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(-) Description

Title :  CRYSTAL STRUCTURE OF PLASMODIUM FALCIPARUM OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE COVALENTLY MODIFIED BY 2-PRIME-FLUORO-6-IODO-UMP
 
Authors :  Y. Liu, L. P. Kotra, E. F. Pai
Date :  05 May 10  (Deposition) - 06 Apr 11  (Release) - 15 Jun 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Crystal Structure, Plasmodium Falciparum, Orotidine 5'-Monophosphate Decarboxylase, Covalently, 2-Prime-Fluoro-6-Iodo-Ump, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Liu, L. P. Kotra, E. F. Pai
Crystal Structure Of Plasmodium Falciparum Orotidine 5'-Monophosphate Decarboxylase Covalently Modified By 2-Prime-Fluoro-6-Iodo-Ump
To Be Published
PubMed: search

(-) 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: PET28A-LIC
    Expression System Strain: BL21-RIL(DE23)
    Expression System Taxid: 469008
    Expression System Vector Type: PLSMID
    Gene: GI|9310996, PF10_0225
    Organism Scientific: PLASMODIUM FALCIPARUM 3D7
    Organism Taxid: 36329
    Strain: 3D7

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
2PO41Ligand/IonPHOSPHATE ION
3UFT2Ligand/Ion2'-DEOXY-2'-FLUOROURIDINE 5'-(DIHYDROGEN PHOSPHATE)

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
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 , GLN A:269 , ASN A:291 , GLY A:293 , ARG A:294 , HOH A:337 , HOH A:347 , HOH A:361 , HOH A:374 , HOH A:399 , ASP B:141 , ILE B:142 , THR B:145BINDING SITE FOR RESIDUE UFT A 1000
2AC2SOFTWAREASP A:141 , ILE A:142 , THR A:145 , ASP B:23 , LYS B:102 , ASN B:104 , ASP B:136 , LYS B:138 , THR B:194 , THR B:195 , PRO B:264 , GLN B:269 , ASN B:291 , GLY B:293 , ARG B:294 , HOH B:329 , HOH B:335 , HOH B:343 , HOH B:348 , HOH B:356BINDING SITE FOR RESIDUE UFT B 1000
3AC3SOFTWAREASN A:299 , PRO A:300 , MET A:308 , GLN A:312BINDING SITE FOR RESIDUE PEG A 2000
4AC4SOFTWARELYS B:147 , ARG B:150 , ASP B:179 , GLU B:180 , GLU B:181 , HOH B:475BINDING SITE FOR RESIDUE PO4 B 3000

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3MWA)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3MWA)

(-) 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:330
 aligned with Q8IJH3_PLAF7 | Q8IJH3 from UniProtKB/TrEMBL  Length:323

    Alignment length:330
                                   1                                                                                                                                                                                                                                                                                                                                  
                                   | 3        13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323
         Q8IJH3_PLAF7     - -------MGFKVKLEKRRNAINTCLCIGLDPDEKDIENFMKNEKENNYNNIKKNLKEKYINNVSIKKDILLKAPDNIIREEKSEEFFYFFNHFCFYIINETNKYALTFKMNFAFYIPYGSVGIDVLKNVFDYLYELNIPTILDMKINDIGNTVKNYRKFIFEYLKSDSCTVNIYMGTNMLKDICYDEEKNKYYSAFVLVKTTNPDSAIFQKNLSLDNKQAYVIMAQEALNMSSYLNLEQNNEFIGFVVGANSYDEMNYIRTYFPNCYILSPGIGAQNGDLHKTLTNGYHKSYEKILINIGRAITKNPYPQKAAQMYYDQINAILKQNMES 323
               SCOP domains d3mwaa_ A: automated matches                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhh.hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.eeeee.hhh...hhhhhhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhhhh.....eeee.....hhhhhhh.ee....ee.eeeeeee.....hhhhhh..ee..eehhhhhhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhh....eee........hhhhhhhhhh..hhh.eeeeehhhhhh..hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3mwa A  -6 GLVPRGSMGFKVKLEKRRNAINTCLCIGLDPDEKDIENFMKNEKENNYNNIKKNLKEKYINNVSIKKDILLKAPDNIIREEKSEEFFYFFNHFCFYIINETNKYALTFKMNFAFYIPYGSVGIDVLKNVFDYLYELNIPTILDMKINDIGNTVKNYRKFIFEYLKSDSCTVNIYMGTNMLKDICYDEEKNKYYSAFVLVKTTNPDSAIFQKNLSLDNKQAYVIMAQEALNMSSYLNLEQNNEFIGFVVGANSYDEMNYIRTYFPNCYILSPGIGAQNGDLHKTLTNGYHKSYEKILINIGRAITKNPYPQKAAQMYYDQINAILKQNMES 323
                                     3        13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323


Chain B from PDB  Type:PROTEIN  Length:322
 aligned with Q8IJH3_PLAF7 | Q8IJH3 from UniProtKB/TrEMBL  Length:323

    Alignment length:322
                             1                                                                                                                                                                                                                                                                                                                                
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319  
         Q8IJH3_PLAF7     - -MGFKVKLEKRRNAINTCLCIGLDPDEKDIENFMKNEKENNYNNIKKNLKEKYINNVSIKKDILLKAPDNIIREEKSEEFFYFFNHFCFYIINETNKYALTFKMNFAFYIPYGSVGIDVLKNVFDYLYELNIPTILDMKINDIGNTVKNYRKFIFEYLKSDSCTVNIYMGTNMLKDICYDEEKNKYYSAFVLVKTTNPDSAIFQKNLSLDNKQAYVIMAQEALNMSSYLNLEQNNEFIGFVVGANSYDEMNYIRTYFPNCYILSPGIGAQNGDLHKTLTNGYHKSYEKILINIGRAITKNPYPQKAAQMYYDQINAILKQNM 321
               SCOP domains d3mwab_ B: automated matches                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------------OMPdecase-3mwaB01 B:16-309                                                                                                                                                                                                                                                                            ------------ Pfam domains (1)
           Pfam domains (2) ----------------OMPdecase-3mwaB02 B:16-309                                                                                                                                                                                                                                                                            ------------ Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.eeeee.hhh...hhhhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhh.....eeee.....hhhhhhh.ee....ee.eeeeeee.....hhhhhh..ee..eehhhhhhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhh....eee........hhhhhhhhhh..hhh.eeeeehhhhhh..hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mwa B   0 SMGFKVKLEKRRNAINTCLCIGLDPDEKDIENFMKNEKENNYNNIKKNLKEKYINNVSIKKDILLKAPDNIIREEKSEEFFYFFNHFCFYIINETNKYALTFKMNFAFYIPYGSVGIDVLKNVFDYLYELNIPTILDMKINDIGNTVKNYRKFIFEYLKSDSCTVNIYMGTNMLKDICYDEEKNKYYSAFVLVKTTNPDSAIFQKNLSLDNKQAYVIMAQEALNMSSYLNLEQNNEFIGFVVGANSYDEMNYIRTYFPNCYILSPGIGAQNGDLHKTLTNGYHKSYEKILINIGRAITKNPYPQKAAQMYYDQINAILKQNM 321
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319
   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 3MWA)

(-) 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   (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 2q8l 2q8z 2qaf 3bar 3bpw 3n2m 3n34 3n3m 3s9y

(-) Related Entries Specified in the PDB File

3mw7