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(-) Description

Title :  CRYSTAL STRUCTURE OF THE METAL-BOUND SUPEROXIDE DISMUTASE FROM PYROBACULUM AEROPHILUM
 
Authors :  S. Lee
Date :  13 Oct 08  (Deposition) - 25 Aug 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Alpha-Beta, Iron, Metal-Binding, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Lee
Crystal Structure Of The Metal-Bound Superoxide Dismutase From Pyrobaculum Aerophilum And Comparison With The Metal-Free Form
Bull. Korean Chem. Soc. V. 29 2399 2008
PubMed: search

(-) Compounds

Molecule 1 - SUPEROXIDE DISMUTASE [FE]
    Chains: A, B, C, D
    EC Number: 1.15.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE30
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: SOD, PAE0274
    Organism Scientific: PYROBACULUM AEROPHILUM
    Organism Taxid: 13773

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1MN4Ligand/IonMANGANESE (II) ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:42 , HIS A:90 , ASP A:176 , HIS A:180 , HOH A:302BINDING SITE FOR RESIDUE MN A 301
2AC2SOFTWAREHIS B:42 , HIS B:90 , ASP B:176 , HIS B:180 , HOH B:302BINDING SITE FOR RESIDUE MN B 301
3AC3SOFTWAREHIS C:42 , HIS C:90 , ASP C:176 , HIS C:180 , HOH C:302BINDING SITE FOR RESIDUE MN C 301
4AC4SOFTWAREHIS D:42 , HIS D:90 , ASP D:176 , HIS D:180BINDING SITE FOR RESIDUE MN D 301

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Glu A:31 -Pro A:32
2Glu B:31 -Pro B:32
3Glu C:31 -Pro C:32
4Glu D:31 -Pro D:32

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 4)

Asymmetric/Biological Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SOD_MNPS00088 Manganese and iron superoxide dismutases signature.SODF_PYRAE165-172
 
 
 		  4A:176-183
B:176-183
C:176-183
D:176-183

(-) Exons   (0, 0)

(no "Exon" information available for 3EVK)

(-) 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:211
 aligned with SODF_PYRAE | O93724 from UniProtKB/Swiss-Prot  Length:211

    Alignment length:211
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210 
           SODF_PYRAE     1 MVTTKRYTLPPLPYAYNALEPYISAEIMQLHHQKHHQGYVNGANAALEKLEKFRKGEAQIDIRAVLRDLSFHLNGHILHSIFWPNMAPPGKGGGKPGGKIADLINKFFGSFEKFKEEFSQAAKNVEGVGWAILVYEPLEEQLLILQIEKHNLMHAADAQVLLALDVWEHAYYLQYKNDRGSYVDNWWNVVNWDDVERRLQKALNGQIALKL 211
               SCOP domains d3evka1 A:12-103 Fe superoxide dismutase (FeSOD)                                            d3evka2 A:104-222 Fe superoxide dismutase (FeSOD)                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeee....eeeeeeee..........eeeeeee.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  --------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3evk A  12 SVTTKRYTLPPLPYAYNALEPYISAEIMQLHHQKHHQGYVNGANAALEKLEKFRKGEAQIDIRAVLRDLSFHLNGHILHSIFWPNMAPPGKGGGKPGGKIADLINKFFGSFEKFKEEFSQAAKNVEGVGWAILVYEPLEEQLLILQIEKHNLMHAADAQVLLALDVWEHAYYLQYKNDRGSYVDNWWNVVNWDDVERRLQKALNGQIALKL 222
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221 


Chain B from PDB  Type:PROTEIN  Length:211
 aligned with SODF_PYRAE | O93724 from UniProtKB/Swiss-Prot  Length:211

