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(-) Description

Title :  STRUCTURE OF IRON DEPENDENT SUPEROXIDE DISMUTASE FROM P. FALCIPARUM.
 
Authors :  I. W. Boucher, J. A. Brannigan, A. J. Wilkinson, A. M. Brzozowski
Date :  20 Apr 05  (Deposition) - 11 Oct 06  (Release) - 15 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.52
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Dismutase, Oxidoreductase, Metal-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  I. W. Boucher, A. M. Brzozowski, J. A. Brannigan, C. Schnick, D. J. Smith, S. A. Kyes, A. J. Wilkinson
The Crystal Structure Of Superoxide Dismutase From Plasmodium Falciparum.
Bmc Struct. Biol. V. 6 20 2006
PubMed-ID: 17020617  |  Reference-DOI: 10.1186/1472-6807-6-20

(-) Compounds

Molecule 1 - FE-SUPEROXIDE DISMUTASE
    ChainsA, B
    EC Number1.15.1.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET 28C
    Expression System StrainBL21
    Expression System Taxid511693
    Organism ScientificPLASMODIUM FALCIPARUM
    Organism Taxid36329
    Strain3D7

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1FE2Ligand/IonFE (III) ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1FE-1Ligand/IonFE (III) ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1FE-1Ligand/IonFE (III) ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:26 , HIS A:73 , ASP A:157 , HIS A:161 , HOH A:2055BINDING SITE FOR RESIDUE FE A1198
2AC2SOFTWAREHIS B:26 , HIS B:73 , ASP B:157 , HIS B:161 , HOH B:2054BINDING SITE FOR RESIDUE FE B1198

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ser A:15 -Pro A:16
2Ser B:15 -Pro B:16

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SOD_MNPS00088 Manganese and iron superoxide dismutases signature.SODF_PLAF7158-165
 
  2A:157-164
B:157-164
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SOD_MNPS00088 Manganese and iron superoxide dismutases signature.SODF_PLAF7158-165
 
  1A:157-164
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SOD_MNPS00088 Manganese and iron superoxide dismutases signature.SODF_PLAF7158-165
 
  1-
B:157-164

(-) Exons   (0, 0)

(no "Exon" information available for 2BPI)

(-) 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:197
 aligned with SODF_PLAF7 | Q8IAY6 from UniProtKB/Swiss-Prot  Length:198

    Alignment length:197
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       
           SODF_PLAF7     2 VITLPKLKYALNALSPHISEETLNFHYNKHHAGYVNKLNTLIKDTPFAEKSLLDIVKESSGAIFNNAAQIWNHTFYWDSMGPDCGGEPHGEIKEKIQEDFGSFNNFKEQFSNILCGHFGSGWGWLALNNNNKLVILQTHDAGNPIKDNTGIPILTCDIWEHAYYIDYRNDRASYVKAWWNLVNWNFANENLKKAMQK 198
               SCOP domains d2bpia1 A:1-83 automated matches                                                   d2bpia2 A:84-197 automated matches                                                                                 SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................hhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee.....eeeeeee...........eeeeeee.hhhhhhhhhh.hhhhhhhhhh...hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  --------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bpi A   1 VITLPKLKYALNALSPHISEETLNFHYNKHHAGYVNKLNTLIKDTPFAEKSLLDIVKESSGAIFNNAAQIWNHTFYWDSMGPDCGGEPHGEIKEKIQEDFGSFNNFKEQFSNILCGHFGSGWGWLALNNNNKLVILQTHDAGNPIKDNTGIPILTCDIWEHAYYIDYRNDRASYVKAWWNLVNWNFANENLKKAMQK 197
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       

Chain B from PDB  Type:PROTEIN  Length:197
 aligned with SODF_PLAF7 | Q8IAY6 from UniProtKB/Swiss-Prot  Length:198

    Alignment length:197
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       
           SODF_PLAF7     2 VITLPKLKYALNALSPHISEETLNFHYNKHHAGYVNKLNTLIKDTPFAEKSLLDIVKESSGAIFNNAAQIWNHTFYWDSMGPDCGGEPHGEIKEKIQEDFGSFNNFKEQFSNILCGHFGSGWGWLALNNNNKLVILQTHDAGNPIKDNTGIPILTCDIWEHAYYIDYRNDRASYVKAWWNLVNWNFANENLKKAMQK 198
               SCOP domains d2bpib1 B:1-83 automated matches                                                   d2bpib2 B:84-197 automated matches                                                                                 SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeee.....eeeeeee...hhhhhh..eeeeeee.hhhhhhhhhh.hhhhhhhhhh...hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  --------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bpi B   1 VITLPKLKYALNALSPHISEETLNFHYNKHHAGYVNKLNTLIKDTPFAEKSLLDIVKESSGAIFNNAAQIWNHTFYWDSMGPDCGGEPHGEIKEKIQEDFGSFNNFKEQFSNILCGHFGSGWGWLALNNNNKLVILQTHDAGNPIKDNTGIPILTCDIWEHAYYIDYRNDRASYVKAWWNLVNWNFANENLKKAMQK 197
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       

   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, 4)

Asymmetric Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (SODF_PLAF7 | Q8IAY6)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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: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).
    GO:0004784    superoxide dismutase activity    Catalysis of the reaction: 2 superoxide + 2 H+ = O2 + hydrogen peroxide.
biological process
    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.
    GO:0019430    removal of superoxide radicals    Any process, acting at the cellular level, involved in removing superoxide radicals (O2-) from a cell or organism, e.g. by conversion to dioxygen (O2) and hydrogen peroxide (H2O2).
    GO:0006979    response to oxidative stress    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
    GO:0006801    superoxide metabolic process    The chemical reactions and pathways involving superoxide, the superoxide anion O2- (superoxide free radical), or any compound containing this species.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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