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(-) Description

Title :  NICKEL SUPEROXIDE DISMUTASE (NISOD) APO STRUCTURE
 
Authors :  D. P. Barondeau, C. J. Kassmann, C. K. Bruns, J. A. Tainer, E. D. Getzoff
Date :  06 May 04  (Deposition) - 13 Jul 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.81
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (2x)
Keywords :  Nickel, 4-Helix Bundle, Hexamer, Superoxide Dismutase, Nisod, Sod, Apo, 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: PET11A
    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  (1, 6)

Asymmetric Unit (1, 6)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 12)
No.NameCountTypeFull Name
1MSE12Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1T6I)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1T6I)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1T6I)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1T6I)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1T6I)

(-) Exons   (0, 0)

(no "Exon" information available for 1T6I)

(-) 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:111
 aligned with SODN_STRCO | P80735 from UniProtKB/Swiss-Prot  Length:131

    Alignment length:111
                                    30        40        50        60        70        80        90       100       110       120       130 
           SODN_STRCO    21 GVYDPAQARIEAESVKAVQEKMAGNDDPHFQTRATVIKEQRAELAKHHVSVLWSDYFKPPHFEKYPELHQLVNDTLKALSAAKGSKDPATGQKALDYIAQIDKIFWETKKA 131
               SCOP domains d1t6ia_ A: Nickel-containing superoxide dismutase, NiSOD                                                        SCOP domains
               CATH domains 1t6iA00 A:7-117 Nickel-containing superoxide dismutase, NiSOD                                                   CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhh.hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                 1t6i A   7 GVYDPAQARIEAESVKAVQEKmAGNDDPHFQTRATVIKEQRAELAKHHVSVLWSDYFKPPHFEKYPELHQLVNDTLKAmSAAKGSKDPATGQKALDYIAQIDKIFWETKKA 117
                                    16        26 |      36        46        56        66        76        86        96       106       116 
                                                28-MSE                                                   85-MSE                            


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

    Alignment length:110
                                    31        41        51        61        71        81        91       101       111       121       131
           SODN_STRCO    22 VYDPAQARIEAESVKAVQEKMAGNDDPHFQTRATVIKEQRAELAKHHVSVLWSDYFKPPHFEKYPELHQLVNDTLKALSAAKGSKDPATGQKALDYIAQIDKIFWETKKA 131
               SCOP domains d1t6ib_ B: Nickel-containing superoxide dismutase, NiSOD                                                       SCOP domains
               CATH domains 1t6iB00 B:8-117 Nickel-containing superoxide dismutase, NiSOD                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh.hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 1t6i B   8 VYDPAQARIEAESVKAVQEKmAGNDDPHFQTRATVIKEQRAELAKHHVSVLWSDYFKPPHFEKYPELHQLVNDTLKAmSAAKGSKDPATGQKALDYIAQIDKIFWETKKA 117
                                    17        27|       37        47        57        67        77       |87        97       107       117
                                               28-MSE                                                   85-MSE                            


Chain C from PDB  Type:PROTEIN  Length:109
 aligned with SODN_STRCO | P80735 from UniProtKB/Swiss-Prot  Length:131

    Alignment length:109
                                    31        41        51        61        71        81        91       101       111       121         
           SODN_STRCO    22 VYDPAQARIEAESVKAVQEKMAGNDDPHFQTRATVIKEQRAELAKHHVSVLWSDYFKPPHFEKYPELHQLVNDTLKALSAAKGSKDPATGQKALDYIAQIDKIFWETKK 130
               SCOP domains d1t6ic_ C: Nickel-containing superoxide dismutase, NiSOD                                                      SCOP domains
               CATH domains 1t6iC00 C:8-116 Nickel-containing superoxide dismutase, NiSOD                                                 CATH domains
           Pfam domains (1) Sod_Ni-1t6iC01 C:8-115                                                                                      - Pfam domains (1)
           Pfam domains (2) Sod_Ni-1t6iC02 C:8-115                                                                                      - Pfam domains (2)
           Pfam domains (3) Sod_Ni-1t6iC03 C:8-115                                                                                      - Pfam domains (3)
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh.hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                 1t6i C   8 VYDPAQARIEAESVKAVQEKmAGNDDPHFQTRATVIKEQRAELAKHHVSVLWSDYFKPPHFEKYPELHQLVNDTLKAmSAAKGSKDPATGQKALDYIAQIDKIFWETKK 116
                                    17        27|       37        47        57        67        77       |87        97       107         
                                               28-MSE                                                   85-MSE
   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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 Related Entries

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

UniProtKB/Swiss-Prot
        SODN_STRCO | P80735: 1t6q 1t6u 3g4x 3g4z 3g50 4ncq

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