Q4QEW7_LEIMA | Q4QEW7: 3gye 3gz3 3mhu 3tjx 3tq0 3tro 4ef8 4ef9

(-) Related Entries Specified in the PDB File

3c3n DIHYDROOROTATE DEHYDROGENASE FROM TRYPANOSOMA CRUZI FROM Y STRAIN
3gye DIHYDROOROTATE DEHYDROGENASE FROM LEISHMANIA MAJOR
3mhu DIHYDROOROTATE DEHYDROGENASE FROM LEISHMANIA MAJOR IN COMPLEX WITH 5-NITROOROTIC ACID