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(-) Description

Title :  STRUCTURE AND PROPERTIES OF THE ATYPICAL IRON SUPEROXIDE DISMUTASE FROM METHANOBACTERIUM THERMOAUTOTROPHICUM
 
Authors :  J. J. Adams, B. F. Anderson, J. P. Renault, C. Verchere-Beaur, I. Morgenstern-Badarau, G. B. Jameson
Date :  31 Jul 02  (Deposition) - 21 Aug 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B  (2x)
Biol. Unit 2:  C,D,E,F  (1x)
Keywords :  Iron Superoxide Dismutase, Metal Specificity, Azide Inhibition, Peroxide Inactivation, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. J. Adams, B. F. Anderson, J. P. Renault, C. Verchere-Beaur, I. Morgenstern-Badarau, G. B. Jameson
Structure And Properties Of The Atypical Iron Superoxide Dismutase From Methanobacterium Thermoautotrophicum
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SUPEROXIDE DISMUTASE
    Chains: A, B, C, D, E, F
    EC Number: 1.15.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PETS1
    Expression System Strain: BL21 (DE1)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: SODF
    Organism Scientific: METHANOTHERMOBACTER THERMAUTOTROPHICUS
    Organism Taxid: 145262

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (2x): AB    
Biological Unit 2 (1x):   CDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric Unit (1, 6)
No.NameCountTypeFull Name
1FE6Ligand/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  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:32 , HIS A:80 , ASP A:166 , HIS A:170 , HOH A:272BINDING SITE FOR RESIDUE FE A 206
2AC2SOFTWAREHIS B:32 , HIS B:80 , ASP B:166 , HIS B:170 , HOH B:246BINDING SITE FOR RESIDUE FE B 206
3AC3SOFTWAREHIS C:32 , HIS C:80 , ASP C:166 , HIS C:170 , HOH C:290BINDING SITE FOR RESIDUE FE C 206
4AC4SOFTWAREHIS D:32 , HIS D:80 , ASP D:166 , HIS D:170 , HOH D:286BINDING SITE FOR RESIDUE FE D 206
5AC5SOFTWAREHIS E:32 , HIS E:80 , ASP E:166 , HIS E:170 , HOH E:299BINDING SITE FOR RESIDUE FE E 206
6AC6SOFTWAREHIS F:32 , HIS F:80 , ASP F:166 , HIS F:170 , HOH F:265BINDING SITE FOR RESIDUE FE F 206

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1MA1)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Glu A:21 -Pro A:22
2Glu B:21 -Pro B:22
3Glu C:21 -Pro C:22
4Glu D:21 -Pro D:22
5Glu E:21 -Pro E:22
6Glu F:21 -Pro F:22

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1MA1)

(-) PROSITE Motifs  (1, 6)

Asymmetric Unit (1, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SOD_MNPS00088 Manganese and iron superoxide dismutases signature.SODF_METTH167-174
 
 
 
 
 		  6A:166-173
B:166-173
C:166-173
D:166-173
E:166-173
F:166-173
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SOD_MNPS00088 Manganese and iron superoxide dismutases signature.SODF_METTH167-174
 
 
 
 
 		  4A:166-173
B:166-173
-
-
-
-
Biological Unit 2 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SOD_MNPS00088 Manganese and iron superoxide dismutases signature.SODF_METTH167-174
 
 
 
 
 		  4-
-
C:166-173
D:166-173
E:166-173
F:166-173

(-) Exons   (0, 0)

(no "Exon" information available for 1MA1)

(-) 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:201
 aligned with SODF_METTH | P18868 from UniProtKB/Swiss-Prot  Length:205

    Alignment length:201
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204 
           SODF_METTH     5 EKKFYELPELPYPYDALEPHISREQLTIHHQKHHQAYVDGANALLRKLDEARESDTDVDIKAALKELSFHVGGYVLHLFFWGNMGPADECGGEPSGKLAEYIEKDFGSFERFRKEFSQAAISAEGSGWAVLTYCQRTDRLFIMQVEKHNVNVIPHFRILLVLDVWEHAYYIDYRNVRPDYVEAFWNIVNWKEVEKRFEDIL 205
               SCOP domains d1ma1a1 A:4-91 Fe superoxide dismutase (FeSOD)                                          d1ma1a2 A:92-204 Fe superoxide dismutase (FeSOD)                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeee....eeeeeeee.............eeee.hhhhhhhhhh.hhhhhhhhhh...hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  ------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ma1 A   4 EKKFYELPELPYPYDALEPHISREQLTIHHQKHHQAYVDGANALLRKLDEARESDTDVDIKAALKELSFHVGGYVLHLFFWGNMGPADECGGEPSGKLAEYIEKDFGSFERFRKEFSQAAISAEGSGWAVLTYCQRTDRLFIMQVEKHNVNVIPHFRILLVLDVWEHAYYIDYRNVRPDYVEAFWNIVNWKEVEKRFEDIL 204
                                    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:201
 aligned with SODF_METTH | P18868 from UniProtKB/Swiss-Prot  Length:205

