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(-) Description

Title :  CRYSTAL STRUCTURE OF NISOD Y9F MUTANT AT 1.9 A
 
Authors :  S. C. Garman, A. I. Guce, R. W. Herbst, P. A. Bryngelson, D. E. Cabelli, K. A. Higgins, K. C. Ryan, M. J. Maroney
Date :  04 Feb 09  (Deposition) - 28 Apr 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.87
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (2x)
Keywords :  Nickel, Hexamer, Superoxide Dismutase, Nisod, Sod, Antioxidant, Metal-Binding, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. W. Herbst, A. Guce, P. A. Bryngelson, K. A. Higgins, K. C. Ryan, D. E. Cabelli, S. C. Garman, M. J. Maroney
Role Of Conserved Tyrosine Residues In Nisod Catalysis: A Case Of Convergent Evolution
Biochemistry V. 48 3354 2009
PubMed-ID: 19183068  |  Reference-DOI: 10.1021/BI802029T

(-) 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: PET30
    Expression System Strain: BL21(DE3) PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: NISOD (UNP RESIDUES 15 TO 131)
    Gene: 2SC7G11.16C, SCO5254, SOD1, SODN
    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  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1BR3Ligand/IonBROMIDE ION
2NI3Ligand/IonNICKEL (II) ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1BR-1Ligand/IonBROMIDE ION
2NI-1Ligand/IonNICKEL (II) ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:1 , CYS A:2 , ASP A:3 , CYS A:6BINDING SITE FOR RESIDUE NI A 201
2AC2SOFTWAREASP A:3 , PRO A:5 , CYS A:6 , PHE A:9 , HOH A:355BINDING SITE FOR RESIDUE BR A 301
3AC3SOFTWAREPRO B:5 , PHE B:9 , ASP B:61BINDING SITE FOR RESIDUE BR B 302
4AC4SOFTWAREHIS B:1 , CYS B:2 , ASP B:3 , CYS B:6BINDING SITE FOR RESIDUE NI B 202
5AC5SOFTWAREHIS C:1 , CYS C:2 , CYS C:6BINDING SITE FOR RESIDUE NI C 203
6AC6SOFTWAREASP C:3 , PRO C:5 , CYS C:6 , PHE C:9BINDING SITE FOR RESIDUE BR C 303

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3G4Z)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Leu A:4 -Pro A:5
2Leu B:4 -Pro B:5
3Leu C:4 -Pro C:5

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3G4Z)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3G4Z)

(-) Exons   (0, 0)

(no "Exon" information available for 3G4Z)

(-) 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:117
 aligned with SODN_STRCO | P80735 from UniProtKB/Swiss-Prot  Length:131

    Alignment length:117
                                    24        34        44        54        64        74        84        94       104       114       124       
           SODN_STRCO    15 HCDLPCGVYDPAQARIEAESVKAVQEKMAGNDDPHFQTRATVIKEQRAELAKHHVSVLWSDYFKPPHFEKYPELHQLVNDTLKALSAAKGSKDPATGQKALDYIAQIDKIFWETKKA 131
               SCOP domains d3g4za_ A: automated matches                                                                                          SCOP domains
               CATH domains 3g4zA00 A:1-117 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
                 3g4z A   1 HCDLPCGVFDPAQARIEAESVKAVQEKMAGNDDPHFQTRATVIKEQRAELAKHHVSVLWSDYFKPPHFEKYPELHQLVNDTLKALSAAKGSKDPATGQKALDYIAQIDKIFWETKKA 117
                                    10        20        30        40        50        60        70        80        90       100       110       


Chain B from PDB  Type:PROTEIN  Length:117
 aligned with SODN_STRCO | P80735 from UniProtKB/Swiss-Prot  Length:131

    Alignment length:117
                                    24        34        44        54        64        74        84        94       104       114       124       
           SODN_STRCO    15 HCDLPCGVYDPAQARIEAESVKAVQEKMAGNDDPHFQTRATVIKEQRAELAKHHVSVLWSDYFKPPHFEKYPELHQLVNDTLKALSAAKGSKDPATGQKALDYIAQIDKIFWETKKA 131
               SCOP domains d3g4zb_ B: automated matches                                                                                          SCOP domains
               CATH domains 3g4zB00 B:1-117 Nickel-containing superoxide dismutase, NiSOD                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh.hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 3g4z B   1 HCDLPCGVFDPAQARIEAESVKAVQEKMAGNDDPHFQTRATVIKEQRAELAKHHVSVLWSDYFKPPHFEKYPELHQLVNDTLKALSAAKGSKDPATGQKALDYIAQIDKIFWETKKA 117
                                    10        20        30        40        50        60        70        80        90       100       110       


Chain C from PDB  Type:PROTEIN  Length:117
 aligned with SODN_STRCO | P80735 from UniProtKB/Swiss-Prot  Length:131

    Alignment length:117
                                    24        34        44        54        64        74        84        94       104       114       124       
           SODN_STRCO    15 HCDLPCGVYDPAQARIEAESVKAVQEKMAGNDDPHFQTRATVIKEQRAELAKHHVSVLWSDYFKPPHFEKYPELHQLVNDTLKALSAAKGSKDPATGQKALDYIAQIDKIFWETKKA 131
               SCOP domains d3g4zc_ C: automated matches                                                                                          SCOP domains
               CATH domains 3g4zC00 C:1-117 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
                 3g4z C   1 HCDLPCGVFDPAQARIEAESVKAVQEKMAGNDDPHFQTRATVIKEQRAELAKHHVSVLWSDYFKPPHFEKYPELHQLVNDTLKALSAAKGSKDPATGQKALDYIAQIDKIFWETKKA 117
                                    10        20        30        40        50        60        70        80        90       100       110
   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  (0, 0)

(no "Pfam Domain" information available for 3G4Z)

(-) 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: 1t6i 1t6q 1t6u 3g4x 3g50 4ncq

(-) Related Entries Specified in the PDB File

3g4x CRYSTAL STRUCTURE OF NISOD Y9F MUTANT
3g50 CRYSTAL STRUCTURE OF NISOD D3A MUTANT AT 1.9 A
it6u NICKEL SUPEROXIDE DISMUTASE (NISOD) NATIVE AT 1.30 A