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(-) Description

Title :  CRYSTAL STRUCTURE OF LEISHMANIA MAJOR DIHYDROOROTATE DEHYDROGENASE MUTANT D171A
 
Authors :  A. L. De Souza, M. P. Pinheiro, M. C. Nonato
Date :  09 Sep 11  (Deposition) - 12 Sep 12  (Release) - 12 Sep 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.86
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Pyrd, Dhodh, Lmdhodh, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. L. De Souza, M. P. Pinheiro, M. C. Nonato
Crystal Structure Of Leishmania Major Dihydroorotate Dehydrogenase Mutant D171A
To Be Published
PubMed: search

(-) 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: 469008
    Expression System Vector Type: PLASMID
    Gene: DHODH, LMJF16.0530, LMJF_16_0530
    Mutation: YES
    Organism Scientific: LEISHMANIA MAJOR
    Organism Taxid: 347515
    Strain: FRIEDLIN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 12)

Asymmetric/Biological Unit (3, 12)
No.NameCountTypeFull Name
1FMN2Ligand/IonFLAVIN MONONUCLEOTIDE
2GOL8Ligand/IonGLYCEROL
3SO42Ligand/IonSULFATE ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREALA A:19 , ALA A:20 , GLY A:21 , LYS A:44 , SER A:45 , 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 , HOH A:339 , HOH A:342 , HOH A:358BINDING SITE FOR RESIDUE FMN A 321
02AC2SOFTWAREHIS A:160 , SER A:161 , HOH A:427BINDING SITE FOR RESIDUE SO4 A 322
03AC3SOFTWAREPRO A:159 , LYS A:187BINDING SITE FOR RESIDUE SO4 A 323
04AC4SOFTWAREPHE A:172 , ALA A:173 , PRO B:138 , ASN B:199 , LYS B:215BINDING SITE FOR RESIDUE GOL A 324
05AC5SOFTWAREARG A:239 , THR A:311BINDING SITE FOR RESIDUE GOL A 325
06AC6SOFTWAREARG A:298 , GOL A:327BINDING SITE FOR RESIDUE GOL A 326
07AC7SOFTWAREILE A:203 , GOL A:326 , HOH A:377 , HOH A:497 , LEU B:231BINDING SITE FOR RESIDUE GOL A 327
08AC8SOFTWAREALA B:19 , ALA B:20 , GLY B:21 , LYS B:44 , SER B:45 , 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 , HOH B:333 , HOH B:367 , HOH B:409BINDING SITE FOR RESIDUE FMN B 321
09AC9SOFTWAREASN A:199 , LYS A:215 , HOH A:537 , ALA B:171 , PHE B:172 , ALA B:173 , HOH B:510BINDING SITE FOR RESIDUE GOL B 322
10BC1SOFTWAREGOL B:324BINDING SITE FOR RESIDUE GOL B 323
11BC2SOFTWARELEU A:227 , HOH A:408 , HOH A:429 , VAL B:202 , ILE B:203 , GOL B:323 , HOH B:481BINDING SITE FOR RESIDUE GOL B 324
12BC3SOFTWAREGLN A:216 , ARG B:239 , THR B:311 , HOH B:450BINDING SITE FOR RESIDUE GOL B 325

(-) SS Bonds  (0, 0)

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

(-) 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 3TRO)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3TRO)

(-) 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:307
 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 d3troa_ 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.hhhhhhhhhhhhhhhhh...hhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tro A  -1 GSMSLQVNLLNNTFANPFMNAAGVMCTTTEELVAMTESASGSLVSKSCTPALREGNPTPRYQALPLGSINSMGLPNNGFDFYLAYAAEQHDYGKKPLFLSMSGLSMRENVEMCKRLAAVATEKGVILELNLS-------PQVAYDFDAMRQCLTAVSEVYPHSFGVKMPPYFAFAHFDAAAEILNEFPKVQFITCINSIGNGLVIDAETESVVIKPKQGFGGLGGRYVLPTALANINAFYRRCPGKLIFGCGGVYTGEDAFLHVLAGASMVQVGTALQEEGPSIFERLTSELLGVMAKKRYQTLDEFRGKVRTL 312
                                     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    
                                                                                                                                                             130     138                                                                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:307
 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 d3trob_ B: 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....hhhhhhhhhhhhh....eeeeee...eeeee.ee....ee..hhhh.eeeeehhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhheeeeeehhhhhhhh.hhhhhhhhhhhhhhhhhh..hhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tro B  -1 GSMSLQVNLLNNTFANPFMNAAGVMCTTTEELVAMTESASGSLVSKSCTPALREGNPTPRYQALPLGSINSMGLPNNGFDFYLAYAAEQHDYGKKPLFLSMSGLSMRENVEMCKRLAAVATEKGVILELNLS-------PQVAYDFDAMRQCLTAVSEVYPHSFGVKMPPYFAFAHFDAAAEILNEFPKVQFITCINSIGNGLVIDAETESVVIKPKQGFGGLGGRYVLPTALANINAFYRRCPGKLIFGCGGVYTGEDAFLHVLAGASMVQVGTALQEEGPSIFERLTSELLGVMAKKRYQTLDEFRGKVRTL 312
                                     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    
                                                                                                                                                             130     138
   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 3TRO)

(-) Pfam Domains  (0, 0)

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

(-) 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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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

3gye DIDYDROOROTATE DEHYDROGENASE FROM LEISHMANIA MAJOR
3gz3 LEISHMANIA MAJOR DIHYDROOROTATE DEHYDROGENASE IN COMPLEX WITH OROTATE
3mhu CRYSTAL STRUCTURE OF DIHYDROOROTATE DEHYDROGENASE FROM LEISHMANIA MAJOR IN COMPLEX WITH 5-NITROOROTIC ACID
3mjy CRYSTAL STRUCTURE OF DIHYDROOROTATE DEHYDROGENASE FROM LEISHMANIA MAJOR IN COMPLEX WITH 5-AMINOOROTIC ACID
3snq LEISHMANIA MAJOR DIHYDROOROTATE DEHYDROGENASE IN COMPLEX WITH 5-AMINO-2-(1H-PYRROL-1-YL)BENZONITRILE
3snu LEISHMANIA MAJOR DIHYDROOROTATE DEHYDROGENASE IN COMPLEX WITH 4-(1H-PYRROL-1-YL)ANILINE