    Alignment length:201
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204 
           SODF_METTH     5 EKKFYELPELPYPYDALEPHISREQLTIHHQKHHQAYVDGANALLRKLDEARESDTDVDIKAALKELSFHVGGYVLHLFFWGNMGPADECGGEPSGKLAEYIEKDFGSFERFRKEFSQAAISAEGSGWAVLTYCQRTDRLFIMQVEKHNVNVIPHFRILLVLDVWEHAYYIDYRNVRPDYVEAFWNIVNWKEVEKRFEDIL 205
               SCOP domains d1ma1b1 B:4-91 Fe superoxide dismutase (FeSOD)                                          d1ma1b2 B:92-204 Fe superoxide dismutase (FeSOD)                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeee....eeeeeeee.............eeee.hhhhhhhhhh.hhhhhhhhhh...hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  ------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ma1 B   4 EKKFYELPELPYPYDALEPHISREQLTIHHQKHHQAYVDGANALLRKLDEARESDTDVDIKAALKELSFHVGGYVLHLFFWGNMGPADECGGEPSGKLAEYIEKDFGSFERFRKEFSQAAISAEGSGWAVLTYCQRTDRLFIMQVEKHNVNVIPHFRILLVLDVWEHAYYIDYRNVRPDYVEAFWNIVNWKEVEKRFEDIL 204
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203 


Chain C from PDB  Type:PROTEIN  Length:201
 aligned with SODF_METTH | P18868 from UniProtKB/Swiss-Prot  Length:205

    Alignment length:201
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204 
           SODF_METTH     5 EKKFYELPELPYPYDALEPHISREQLTIHHQKHHQAYVDGANALLRKLDEARESDTDVDIKAALKELSFHVGGYVLHLFFWGNMGPADECGGEPSGKLAEYIEKDFGSFERFRKEFSQAAISAEGSGWAVLTYCQRTDRLFIMQVEKHNVNVIPHFRILLVLDVWEHAYYIDYRNVRPDYVEAFWNIVNWKEVEKRFEDIL 205
               SCOP domains d1ma1c1 C:4-91 Fe superoxide dismutase (FeSOD)                                          d1ma1c2 C:92-204 Fe superoxide dismutase (FeSOD)                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeee....eeeeeeee.............eeee.hhhhhhhhhh.hhhhhhhhhh...hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  ------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ma1 C   4 EKKFYELPELPYPYDALEPHISREQLTIHHQKHHQAYVDGANALLRKLDEARESDTDVDIKAALKELSFHVGGYVLHLFFWGNMGPADECGGEPSGKLAEYIEKDFGSFERFRKEFSQAAISAEGSGWAVLTYCQRTDRLFIMQVEKHNVNVIPHFRILLVLDVWEHAYYIDYRNVRPDYVEAFWNIVNWKEVEKRFEDIL 204
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203 


Chain D from PDB  Type:PROTEIN  Length:201
 aligned with SODF_METTH | P18868 from UniProtKB/Swiss-Prot  Length:205

    Alignment length:201
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204 
           SODF_METTH     5 EKKFYELPELPYPYDALEPHISREQLTIHHQKHHQAYVDGANALLRKLDEARESDTDVDIKAALKELSFHVGGYVLHLFFWGNMGPADECGGEPSGKLAEYIEKDFGSFERFRKEFSQAAISAEGSGWAVLTYCQRTDRLFIMQVEKHNVNVIPHFRILLVLDVWEHAYYIDYRNVRPDYVEAFWNIVNWKEVEKRFEDIL 205
               SCOP domains d1ma1d1 D:4-91 Fe superoxide dismutase (FeSOD)                                          d1ma1d2 D:92-204 Fe superoxide dismutase (FeSOD)                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeee....eeeeeeee.............eeee.hhhhhhhhhh.hhhhhhhhhh...hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  ------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ma1 D   4 EKKFYELPELPYPYDALEPHISREQLTIHHQKHHQAYVDGANALLRKLDEARESDTDVDIKAALKELSFHVGGYVLHLFFWGNMGPADECGGEPSGKLAEYIEKDFGSFERFRKEFSQAAISAEGSGWAVLTYCQRTDRLFIMQVEKHNVNVIPHFRILLVLDVWEHAYYIDYRNVRPDYVEAFWNIVNWKEVEKRFEDIL 204
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203 