    Alignment length:211
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210 
           SODF_PYRAE     1 MVTTKRYTLPPLPYAYNALEPYISAEIMQLHHQKHHQGYVNGANAALEKLEKFRKGEAQIDIRAVLRDLSFHLNGHILHSIFWPNMAPPGKGGGKPGGKIADLINKFFGSFEKFKEEFSQAAKNVEGVGWAILVYEPLEEQLLILQIEKHNLMHAADAQVLLALDVWEHAYYLQYKNDRGSYVDNWWNVVNWDDVERRLQKALNGQIALKL 211
               SCOP domains d3evkb1 B:12-103 Fe superoxide dismutase (FeSOD)                                            d3evkb2 B:104-222 Fe superoxide dismutase (FeSOD)                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeee....eeeeeeee..........eeeeeee.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  --------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3evk B  12 SVTTKRYTLPPLPYAYNALEPYISAEIMQLHHQKHHQGYVNGANAALEKLEKFRKGEAQIDIRAVLRDLSFHLNGHILHSIFWPNMAPPGKGGGKPGGKIADLINKFFGSFEKFKEEFSQAAKNVEGVGWAILVYEPLEEQLLILQIEKHNLMHAADAQVLLALDVWEHAYYLQYKNDRGSYVDNWWNVVNWDDVERRLQKALNGQIALKL 222
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221 


Chain C from PDB  Type:PROTEIN  Length:211
 aligned with SODF_PYRAE | O93724 from UniProtKB/Swiss-Prot  Length:211

    Alignment length:211
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210 
           SODF_PYRAE     1 MVTTKRYTLPPLPYAYNALEPYISAEIMQLHHQKHHQGYVNGANAALEKLEKFRKGEAQIDIRAVLRDLSFHLNGHILHSIFWPNMAPPGKGGGKPGGKIADLINKFFGSFEKFKEEFSQAAKNVEGVGWAILVYEPLEEQLLILQIEKHNLMHAADAQVLLALDVWEHAYYLQYKNDRGSYVDNWWNVVNWDDVERRLQKALNGQIALKL 211
               SCOP domains d3evkc1 C:12-103 Fe superoxide dismutase (FeSOD)                                            d3evkc2 C:104-222 Fe superoxide dismutase (FeSOD)                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeee....eeeeeeee..........eeeeeee.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  --------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3evk C  12 SVTTKRYTLPPLPYAYNALEPYISAEIMQLHHQKHHQGYVNGANAALEKLEKFRKGEAQIDIRAVLRDLSFHLNGHILHSIFWPNMAPPGKGGGKPGGKIADLINKFFGSFEKFKEEFSQAAKNVEGVGWAILVYEPLEEQLLILQIEKHNLMHAADAQVLLALDVWEHAYYLQYKNDRGSYVDNWWNVVNWDDVERRLQKALNGQIALKL 222
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221 


Chain D from PDB  Type:PROTEIN  Length:211
 aligned with SODF_PYRAE | O93724 from UniProtKB/Swiss-Prot  Length:211

    Alignment length:211
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210 
           SODF_PYRAE     1 MVTTKRYTLPPLPYAYNALEPYISAEIMQLHHQKHHQGYVNGANAALEKLEKFRKGEAQIDIRAVLRDLSFHLNGHILHSIFWPNMAPPGKGGGKPGGKIADLINKFFGSFEKFKEEFSQAAKNVEGVGWAILVYEPLEEQLLILQIEKHNLMHAADAQVLLALDVWEHAYYLQYKNDRGSYVDNWWNVVNWDDVERRLQKALNGQIALKL 211
               SCOP domains d3evkd1 D:12-103 Fe superoxide dismutase (FeSOD)                                            d3evkd2 D:104-222 Fe superoxide dismutase (FeSOD)                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeee....eeeeeeee..........eeeeeee.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  --------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3evk D  12 SVTTKRYTLPPLPYAYNALEPYISAEIMQLHHQKHHQGYVNGANAALEKLEKFRKGEAQIDIRAVLRDLSFHLNGHILHSIFWPNMAPPGKGGGKPGGKIADLINKFFGSFEKFKEEFSQAAKNVEGVGWAILVYEPLEEQLLILQIEKHNLMHAADAQVLLALDVWEHAYYLQYKNDRGSYVDNWWNVVNWDDVERRLQKALNGQIALKL 222
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221
   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, 8)

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 3EVK)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3EVK)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (SODF_PYRAE | O93724)
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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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        SODF_PYRAE | O93724: 1p7g

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