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(-) Description

Title :  THE CRYSTAL STRUCTURE OF THE ENZYME FE-SUPEROXIDE DISMUTASE FROM PLASMODIUM FALCIPARUM
 
Authors :  M. V. A. S. Navarro, R. C. Garratt
Date :  13 Apr 06  (Deposition) - 28 Aug 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Beta+Alpha Structure, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. F. Bachega, M. V. Navarro, L. Bleicher, R. K. Bortoleto-Bugs, D. Dive, P. Hoffmann, E. Viscogliosi, R. C. Garratt
Systematic Structural Studies Of Iron Superoxide Dismutases From Human Parasites And A Statistical Coupling Analysis Of Metal Binding Specificity
Proteins V. 77 26 2009
PubMed-ID: 19384994  |  Reference-DOI: 10.1002/PROT.22412

(-) Compounds

Molecule 1 - FE-SUPEROXIDE DISMUTASE
    ChainsA, B
    EC Number1.15.1.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI K12
    Expression System StrainK12
    Expression System Taxid83333
    Expression System Vector TypePLASMID
    GeneSOD
    Organism ScientificPLASMODIUM FALCIPARUM
    Organism Taxid137071
    StrainHB3

 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
1FE22Ligand/IonFE (II) ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:26 , HIS A:73 , ASP A:157 , HIS A:161 , HOH A:199BINDING SITE FOR RESIDUE FE2 A 198
2AC2SOFTWAREHIS B:26 , HIS B:73 , ASP B:157 , HIS B:161 , HOH B:199BINDING SITE FOR RESIDUE FE2 B 198

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological 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 2GOJ)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SOD_MNPS00088 Manganese and iron superoxide dismutases signature.SODF_PLAFX158-165
 
  2A:157-164
B:157-164

(-) Exons   (0, 0)

(no "Exon" information available for 2GOJ)

(-) 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:196
 aligned with SODF_PLAFX | Q27740 from UniProtKB/Swiss-Prot  Length:198

    Alignment length:196
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191      
           SODF_PLAFX     2 VITLPKLKYALNALSPHISEETLNFHYNKHHAGYVNKLNTLIKDTPFAEKSLLDIVKESSGAIFNNAAQIWNHTFYWDSMGPDCGGEPHGEIKEKIQEDFGSFNNFKEQFSNILCGHFGSGWGWLALNNNNKLVILQTHDAGNPIKDNTGIPILTCDIWEHAYYIDYRNDRASYVKAWWNLVNWNFANENLKKAMK 197
               SCOP domains d2goja1 A:1-82 automated matches                                                  d2goja2 A:83-196 automated matches                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................hhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee.....eeeeeee...........eeeeeee.hhhhhhhhhh.hhhhhhhhhh...hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  -------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2goj A   1 VITLPKLKYALNALSPHISEETLNFHYNKHHAGYVNKLNTLIKDTPFAEKSLLDIVKESSGAIFNNAAQIWNHTFYWDSMGPDCGGEPHGEIKEKIQEDFGSFNNFKEQFSNILCGHFGSGWGWLALNNNNKLVILQTHDAGNPIKDNTGIPILTCDIWEHAYYIDYRNDRASYVKAWWNLVNWNFANENLKKAMK 196
                                    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:195
 aligned with SODF_PLAFX | Q27740 from UniProtKB/Swiss-Prot  Length:198

    Alignment length:195
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191     
           SODF_PLAFX     2 VITLPKLKYALNALSPHISEETLNFHYNKHHAGYVNKLNTLIKDTPFAEKSLLDIVKESSGAIFNNAAQIWNHTFYWDSMGPDCGGEPHGEIKEKIQEDFGSFNNFKEQFSNILCGHFGSGWGWLALNNNNKLVILQTHDAGNPIKDNTGIPILTCDIWEHAYYIDYRNDRASYVKAWWNLVNWNFANENLKKAM 196
               SCOP domains d2gojb1 B:1-82 automated matches                                                  d2gojb2 B:83-195 automated matches                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee.....eeeeeee...hhhhhh..eeeeeee.hhhhhhhhhh.hhhhhhhhhh...hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  ------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2goj B   1 VITLPKLKYALNALSPHISEETLNFHYNKHHAGYVNKLNTLIKDTPFAEKSLLDIVKESSGAIFNNAAQIWNHTFYWDSMGPDCGGEPHGEIKEKIQEDFGSFNNFKEQFSNILCGHFGSGWGWLALNNNNKLVILQTHDAGNPIKDNTGIPILTCDIWEHAYYIDYRNDRASYVKAWWNLVNWNFANENLKKAM 195
                                    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)
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  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/Biological Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (SODF_PLAFX | Q27740)
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: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: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.

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