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(-) Description

Title :  CRYSTAL STRUCTURE OF OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE COMPLEXED WITH OROTIDINE 5'-MONOPHOSPHATE FROM P.FALCIPARUM
 
Authors :  K. Tokuoka, T. Inoue
Date :  26 Sep 07  (Deposition) - 04 Dec 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.65
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Orotidine 5'-Monophosphate Decarboxylase, Plasmodium Falciparum, Orotidine 5'-Monophosphate, Lyase, Pyrimidine Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Tokuoka, Y. Kusakari, S. R. Krungkrai, H. Matsumura, Y. Kai, J. Krungkrai, T. Horii, T. Inoue
Structural Basis For The Decarboxylation Of Orotidine 5'-Monophosphate (Omp) By Plasmodium Falciparum Omp Decarboxylase
J. Biochem. (Tokyo) V. 143 69 2008
PubMed-ID: 17981823  |  Reference-DOI: 10.1093/JB/MVM193
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - OROTIDINE 5'-PHOSPHATE DECARBOXYLASE
    Chains: A, B
    EC Number: 4.1.1.23
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTRCHIS-TOPO
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Common: MALARIA PARASITE P. FALCIPARUM
    Organism Scientific: PLASMODIUM FALCIPARUM
    Organism Taxid: 5833

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1OMP2Ligand/IonOROTIDINE-5'-MONOPHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:23 , LYS A:102 , ASN A:104 , ASP A:136 , LYS A:138 , THR A:194 , THR A:195 , PRO A:264 , GLY A:267 , ALA A:268 , GLN A:269 , ASN A:291 , GLY A:293 , ARG A:294 , HOH A:501 , HOH A:506 , HOH A:564 , ASP B:141BINDING SITE FOR RESIDUE OMP A 500
2AC2SOFTWAREILE A:142 , ASP B:23 , LYS B:102 , ASN B:104 , ASP B:136 , THR B:194 , THR B:195 , VAL B:240 , PRO B:264 , GLY B:267 , GLN B:269 , ASN B:291 , GLY B:293 , ARG B:294 , HOH B:647 , HOH B:648 , HOH B:651 , HOH B:652BINDING SITE FOR RESIDUE OMP B 600

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2ZA1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2ZA1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2ZA1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2ZA1)

(-) Exons   (0, 0)

(no "Exon" information available for 2ZA1)

(-) 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:318
 aligned with Q8T6J6_PLAFA | Q8T6J6 from UniProtKB/TrEMBL  Length:323

    Alignment length:318
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310        
         Q8T6J6_PLAFA     1 MGFKVKLEKRRNAINTCLCIGLDPDEKDIENFMKNEKENNYNNIKKNLKEKYINNVSIKKDILLKAPDNIIREEKSEEFFYFFNHFCFYIINETNKYALTFKMNFAFYIPYGSVGIDVLKNVFDYLYELNIPTILDMKINDIGNTVKNYRKFIFEYLKSDSCTVNIYMGTNMLKDICYDEEKNKYYSAFVLVKTTNPDSAIFQKNLSLDNKQAYVIMAQEALNMSSYLNLEQNNEFIGFVVGANSYDEMNYIRTYFPNCYILSPGIGAQNGDLHKTLTNGYHKSYEKILINIGRAITKNPYPQKAAQMYYDQINAILK 318
               SCOP domains d2za1a_ A: automated matches                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhh............hhhhhhhhhhhhhhhhhhhhhh.eeeee.hhh....hhhhhhhhhhhhhhhhhh..eeeeeee.....hhhhhhhhhhh.....eeee......hhhhhhh.........eeeeeee..................hhhhhhhhhhhhhhhhh........eeeee...hhhhhhhhhhhh....eeee..........hhhhhh...hhh.eeeeehhhhhh..hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2za1 A   1 MGFKVKLEKRRNAINTCLCIGLDPDEKDIENFMKNEKENNYNNIKKNLKEKYINNVSIKKDILLKAPDNIIREEKSEEFFYFFNHFCFYIINETNKYALTFKMNFAFYIPYGSVGIDVLKNVFDYLYELNIPTILDMKINDIGNTVKNYRKFIFEYLKSDSCTVNIYMGTNMLKDICYDEEKNKYYSAFVLVKTTNPDSAIFQKNLSLDNKQAYVIMAQEALNMSSYLNLEQNNEFIGFVVGANSYDEMNYIRTYFPNCYILSPGIGAQNGDLHKTLTNGYHKSYEKILINIGRAITKNPYPQKAAQMYYDQINAILK 318
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310        