Chain E from PDB  Type:PROTEIN  Length:201
 aligned with SODF_METTH | P18868 from UniProtKB/Swiss-Prot  Length:205

    Alignment length:201
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204 
           SODF_METTH     5 EKKFYELPELPYPYDALEPHISREQLTIHHQKHHQAYVDGANALLRKLDEARESDTDVDIKAALKELSFHVGGYVLHLFFWGNMGPADECGGEPSGKLAEYIEKDFGSFERFRKEFSQAAISAEGSGWAVLTYCQRTDRLFIMQVEKHNVNVIPHFRILLVLDVWEHAYYIDYRNVRPDYVEAFWNIVNWKEVEKRFEDIL 205
               SCOP domains d1ma1e1 E:4-91 Fe superoxide dismutase (FeSOD)                                          d1ma1e2 E:92-204 Fe superoxide dismutase (FeSOD)                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeee....eeeeeeee.............eeee.hhhhhhhhhh.hhhhhhhhhh...hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  ------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ma1 E   4 EKKFYELPELPYPYDALEPHISREQLTIHHQKHHQAYVDGANALLRKLDEARESDTDVDIKAALKELSFHVGGYVLHLFFWGNMGPADECGGEPSGKLAEYIEKDFGSFERFRKEFSQAAISAEGSGWAVLTYCQRTDRLFIMQVEKHNVNVIPHFRILLVLDVWEHAYYIDYRNVRPDYVEAFWNIVNWKEVEKRFEDIL 204
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203 


Chain F from PDB  Type:PROTEIN  Length:201
 aligned with SODF_METTH | P18868 from UniProtKB/Swiss-Prot  Length:205

    Alignment length:201
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204 
           SODF_METTH     5 EKKFYELPELPYPYDALEPHISREQLTIHHQKHHQAYVDGANALLRKLDEARESDTDVDIKAALKELSFHVGGYVLHLFFWGNMGPADECGGEPSGKLAEYIEKDFGSFERFRKEFSQAAISAEGSGWAVLTYCQRTDRLFIMQVEKHNVNVIPHFRILLVLDVWEHAYYIDYRNVRPDYVEAFWNIVNWKEVEKRFEDIL 205
               SCOP domains d1ma1f1 F:4-91 Fe superoxide dismutase (FeSOD)                                          d1ma1f2 F:92-204 Fe superoxide dismutase (FeSOD)                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---Sod_Fe_N-1ma1F07 F:7-88                                                           ------Sod_Fe_C-1ma1F01 F:95-200                                                                                 ---- Pfam domains (1)
           Pfam domains (2) ---Sod_Fe_N-1ma1F08 F:7-88                                                           ------Sod_Fe_C-1ma1F02 F:95-200                                                                                 ---- Pfam domains (2)
           Pfam domains (3) ---Sod_Fe_N-1ma1F09 F:7-88                                                           ------Sod_Fe_C-1ma1F03 F:95-200                                                                                 ---- Pfam domains (3)
           Pfam domains (4) ---Sod_Fe_N-1ma1F10 F:7-88                                                           ------Sod_Fe_C-1ma1F04 F:95-200                                                                                 ---- Pfam domains (4)
           Pfam domains (5) ---Sod_Fe_N-1ma1F11 F:7-88                                                           ------Sod_Fe_C-1ma1F05 F:95-200                                                                                 ---- Pfam domains (5)
           Pfam domains (6) ---Sod_Fe_N-1ma1F12 F:7-88                                                           ------Sod_Fe_C-1ma1F06 F:95-200                                                                                 ---- Pfam domains (6)
         Sec.struct. author .....................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeee....eeeeeeee.............eeee.hhhhhhhhhh.hhhhhhhhhh...hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  ------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ma1 F   4 EKKFYELPELPYPYDALEPHISREQLTIHHQKHHQAYVDGANALLRKLDEARESDTDVDIKAALKELSFHVGGYVLHLFFWGNMGPADECGGEPSGKLAEYIEKDFGSFERFRKEFSQAAISAEGSGWAVLTYCQRTDRLFIMQVEKHNVNVIPHFRILLVLDVWEHAYYIDYRNVRPDYVEAFWNIVNWKEVEKRFEDIL 204
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203
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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, 12)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1MA1)

(-) Pfam Domains  (2, 12)

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

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (SODF_METTH | P18868)
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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  1ma1
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  SODF_METTH | P18868
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  1.15.1.1
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 Related Entries

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