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(-) Description

Title :  CRYSTAL STRUCTURE OF NI-CONTAINING SUPEROXIDE DISMUTASE WITH NI-LIGATION CORRESPONDING TO THE STATE AFTER FULL X-RAY-INDUCED REDUCTION
 
Authors :  J. Wuerges, J. -W. Lee, Y. -I. Yim, H. -S. Yim, S. -O. Kang, K. Djinovic Carugo
Date :  16 Jul 03  (Deposition) - 18 May 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.68
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Homohexamer Of Four-Helix Bundles, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Wuerges, J. -W. Lee, Y. -I. Yim, H. -S. Yim, S. -O. Kang, K. Djinovic Carugo
Crystal Structure Of Nickel-Containing Superoxide Dismutase Reveals Another Type Of Active Site
Proc. Natl. Acad. Sci. Usa V. 101 8569 2004
PubMed-ID: 15173586  |  Reference-DOI: 10.1073/PNAS.0308514101
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SUPEROXIDE DISMUTASE [NI]
    Chains: A, B, C, D, E, F
    EC Number: 1.15.1.1
    Organism Scientific: STREPTOMYCES SEOULENSIS
    Organism Taxid: 73044
    Other Details: THE ASYMMETRIC UNIT CONTAINS ONE HEXAMER
    Synonym: NICKEL-CONTAINING SUPEROXIDE DISMUTASE

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 17)

Asymmetric/Biological Unit (3, 17)
No.NameCountTypeFull Name
1ACY3Ligand/IonACETIC ACID
2NI6Ligand/IonNICKEL (II) ION
3SO48Ligand/IonSULFATE ION

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:1 , CYS A:2 , ASP A:3 , CYS A:6BINDING SITE FOR RESIDUE NI A 118
02AC2SOFTWAREHIS B:1 , CYS B:2 , ASP B:3 , CYS B:6BINDING SITE FOR RESIDUE NI B 118
03AC3SOFTWAREHIS C:1 , CYS C:2 , ASP C:3 , CYS C:6BINDING SITE FOR RESIDUE NI C 118
04AC4SOFTWAREHIS D:1 , CYS D:2 , ASP D:3 , CYS D:6BINDING SITE FOR RESIDUE NI D 118
05AC5SOFTWAREHIS E:1 , CYS E:2 , ASP E:3 , CYS E:6BINDING SITE FOR RESIDUE NI E 118
06AC6SOFTWAREHIS F:1 , CYS F:2 , ASP F:3 , CYS F:6BINDING SITE FOR RESIDUE NI F 118
07AC7SOFTWAREPRO A:5 , GLY A:7 , TYR A:9 , LYS A:64 , HOH A:9143BINDING SITE FOR RESIDUE SO4 A 9001
08AC8SOFTWAREPRO B:5 , GLY B:7 , TYR B:9 , ASP B:61 , LYS B:64 , HOH B:9046 , HOH B:9060 , HOH B:9119 , HOH B:9151BINDING SITE FOR RESIDUE SO4 B 9002
09AC9SOFTWAREPRO C:5 , GLY C:7 , TYR C:9 , ASP C:61 , LYS C:64 , HOH C:9083 , HOH C:9128 , HOH C:9137BINDING SITE FOR RESIDUE SO4 C 9003
10BC1SOFTWAREPRO D:5 , GLY D:7 , TYR D:9 , ASP D:61 , LYS D:64 , HOH D:9063BINDING SITE FOR RESIDUE SO4 D 9004
11BC2SOFTWAREPRO E:5 , GLY E:7 , TYR E:9 , ASP E:61 , LYS E:64 , HOH E:9079 , HOH E:9113BINDING SITE FOR RESIDUE SO4 E 9005
12BC3SOFTWAREPRO F:5 , GLY F:7 , TYR F:9 , LYS F:64 , HOH F:9076 , HOH F:9108BINDING SITE FOR RESIDUE SO4 F 9006
13BC4SOFTWAREGLN A:46 , GLN B:46 , GLN D:46 , HOH D:9071 , HOH D:9077BINDING SITE FOR RESIDUE SO4 D 9007
14BC5SOFTWAREGLN C:46 , HOH C:9068 , GLN E:46 , GLN F:46BINDING SITE FOR RESIDUE SO4 C 9008
15BC6SOFTWAREGLU C:69 , PRO D:65 , PHE D:68 , ASN E:79 , HOH E:9059 , HOH E:9074BINDING SITE FOR RESIDUE ACY C 7001
16BC7SOFTWARETHR B:76 , ASN B:79 , HOH B:9043 , PRO C:65 , HIS C:75 , GLU D:69BINDING SITE FOR RESIDUE ACY D 7002
17BC8SOFTWAREPRO B:65 , PHE B:68 , ASN C:79 , LYS C:83 , HOH C:9025 , HOH C:9066 , GLU F:69BINDING SITE FOR RESIDUE ACY F 7003