Chain B from PDB  Type:PROTEIN  Length:315
 aligned with Q8T6J6_PLAFA | Q8T6J6 from UniProtKB/TrEMBL  Length:323

    Alignment length:318
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310        
         Q8T6J6_PLAFA     1 MGFKVKLEKRRNAINTCLCIGLDPDEKDIENFMKNEKENNYNNIKKNLKEKYINNVSIKKDILLKAPDNIIREEKSEEFFYFFNHFCFYIINETNKYALTFKMNFAFYIPYGSVGIDVLKNVFDYLYELNIPTILDMKINDIGNTVKNYRKFIFEYLKSDSCTVNIYMGTNMLKDICYDEEKNKYYSAFVLVKTTNPDSAIFQKNLSLDNKQAYVIMAQEALNMSSYLNLEQNNEFIGFVVGANSYDEMNYIRTYFPNCYILSPGIGAQNGDLHKTLTNGYHKSYEKILINIGRAITKNPYPQKAAQMYYDQINAILK 318
               SCOP domains d2za1b_ B: automated matches                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) ---------------OMPdecase-2za1B01 B:16-309                                                                                                                                                                                                                                                                            --------- Pfam domains (1)
           Pfam domains (2) ---------------OMPdecase-2za1B02 B:16-309                                                                                                                                                                                                                                                                            --------- Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh......---.....hhhhhhhhhhhhhhhhhhhh.eeeee.hhhh...hhhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhh.....eeee.hhhhhhhhhhhhee...eee.eeeeeee.............ee..eehhhhhhhhhhhhhhh...hhhhh.eeeee...hhhhhhhhhhhh....eeee...................hhh.eeeeehhhhhh....hhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2za1 B   1 MGFKVKLEKRRNAINTCLCIGLDPDEKDIENFMKNEKENNYNNIKKNLKEKYINNVSIKKDILLKAPDNI---EKSEEFFYFFNHFCFYIINETNKYALTFKMNFAFYIPYGSVGIDVLKNVFDYLYELNIPTILDMKINDIGNTVKNYRKFIFEYLKSDSCTVNIYMGTNMLKDICYDEEKNKYYSAFVLVKTTNPDSAIFQKNLSLDNKQAYVIMAQEALNMSSYLNLEQNNEFIGFVVGANSYDEMNYIRTYFPNCYILSPGIGAQNGDLHKTLTNGYHKSYEKILINIGRAITKNPYPQKAAQMYYDQINAILK 318
                                    10        20        30        40        50        60        70   |    80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310        
                                                                                                70  74
   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 2ZA1)

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q8T6J6_PLAFA | Q8T6J6)
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:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0004590    orotidine-5'-phosphate decarboxylase activity    Catalysis of the reaction: H(+) + orotidine 5'-phosphate = CO(2) + UMP.
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:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        Q8T6J6_PLAFA | Q8T6J6: 2qaf 3bar 3bpw
UniProtKB/TrEMBL
        Q8T6J6_PLAFA | Q8T6J6: 2za2 2za3 2zcg 3vi2

(-) Related Entries Specified in the PDB File

2f84 THE SAME PROTEIN COMPLEXED WITH PO4 ION
2za2 THE SAME PROTEIN, APO-FORM
2za3 THE SAME PROTEIN COMPLEXED WITH 2'-DEOXYURIDINE 5'- MONOPHOSPHATE