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(-) Description

Title :  IRON SUPEROXIDE DISMUTASE (FE-SOD) FROM THE HYPERTHERMOPHILE SULFOLOBUS SOLFATARICUS. 2.3 A RESOLUTION STRUCTURE OF RECOMBINANT PROTEIN WITH A COVALENTLY MODIFIED TYROSIN IN THE ACTIVE SITE.
 
Authors :  T. Ursby, B. S. Adinolfi, S. Al-Karadaghi, E. De Vendittis, V. Bocchini
Date :  31 Oct 04  (Deposition) - 08 Nov 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Superoxide Dismutase, Sod, Iron, Oxidoreductase, Superoxide Radical Disproportionation, Sulfolobus Solftaricus, Thermostable (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Ursby, B. S. Adinolfi, S. Al-Karadaghi, E. De Vendittis, V. Bocchini
Iron Superoxide Dismutase From The Archaeon Sulfolobus Solfataricus: Analysis Of Structure And Thermostability
J. Mol. Biol. V. 286 189 1999
PubMed-ID: 9931259  |  Reference-DOI: 10.1006/JMBI.1998.2471
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SUPEROXIDE DISMUTASE [FE]
    Chains: A, B
    EC Number: 1.15.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PT7-7
    Expression System Strain: JM109(DE3)
    Expression System Taxid: 562
    Expression System Vector: VSOD
    Organism Scientific: SULFOLOBUS SOLFATARICUS
    Organism Taxid: 2287
    Other Details: COVALENT MODIFICATION OF TYR 41 CONSISTING OF HET GROUP PMS (PHENYL METHYL SULFONATE, BENZYLSULFINIC ACID)

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1FE2Ligand/IonFE (III) ION
2PMS2Ligand/IonBENZYLSULFINIC ACID
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1FE-1Ligand/IonFE (III) ION
2PMS4Ligand/IonBENZYLSULFINIC ACID

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:33 , HIS A:84 , ASP A:170 , HIS A:174 , HOH A:2077BINDING SITE FOR RESIDUE FE A 212
2AC2SOFTWAREHIS B:33 , HIS B:84 , ASP B:170 , HIS B:174 , HOH B:2065BINDING SITE FOR RESIDUE FE B 211
3AC3SOFTWAREHIS A:37 , TYR A:41 , PHE A:76 , PHE A:172 , HIS A:174 , LEU B:130 , GLY B:132 , ARG B:184BINDING SITE FOR RESIDUE PMS A 213
4AC4SOFTWARELEU A:130 , GLY A:132 , ARG A:184 , HIS B:37 , TYR B:41 , PHE B:76 , PHE B:172 , HIS B:174BINDING SITE FOR RESIDUE PMS B 214

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1WB8)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Glu A:22 -Pro A:23
2Glu B:22 -Pro B:23

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1WB8)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SOD_MNPS00088 Manganese and iron superoxide dismutases signature.SODF_SULSO171-178
 		  2A:170-177
B:170-177
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SOD_MNPS00088 Manganese and iron superoxide dismutases signature.SODF_SULSO171-178
 		  4A:170-177
B:170-177

(-) Exons   (0, 0)

(no "Exon" information available for 1WB8)

(-) 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:205
 aligned with SODF_SULSO | P80857 from UniProtKB/Swiss-Prot  Length:211

    Alignment length:205
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204     
           SODF_SULSO     5 IQFKKYELPPLPYKIDALEPYISKDIIDVHYNGHHKGYVNGANSLLERLEKVVKGDLQTGQYDIQGIIRGLTFNINGHKLHALYWENMAPSGKGGGKPGGALADLINKQYGSFDRFKQVFTETANSLPGTGWAVLYYDTESGNLQIMTFENHFQNHIAEIPIILILDEFEHAYYLQYKNKRADYVNAWWNVVNWDAAEKKLQKYL 209
               SCOP domains d1wb8a1 A:4-92 Fe superoxide dismutase (FeSOD)                                           d1wb8a2 A:93-208 Fe superoxide dismutase (FeSOD)                                                                     SCOP domains
               CATH domains ----------------------1wb8A01 A:26-92 Fe,Mn superoxide dismutase (SOD) domain            -------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeee......eeeeeee...........eeeeee.hhhhhhhhhh.hhhhhhhhhh...hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  ------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wb8 A   4 IQFKKYELPPLPYKIDALEPYISKDIIDVHYNGHHKGYVNGANSLLERLEKVVKGDLQTGQYDIQGIIRGLTFNINGHKLHALYWENMAPSGKGGGKPGGALADLINKQYGSFDRFKQVFTETANSLPGTGWAVLYYDTESGNLQIMTFENHFQNHIAEIPIILILDEFEHAYYLQYKNKRADYVNAWWNVVNWDAAEKKLQKYL 208
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203     


Chain B from PDB  Type:PROTEIN  Length:205
 aligned with SODF_SULSO | P80857 from UniProtKB/Swiss-Prot  Length:211

    Alignment length:205
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204     
           SODF_SULSO     5 IQFKKYELPPLPYKIDALEPYISKDIIDVHYNGHHKGYVNGANSLLERLEKVVKGDLQTGQYDIQGIIRGLTFNINGHKLHALYWENMAPSGKGGGKPGGALADLINKQYGSFDRFKQVFTETANSLPGTGWAVLYYDTESGNLQIMTFENHFQNHIAEIPIILILDEFEHAYYLQYKNKRADYVNAWWNVVNWDAAEKKLQKYL 209
               SCOP domains d1wb8b1 B:4-92 Fe superoxide dismutase (FeSOD)                                           d1wb8b2 B:93-208 Fe superoxide dismutase (FeSOD)                                                                     SCOP domains
               CATH domains ----------------------1wb8B01 B:26-92 Fe,Mn superoxide dismutase (SOD) domain            -------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----Sod_Fe_N-1wb8B03 B:8-92                                                              ------Sod_Fe_C-1wb8B01 B:99-204                                                                                 ---- Pfam domains (1)
           Pfam domains (2) ----Sod_Fe_N-1wb8B04 B:8-92                                                              ------Sod_Fe_C-1wb8B02 B:99-204                                                                                 ---- Pfam domains (2)
         Sec.struct. author ......................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeee......eeeeeee...........eeeeee.hhhhhhhhhh.hhhhhhhhhh...hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  ------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wb8 B   4 IQFKKYELPPLPYKIDALEPYISKDIIDVHYNGHHKGYVNGANSLLERLEKVVKGDLQTGQYDIQGIIRGLTFNINGHKLHALYWENMAPSGKGGGKPGGALADLINKQYGSFDRFKQVFTETANSLPGTGWAVLYYDTESGNLQIMTFENHFQNHIAEIPIILILDEFEHAYYLQYKNKRADYVNAWWNVVNWDAAEKKLQKYL 208
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203
   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
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (2, 4)

Asymmetric Unit
(-)
Clan: no clan defined [family: Sod_Fe_C] (46)
(-)
Clan: no clan defined [family: Sod_Fe_N] (46)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (SODF_SULSO | P80857)
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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 Related Entries

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

UniProtKB/Swiss-Prot
        SODF_SULSO | P80857: 1wb7

(-) Related Entries Specified in the PDB File

1wb7 IRON SUPEROXIDE DISMUTASE (FE-SOD) FROM THE HYPERTHERMOPHILE SULFOLOBUS SOLFATARICUS. CRYSTAL STRUCTURE OF THE Y41F MUTANT.