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Q0M)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Leu A:4 -Pro A:5
2Leu B:4 -Pro B:5
3Leu C:4 -Pro C:5
4Leu D:4 -Pro D:5
5Leu E:4 -Pro E:5
6Leu F:4 -Pro F:5

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Q0M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1Q0M)

(-) Exons   (0, 0)

(no "Exon" information available for 1Q0M)

(-) Sequences/Alignments

Asymmetric/Biological 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_STRSO | P80734 from UniProtKB/Swiss-Prot  Length:131

    Alignment length:117
                                    24        34        44        54        64        74        84        94       104       114       124       
           SODN_STRSO    15 HCDLPCGVYDPAQARIEAESVKAIQEKMAANDDLHFQIRATVIKEQRAELAKHHLDVLWSDYFKPPHFESYPELHTLVNEAVKALSAAKASTDPATGQKALDYIAQIDKIFWETKKA 131
               SCOP domains d1q0ma_ A: Nickel-containing superoxide dismutase, NiSOD                                                              SCOP domains
               CATH domains 1q0mA00 A:1-117 Nickel-containing superoxide dismutase, NiSOD                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhh.hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 1q0m A   1 HCDLPCGVYDPAQARIEAESVKAIQEKMAANDDLHFQIRATVIKEQRAELAKHHLDVLWSDYFKPPHFESYPELHTLVNEAVKALSAAKASTDPATGQKALDYIAQIDKIFWETKKA 117
                                    10        20        30        40        50        60        70        80        90       100       110       


Chain B from PDB  Type:PROTEIN  Length:117
 aligned with SODN_STRSO | P80734 from UniProtKB/Swiss-Prot  Length:131

    Alignment length:117
                                    24        34        44        54        64        74        84        94       104       114       124       
           SODN_STRSO    15 HCDLPCGVYDPAQARIEAESVKAIQEKMAANDDLHFQIRATVIKEQRAELAKHHLDVLWSDYFKPPHFESYPELHTLVNEAVKALSAAKASTDPATGQKALDYIAQIDKIFWETKKA 131
               SCOP domains d1q0mb_ B: Nickel-containing superoxide dismutase, NiSOD                                                              SCOP domains
               CATH domains 1q0mB00 B:1-117 Nickel-containing superoxide dismutase, NiSOD                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 1q0m B   1 HCDLPCGVYDPAQARIEAESVKAIQEKMAANDDLHFQIRATVIKEQRAELAKHHLDVLWSDYFKPPHFESYPELHTLVNEAVKALSAAKASTDPATGQKALDYIAQIDKIFWETKKA 117
                                    10        20        30        40        50        60        70        80        90       100       110       


Chain C from PDB  Type:PROTEIN  Length:117
 aligned with SODN_STRSO | P80734 from UniProtKB/Swiss-Prot  Length:131

    Alignment length:117
                                    24        34        44        54        64        74        84        94       104       114       124       
           SODN_STRSO    15 HCDLPCGVYDPAQARIEAESVKAIQEKMAANDDLHFQIRATVIKEQRAELAKHHLDVLWSDYFKPPHFESYPELHTLVNEAVKALSAAKASTDPATGQKALDYIAQIDKIFWETKKA 131
               SCOP domains d1q0mc_ C: Nickel-containing superoxide dismutase, NiSOD                                                              SCOP domains
               CATH domains 1q0mC00 C:1-117 Nickel-containing superoxide dismutase, NiSOD                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhh.hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 1q0m C   1 HCDLPCGVYDPAQARIEAESVKAIQEKMAANDDLHFQIRATVIKEQRAELAKHHLDVLWSDYFKPPHFESYPELHTLVNEAVKALSAAKASTDPATGQKALDYIAQIDKIFWETKKA 117
                                    10        20        30        40        50        60        70        80        90       100       110       


Chain D from PDB  Type:PROTEIN  Length:117
 aligned with SODN_STRSO | P80734 from UniProtKB/Swiss-Prot  Length:131

