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(-) Description

Title :  CRYSTAL STRUCTURE OF OROTIDINE 5'-PHOSPHATE DECARBOXYLASE FROM PLASMODIUM FALCIPARUM
 
Authors :  Y. Liu, W. Lau, J. Lew, M. Amani, R. Hui, E. F. Pai, Structural Genomics Consortium (Sgc)
Date :  11 Jun 07  (Deposition) - 19 Jun 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Plasmodium Falciparum, Orotidine-5'-Monophosphate Decarboxylase, Structural Genomics, Structural Genomics Consortium, Sgc, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Liu, W. Lau, J. Lew, M. Amani, R. Hui, E. F. Pai
Crystal Structure Of Orotidine 5'-Phosphate Decarboxylase From Plasmodium Falciparum.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - OROTIDINE-MONOPHOSPHATE-DECARBOXYLASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A-LIC
    Expression System Strain: BL21-RIL(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PF10_0225
    Organism Scientific: PLASMODIUM FALCIPARUM
    Organism Taxid: 36329
    Strain: 3D7
    Synonym: OROTIDINE 5'-PHOSPHATE DECARBOXYLASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1PO41Ligand/IonPHOSPHATE ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1PO42Ligand/IonPHOSPHATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:267 , ILE A:292 , GLY A:293 , ARG A:294BINDING SITE FOR RESIDUE PO4 A 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Q8L)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2Q8L)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Q8L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Q8L)

(-) Exons   (0, 0)

(no "Exon" information available for 2Q8L)

(-) Sequences/Alignments

Asymmetric 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:314
 aligned with Q8IJH3_PLAF7 | Q8IJH3 from UniProtKB/TrEMBL  Length:323

    Alignment length:323
                                    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       320   
         Q8IJH3_PLAF7     1 MGFKVKLEKRRNAINTCLCIGLDPDEKDIENFMKNEKENNYNNIKKNLKEKYINNVSIKKDILLKAPDNIIREEKSEEFFYFFNHFCFYIINETNKYALTFKMNFAFYIPYGSVGIDVLKNVFDYLYELNIPTILDMKINDIGNTVKNYRKFIFEYLKSDSCTVNIYMGTNMLKDICYDEEKNKYYSAFVLVKTTNPDSAIFQKNLSLDNKQAYVIMAQEALNMSSYLNLEQNNEFIGFVVGANSYDEMNYIRTYFPNCYILSPGIGAQNGDLHKTLTNGYHKSYEKILINIGRAITKNPYPQKAAQMYYDQINAILKQNMES 323
               SCOP domains d2q8la_ A: Protozoan orotidine monophosphate decarboxylase                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhh....hhhhhhhhh.........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.eeeee.hhhh..hhhhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhh.....eeee.....hhhhhhhhee....ee.eeeee....hhhhhhh.-------.hhhhhhhhhhhhhhhhh.hhhhh..eeee....hhhhhhhhhhhh....eee....--..hhhhhhhhhh..hhh.eeeeehhhhhh..hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q8l A   1 MGFKVKLEKRRNAINTCLCIGLDPDEKDIENFMKNEKENNYNNIKKNLKEKYINNVSIKKDILLKAPDNIIREEKSEEFFYFFNHFCFYIINETNKYALTFKMNFAFYIPYGSVGIDVLKNVFDYLYELNIPTILDMKINDIGNTVKNYRKFIFEYLKSDSCTVNIYMGTNMLKDICYDEEKNKYYSAFVLVKTTNPDSAIFQ-------KQAYVIMAQEALNMSSYLNLEQNNEFIGFVVGANSYDEMNYIRTYFPNCYILSPGIG--NGDLHKTLTNGYHKSYEKILINIGRAITKNPYPQKAAQMYYDQINAILKQNMES 323
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200  |      -|      220       230       240       250       260      |270       280       290       300       310       320   
                                                                                                                                                                                                                                    203     211                                                     267  |                                                     
                                                                                                                                                                                                                                                                                                       270
   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2Q8L)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2Q8L)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q8IJH3_PLAF7 | Q8IJH3)
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:0004590    orotidine-5'-phosphate decarboxylase activity    Catalysis of the reaction: H(+) + orotidine 5'-phosphate = CO(2) + UMP.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
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/TrEMBL
        Q8IJH3_PLAF7 | Q8IJH3: 2f84 2q8z 2qaf 3bar 3bpw 3mwa 3n2m 3n34 3n3m 3s9y

(-) Related Entries Specified in the PDB File

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