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(-) Description

Title :  CRYSTAL STRUCTURE OF PLASMODIUM BERGHEI OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE (ORTHOLOG OF PLASMODIUM FALCIPARUM PF10_0225)
 
Authors :  W. Qiu, A. Dong, G. Wasney, M. Vedadi, J. Lew, I. Kozieradski, Z. Alam, M. Melone, J. Weigelt, M. Sundstrom, A. Edwards, C. Arrowsmith, R. Hui M. Gao, A. Bochkarev, J. D. Artz, Structural Genomics Consortium (Sgc)
Date :  14 Dec 05  (Deposition) - 20 Dec 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.72
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Tim Barrel, Structural Genomics, Structural Genomics Consortium, Sgc, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Vedadi, J. Lew, J. Artz, M. Amani, Y. Zhao, A. Dong, G. A. Wasney, M. Gao, T. Hills, S. Brokx, W. Qiu, S. Sharma, A. Diassiti, Z. Alam, M. Melone, A. Mulichak, A. Wernimont, J. Bray, P. Loppnau, O. Plotnikova, K. Newberry, E. Sundararajan, S. Houston, J. Walker, W. Tempel, A. Bochkarev, I. Kozieradzki, A. Edwards, C. Arrowsmith, D. Roos, K. Kain, R. Hui
Genome-Scale Protein Expression And Structural Biology Of Plasmodium Falciparum And Related Apicomplexan Organisms.
Mol. Biochem. Parasitol. V. 151 100 2007
PubMed-ID: 17125854  |  Reference-DOI: 10.1016/J.MOLBIOPARA.2006.10.011
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - OROTIDINE-MONOPHOSPHATE-DECARBOXYLASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: PLASMODIUM BERGHEI
    Organism Taxid: 5821

 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
1IOD2Ligand/IonIODIDE ION

(-) Sites  (0, 0)

(no "Site" information available for 2FDS)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2FDS)

(-) 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 Q4Z4C3_PLABA | Q4Z4C3 from UniProtKB/TrEMBL  Length:334

    Alignment length:324
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321    
         Q4Z4C3_PLABA     2 HFKTKLKNRRNEVNTCLCIGLDPDEDDIKNFMRNEEKNGYKNVKNNMNSNNNRIENVIKIGKEILLTDEENIENLSEEDKFFYFFNHFCFYIINNTKEYALIYKMNFAFYIPYGSVGINALKNVFDYLNSMNIPTMLDMKINDIGNTVKNYRKFIFEYLKSDSCTINVYMGTSMLKDICFDYEKNKYYSAYVLIKTTNKDSFIFQNELSINDKQAYIVMAEETQKMATDLKIDQNNEFIGFVVGSNAFEEMKIIRNKFPDSYILSPGIGAQNGDLYKTLKNGYNKDYEKLLINVGRAITKSPNPKKSSESYYNQIIQIFKDIEN 325
               SCOP domains d2fdsa1 A:1-324 Protozoan orotidine monophosphat e decarboxylase                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhh...hhhhhhhhh-..hhhhhhh..hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee.hhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhh.....eeee.......hhhhhhee....ee.eeeeeee..hhhhhhhhh..ee..eehhhhhhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhh....eee...-----hhhhhhhhhh..hhh.eeeeehhhhhh..hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2fds A   1 HFKTKLKNRRNEVNTCLCIGLDPDEDDIKNFMRNEEKNGYKNVKNNMN-NNNRIENVIKIGKEILLTDEENIENLSEEDKFFYFFNHFCFYIINNTKEYALIYKMNFAFYIPYGSVGINALKNVFDYLNSMNIPTMLDMKINDIGNTVKNYRKFIFEYLKSDSCTINVYMGTSMLKDICFDYEKNKYYSAYVLIKTTNKDSFIFQNELSINDKQAYIVMAEETQKMATDLKIDQNNEFIGFVVGSNAFEEMKIIRNKFPDSYILSPGI-----DLYKTLKNGYNKDYEKLLINVGRAITKSPNPKKSSESYYNQIIQIFKDIEN 324
                                    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       | -   |   280       290       300       310       320    
                                                                          48 |                                                                                                                                                                                                                       268   274                                                  
                                                                            50                                                                                                                                                                                                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:319
 aligned with Q4Z4C3_PLABA | Q4Z4C3 from UniProtKB/TrEMBL  Length:334

    Alignment length:324
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321    
         Q4Z4C3_PLABA     2 HFKTKLKNRRNEVNTCLCIGLDPDEDDIKNFMRNEEKNGYKNVKNNMNSNNNRIENVIKIGKEILLTDEENIENLSEEDKFFYFFNHFCFYIINNTKEYALIYKMNFAFYIPYGSVGINALKNVFDYLNSMNIPTMLDMKINDIGNTVKNYRKFIFEYLKSDSCTINVYMGTSMLKDICFDYEKNKYYSAYVLIKTTNKDSFIFQNELSINDKQAYIVMAEETQKMATDLKIDQNNEFIGFVVGSNAFEEMKIIRNKFPDSYILSPGIGAQNGDLYKTLKNGYNKDYEKLLINVGRAITKSPNPKKSSESYYNQIIQIFKDIEN 325
               SCOP domains d2fdsb_ B: automated matches                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh..eeee...hhhhhhhhhhhhh...hhhhhhhhhh..hhhhhhh..hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee.hhh...hhhhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhh.....eeee.....hhhhhhh.ee....ee.eeeeeee..hhhhhhhhh..ee..eehhhhhhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhh....eee...-----hhhhhhhhhh..hhh.eeeeehhhhhh..hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2fds B   1 HFKTKLKNRRNEVNTCLCIGLDPDEDDIKNFMRNEEKNGYKNVKNNMNSNNNRIENVIKIGKEILLTDEENIENLSEEDKFFYFFNHFCFYIINNTKEYALIYKMNFAFYIPYGSVGINALKNVFDYLNSMNIPTMLDMKINDIGNTVKNYRKFIFEYLKSDSCTINVYMGTSMLKDICFDYEKNKYYSAYVLIKTTNKDSFIFQNELSINDKQAYIVMAEETQKMATDLKIDQNNEFIGFVVGSNAFEEMKIIRNKFPDSYILSPGI-----DLYKTLKNGYNKDYEKLLINVGRAITKSPNPKKSSESYYNQIIQIFKDIEN 324
                                    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       | -   |   280       290       300       310       320    
                                                                                                                                                                                                                                                                                                     268   274
   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  (2, 2)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q4Z4C3_PLABA | Q4Z4C3)
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 Specified in the PDB File

2aqw THE SAME PROTEIN FROM PLASMODIUM YOELII.