    Alignment length:117
                                    24        34        44        54        64        74        84        94       104       114       124       
           SODN_STRSO    15 HCDLPCGVYDPAQARIEAESVKAIQEKMAANDDLHFQIRATVIKEQRAELAKHHLDVLWSDYFKPPHFESYPELHTLVNEAVKALSAAKASTDPATGQKALDYIAQIDKIFWETKKA 131
               SCOP domains d1q0md_ D: Nickel-containing superoxide dismutase, NiSOD                                                              SCOP domains
               CATH domains 1q0mD00 D:1-117 Nickel-containing superoxide dismutase, NiSOD                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhh.hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 1q0m D   1 HCDLPCGVYDPAQARIEAESVKAIQEKMAANDDLHFQIRATVIKEQRAELAKHHLDVLWSDYFKPPHFESYPELHTLVNEAVKALSAAKASTDPATGQKALDYIAQIDKIFWETKKA 117
                                    10        20        30        40        50        60        70        80        90       100       110       


Chain E from PDB  Type:PROTEIN  Length:117
 aligned with SODN_STRSO | P80734 from UniProtKB/Swiss-Prot  Length:131

    Alignment length:117
                                    24        34        44        54        64        74        84        94       104       114       124       
           SODN_STRSO    15 HCDLPCGVYDPAQARIEAESVKAIQEKMAANDDLHFQIRATVIKEQRAELAKHHLDVLWSDYFKPPHFESYPELHTLVNEAVKALSAAKASTDPATGQKALDYIAQIDKIFWETKKA 131
               SCOP domains d1q0me_ E: Nickel-containing superoxide dismutase, NiSOD                                                              SCOP domains
               CATH domains 1q0mE00 E:1-117 Nickel-containing superoxide dismutase, NiSOD                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhh.hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 1q0m E   1 HCDLPCGVYDPAQARIEAESVKAIQEKMAANDDLHFQIRATVIKEQRAELAKHHLDVLWSDYFKPPHFESYPELHTLVNEAVKALSAAKASTDPATGQKALDYIAQIDKIFWETKKA 117
                                    10        20        30        40        50        60        70        80        90       100       110       


Chain F from PDB  Type:PROTEIN  Length:117
 aligned with SODN_STRSO | P80734 from UniProtKB/Swiss-Prot  Length:131

    Alignment length:117
                                    24        34        44        54        64        74        84        94       104       114       124       
           SODN_STRSO    15 HCDLPCGVYDPAQARIEAESVKAIQEKMAANDDLHFQIRATVIKEQRAELAKHHLDVLWSDYFKPPHFESYPELHTLVNEAVKALSAAKASTDPATGQKALDYIAQIDKIFWETKKA 131
               SCOP domains d1q0mf_ F: Nickel-containing superoxide dismutase, NiSOD                                                              SCOP domains
               CATH domains 1q0mF00 F:1-117 Nickel-containing superoxide dismutase, NiSOD                                                         CATH domains
           Pfam domains (1) Sod_Ni-1q0mF01 F:1-115                                                                                             -- Pfam domains (1)
           Pfam domains (2) Sod_Ni-1q0mF02 F:1-115                                                                                             -- Pfam domains (2)
           Pfam domains (3) Sod_Ni-1q0mF03 F:1-115                                                                                             -- Pfam domains (3)
           Pfam domains (4) Sod_Ni-1q0mF04 F:1-115                                                                                             -- Pfam domains (4)
           Pfam domains (5) Sod_Ni-1q0mF05 F:1-115                                                                                             -- Pfam domains (5)
           Pfam domains (6) Sod_Ni-1q0mF06 F:1-115                                                                                             -- Pfam domains (6)
         Sec.struct. author ..........hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh.hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 1q0m F   1 HCDLPCGVYDPAQARIEAESVKAIQEKMAANDDLHFQIRATVIKEQRAELAKHHLDVLWSDYFKPPHFESYPELHTLVNEAVKALSAAKASTDPATGQKALDYIAQIDKIFWETKKA 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, 6)

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

(-) CATH Domains  (1, 6)

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

(-) Pfam Domains  (1, 6)

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

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (SODN_STRSO | P80734)
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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  1q0m
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  SODN_STRSO | P80734
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 Related Entries

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

UniProtKB/Swiss-Prot
        SODN_STRSO | P80734: 1q0d 1q0f 1q0g 1q0k

(-) Related Entries Specified in the PDB File

1q0d 1Q0D CONTAINS THE RESTING ENZYME IN ANOTHER CRYSTAL FORM
1q0f 1Q0F CONTAINS THE PARTIALLY X-RAY REDUCED ENZYME IN ANOTHER CRYSTAL FORM
1q0g 1Q0G CONTAINS THE FULLY X-RAY REDUCED ENZYME IN ANOTHER CRYSTAL FORM
1q0k 1Q0K CONTAINS THE THIOSULFATE-REDUCED ENZYME IN ANOTHER CRYSTAL FORM