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(-) Description

Title :  NICKEL SUPEROXIDE DISMUTASE (NISOD) CN-TREATED APO STRUCTURE
 
Authors :  D. P. Barondeau, C. J. Kassmann, C. K. Bruns, J. A. Tainer, E. D. Getzoff
Date :  07 May 04  (Deposition) - 13 Jul 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (2x)
Keywords :  Nickel, 4-Helix Bundle, Hexamer, Superoxide Dismutase, Nisod, Sod, Apo, Cyanide, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. P. Barondeau, C. J. Kassmann, C. K. Bruns, J. A. Tainer, E. D. Getzoff
Nickel Superoxide Dismutase Structure And Mechanism.
Biochemistry V. 43 8038 2004
PubMed-ID: 15209499  |  Reference-DOI: 10.1021/BI0496081

(-) Compounds

Molecule 1 - SUPEROXIDE DISMUTASE [NI]
    Chains: A, B, C
    EC Number: 1.15.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET26
    Expression System Strain: BL21(DE3)RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: SODN, SOD1, SCO5254, 2SC7G11.16C
    Mutation: YES
    Organism Scientific: STREPTOMYCES COELICOLOR
    Organism Taxid: 1902
    Synonym: NISOD, NICKEL- CONTAINING SUPEROXIDE DISMUTASE

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x): ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1T6Q)

(-) Sites  (0, 0)

(no "Site" information available for 1T6Q)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1T6Q)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1T6Q)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1T6Q)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1T6Q)

(-) Exons   (0, 0)

(no "Exon" information available for 1T6Q)

(-) 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:110
 aligned with SODN_STRCO | P80735 from UniProtKB/Swiss-Prot  Length:131

    Alignment length:110
                                    30        40        50        60        70        80        90       100       110       120       130
           SODN_STRCO    21 GVYDPAQARIEAESVKAVQEKMAGNDDPHFQTRATVIKEQRAELAKHHVSVLWSDYFKPPHFEKYPELHQLVNDTLKALSAAKGSKDPATGQKALDYIAQIDKIFWETKK 130
               SCOP domains d1t6qa_ A: Nickel-containing superoxide dismutase, NiSOD                                                       SCOP domains
               CATH domains 1t6qA00 A:7-116 Nickel-containing superoxide dismutase, NiSOD                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh.hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 1t6q A   7 GVYDPAQARIEAESVKAVQEKMAGNDDPHFQTRATVIKEQRAELAKHHVSVLWSDYFKPPHFEKYPELHQLVNDTLKAMSAAKGSKDPATGQKALDYIAQIDKIFWETKK 116
                                    16        26        36        46        56        66        76        86        96       106       116


Chain B from PDB  Type:PROTEIN  Length:112
 aligned with SODN_STRCO | P80735 from UniProtKB/Swiss-Prot  Length:131

    Alignment length:112
                                    29        39        49        59        69        79        89        99       109       119       129  
           SODN_STRCO    20 CGVYDPAQARIEAESVKAVQEKMAGNDDPHFQTRATVIKEQRAELAKHHVSVLWSDYFKPPHFEKYPELHQLVNDTLKALSAAKGSKDPATGQKALDYIAQIDKIFWETKKA 131
               SCOP domains d1t6qb_ B: Nickel-containing superoxide dismutase, NiSOD                                                         SCOP domains
               CATH domains 1t6qB00 B:6-117 Nickel-containing superoxide dismutase, NiSOD                                                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh.hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 1t6q B   6 CGVYDPAQARIEAESVKAVQEKMAGNDDPHFQTRATVIKEQRAELAKHHVSVLWSDYFKPPHFEKYPELHQLVNDTLKAMSAAKGSKDPATGQKALDYIAQIDKIFWETKKA 117
                                    15        25        35        45        55        65        75        85        95       105       115  


Chain C from PDB  Type:PROTEIN  Length:110
 aligned with SODN_STRCO | P80735 from UniProtKB/Swiss-Prot  Length:131

    Alignment length:110
                                    30        40        50        60        70        80        90       100       110       120       130
           SODN_STRCO    21 GVYDPAQARIEAESVKAVQEKMAGNDDPHFQTRATVIKEQRAELAKHHVSVLWSDYFKPPHFEKYPELHQLVNDTLKALSAAKGSKDPATGQKALDYIAQIDKIFWETKK 130
               SCOP domains d1t6qc_ C: Nickel-containing superoxide dismutase, NiSOD                                                       SCOP domains
               CATH domains 1t6qC00 C:7-116 Nickel-containing superoxide dismutase, NiSOD                                                  CATH domains
           Pfam domains (1) Sod_Ni-1t6qC01 C:7-115                                                                                       - Pfam domains (1)
           Pfam domains (2) Sod_Ni-1t6qC02 C:7-115                                                                                       - Pfam domains (2)
           Pfam domains (3) Sod_Ni-1t6qC03 C:7-115                                                                                       - Pfam domains (3)
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh.hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 1t6q C   7 GVYDPAQARIEAESVKAVQEKMAGNDDPHFQTRATVIKEQRAELAKHHVSVLWSDYFKPPHFEKYPELHQLVNDTLKAMSAAKGSKDPATGQKALDYIAQIDKIFWETKK 116
                                    16        26        36        46        56        66        76        86        96       106       116
   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  (1, 3)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (1, 3)

Asymmetric Unit
(-)
Clan: no clan defined [family: Sod_Ni] (8)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (SODN_STRCO | P80735)
molecular function
    GO:0016209    antioxidant activity    Inhibition of the reactions brought about by dioxygen (O2) or peroxides. Usually the antioxidant is effective because it can itself be more easily oxidized than the substance protected. The term is often applied to components that can trap free radicals, thereby breaking the chain reaction that normally leads to extensive biological damage.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016151    nickel cation binding    Interacting selectively and non-covalently with nickel (Ni) cations.
    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:0098869    cellular oxidant detoxification    Any process carried out at the cellular level that reduces or removes the toxicity superoxide radicals or hydrogen peroxide.
    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).
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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  1t6q
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 Related Entries

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

UniProtKB/Swiss-Prot
        SODN_STRCO | P80735: 1t6i 1t6u 3g4x 3g4z 3g50 4ncq

(-) Related Entries Specified in the PDB File

1t6i NICKEL SUPEROXIDE DISMUTASE (NISOD) APO STRUCTURE
1t6u NICKEL SUPEROXIDE DISMUTASE (NISOD) NATIVE 1.3A STRUCTURE