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(-) Description

Title :  CRYSTAL STRUCTURE OF PLASMODIUM KNOWLESI STRUCTURE OF IRON SUPER-OXIDE DISMUTASE
 
Authors :  A. Dong, Y. Zhao, J. Lew, Z. Alam, M. Melone, G. Wasney, M. Vedadi, I. Koeieradzki, A. M. Edwards, C. H. Arrowsmith, J. Weigelt, M. Sundstrom, A. Bochkarev, R. Hui, M. Amani, Structural Genomics Consortium (Sgc)
Date :  01 Sep 05  (Deposition) - 13 Sep 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Iron Super-Oxide Dismutase, Structural Genomics, Structural Genomics Consortium, Sgc, Oxidoreductase (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 - IRON SUPER-OXIDE DISMUTASE
    Chains: A, B
    EC Number: 1.15.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)RIL
    Expression System Taxid: 562
    Expression System Vector Type: PET28ALIC
    Organism Scientific: PLASMODIUM KNOWLESI
    Organism Taxid: 5850

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2UNX3Ligand/IonUNKNOWN ATOM OR ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:2105 , HIS B:90 , TRP B:185 , HOH B:3060BINDING SITE FOR RESIDUE CL B 2001
2AC2SOFTWAREASN A:25 , HIS B:90 , GLY B:91BINDING SITE FOR RESIDUE CL A 2002
3AC3SOFTWAREHIS A:27 , HIS A:74 , ASP A:158 , HIS A:162 , HOH A:2015BINDING SITE FOR RESIDUE UNX A 1000
4AC4SOFTWAREHIS B:27 , HIS B:74 , ASP B:158 , HIS B:162 , HOH B:3004BINDING SITE FOR RESIDUE UNX B 1001
5AC5SOFTWAREASP B:167BINDING SITE FOR RESIDUE UNX B 3001

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ser A:16 -Pro A:17
2Ser B:16 -Pro B:17

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2AWP)

(-) 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:197
 aligned with D0VWV6_PLAKN | D0VWV6 from UniProtKB/TrEMBL  Length:198

    Alignment length:197
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       
         D0VWV6_PLAKN     1 MAIILPKLKYALNALSPHISEETLNFHYNKHHAGYVNKLNGLIKDTPFATKSLVEIMKESTGAIFNNAAQIWNHSFYWDSMGPNCGGEPHGEIKEKIQEDFGSFNNFKNEFSNVLCGHFGSGWGWLVLNNNNKLVILQTHDAGNPIKDNTGIPILTCDIWEHAYYIDYRNDRPSYVKAWWNLVNWNFANENLKKALQ 197
               SCOP domains d2awpa1 A:1-83 automated matches                                                   d2awpa2 A:84-197 automated matches                                                                                 SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....eeeeeee...hhhhhh.eeeeeeee.hhhhhhhhhh.hhhhhhhhhh...hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2awp A   1 MAIILPKLKYALNALSPHISEETLNFHYNKHHAGYVNKLNGLIKDTPFATKSLVEIMKESTGAIFNNAAQIWNHSFYWDSMGPNCGGEPHGEIKEKIQEDFGSFNNFKNEFSNVLCGHFGSGWGWLVLNNNNKLVILQTHDAGNPIKDNTGIPILTCDIWEHAYYIDYRNDRPSYVKAWWNLVNWNFANENLKKALQ 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:195
 aligned with D0VWV6_PLAKN | D0VWV6 from UniProtKB/TrEMBL  Length:198

    Alignment length:195
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191     
         D0VWV6_PLAKN     2 AIILPKLKYALNALSPHISEETLNFHYNKHHAGYVNKLNGLIKDTPFATKSLVEIMKESTGAIFNNAAQIWNHSFYWDSMGPNCGGEPHGEIKEKIQEDFGSFNNFKNEFSNVLCGHFGSGWGWLVLNNNNKLVILQTHDAGNPIKDNTGIPILTCDIWEHAYYIDYRNDRPSYVKAWWNLVNWNFANENLKKAL 196
               SCOP domains d2awpb1 B:2-83 automated matches                                                  d2awpb2 B:84-196 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 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2awp B   2 AIILPKLKYALNALSPHISEETLNFHYNKHHAGYVNKLNGLIKDTPFATKSLVEIMKESTGAIFNNAAQIWNHSFYWDSMGPNCGGEPHGEIKEKIQEDFGSFNNFKNEFSNVLCGHFGSGWGWLVLNNNNKLVILQTHDAGNPIKDNTGIPILTCDIWEHAYYIDYRNDRPSYVKAWWNLVNWNFANENLKKAL 196
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191
   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/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (D0VWV6_PLAKN | D0VWV6)
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.

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