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PDBsum entry 1t6u

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protein metals Protein-protein interface(s) links
Oxidoreductase PDB id
1t6u
Jmol
Contents
Protein chains
(+ 6 more) 117 a.a. *
Metals
_NI ×12
Waters ×1926
* Residue conservation analysis
PDB id:
1t6u
Name: Oxidoreductase
Title: Nickel superoxide dismutase (nisod) native 1.30 a structure
Structure: Superoxide dismutase [ni]. Chain: a, b, c, d, e, f, g, h, i, j, k, l. Synonym: nisod, nickel- containing superoxide dismutase. Engineered: yes. Mutation: yes
Source: Streptomyces coelicolor. Organism_taxid: 1902. Gene: sodn, sod1, sco5254, 2sc7g11.16c. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Hexamer (from PQS)
Resolution:
1.30Å     R-factor:   0.158     R-free:   0.201
Authors: D.P.Barondeau,C.J.Kassmann,C.K.Bruns,J.A.Tainer,E.D.Getzoff
Key ref:
D.P.Barondeau et al. (2004). Nickel superoxide dismutase structure and mechanism. Biochemistry, 43, 8038-8047. PubMed id: 15209499 DOI: 10.1021/bi0496081
Date:
07-May-04     Release date:   13-Jul-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P80735  (SODN_STRCO) -  Superoxide dismutase [Ni]
Seq:
Struc:
131 a.a.
117 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.1.15.1.1  - Superoxide dismutase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 2 superoxide + 2 H+ = O2 + H2O2
2 × superoxide
+ 2 × H(+)
= O(2)
+ H(2)O(2)
      Cofactor: Fe cation or Mn(2+) or (Zn(2+) and Cu cation)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     antioxidant activity     3 terms  

 

 
    Added reference    
 
 
DOI no: 10.1021/bi0496081 Biochemistry 43:8038-8047 (2004)
PubMed id: 15209499  
 
 
Nickel superoxide dismutase structure and mechanism.
D.P.Barondeau, C.J.Kassmann, C.K.Bruns, J.A.Tainer, E.D.Getzoff.
 
  ABSTRACT  
 
The 1.30 A resolution crystal structure of nickel superoxide dismutase (NiSOD) identifies a novel SOD fold, assembly, and Ni active site. NiSOD is a hexameric assembly of right-handed 4-helix bundles of up-down-up-down topology with N-terminal hooks chelating the active site Ni ions. This newly identified nine-residue Ni-hook structural motif (His-Cys-X-X-Pro-Cys-Gly-X-Tyr) provides almost all interactions critical for metal binding and catalysis, and thus will likely be diagnostic of NiSODs. Conserved lysine residues are positioned for electrostatic guidance of the superoxide anion to the narrow active site channel. Apo structures show that the Ni-hook motif is unfolded prior to metal binding. The active site Ni geometry cycles from square planar Ni(II), with thiolate (Cys2 and Cys6) and backbone nitrogen (His1 and Cys2) ligands, to square pyramidal Ni(III) with an added axial His1 side chain ligand, consistent with electron paramagentic resonance spectroscopy. Analyses of the three NiSOD structures and comparisons to the Cu,Zn and Mn/Fe SODs support specific molecular mechanisms for NiSOD maturation and catalysis, and identify important structure-function relationships conserved among SODs.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
23396808 S.Classen, G.L.Hura, J.M.Holton, R.P.Rambo, I.Rodic, P.J.McGuire, K.Dyer, M.Hammel, G.Meigs, K.A.Frankel, and J.A.Tainer (2013).
Implementation and performance of SIBYLS: a dual endstation small-angle X-ray scattering and macromolecular crystallography beamline at the Advanced Light Source.
  J Appl Crystallogr, 46, 1.  
21513692 J.S.Pap, B.Kripli, T.Váradi, M.Giorgi, J.Kaizer, and G.Speier (2011).
Comparison of the SOD-like activity of hexacoordinate Mn(II), Fe(II) and Ni(II) complexes having isoindoline-based ligands.
  J Inorg Biochem, 105, 911-918.  
  20607091 C.G.Riordan (2010).
Coordination chemistry of poly(thioether)borate ligands.
  Coord Chem Rev, 254, 1815-1825.  
20664856 C.Núñez, R.Bastida, A.Macías, L.Valencia, J.Ribas, J.L.Capelo, and C.Lodeiro (2010).
New dinuclear nickel(II) and iron(II) complexes with a macrocyclic ligand containing a N6S2 donor-set: synthesis, structural, MALDI-TOF-MS, magnetic and spectroscopic studies.
  Dalton Trans, 39, 7673-7683.  
20221519 D.Nakane, S.I.Kuwasako, M.Tsuge, M.Kubo, Y.Funahashi, T.Ozawa, T.Ogura, and H.Masuda (2010).
A square-planar Ni(II) complex with an N2S2 donor set similar to the active centre of nickel-containing superoxide dismutase and its reaction with superoxide.
  Chem Commun (Camb), 46, 2142-2144.  
20461826 D.Tietze, M.Tischler, S.Voigt, D.Imhof, O.Ohlenschläger, M.Görlach, and G.Buntkowsky (2010).
Development of a functional cis-prolyl bond biomimetic and mechanistic implications for nickel superoxide dismutase.
  Chemistry, 16, 7572-7578.  
19707802 H.I.Lee, J.W.Lee, T.C.Yang, S.O.Kang, and B.M.Hoffman (2010).
ENDOR and ESEEM investigation of the Ni-containing superoxide dismutase.
  J Biol Inorg Chem, 15, 175-182.  
20442957 J.S.Iwig, and P.T.Chivers (2010).
Coordinating intracellular nickel-metal-site structure-function relationships and the NikR and RcnR repressors.
  Nat Prod Rep, 27, 658-667.  
20333421 K.C.Ryan, O.E.Johnson, D.E.Cabelli, T.C.Brunold, and M.J.Maroney (2010).
Nickel superoxide dismutase: structural and functional roles of Cys2 and Cys6.
  J Biol Inorg Chem, 15, 795-807.  
20000358 M.E.Krause, A.M.Glass, T.A.Jackson, and J.S.Laurence (2010).
Novel tripeptide model of nickel superoxide dismutase.
  Inorg Chem, 49, 362-364.  
20333422 O.E.Johnson, K.C.Ryan, M.J.Maroney, and T.C.Brunold (2010).
Spectroscopic and computational investigation of three Cys-to-Ser mutants of nickel superoxide dismutase: insight into the roles played by the Cys2 and Cys6 active-site residues.
  J Biol Inorg Chem, 15, 777-793.  
19253325 A.Schmidt, M.Gube, A.Schmidt, and E.Kothe (2009).
In silico analysis of nickel containing superoxide dismutase evolution and regulation.
  J Basic Microbiol, 49, 109-118.  
19063897 D.S.Shin, M.Didonato, D.P.Barondeau, G.L.Hura, C.Hitomi, J.A.Berglund, E.D.Getzoff, S.C.Cary, and J.A.Tainer (2009).
Superoxide dismutase from the eukaryotic thermophile Alvinella pompejana: structures, stability, mechanism, and insights into amyotrophic lateral sclerosis.
  J Mol Biol, 385, 1534-1555.
PDB codes: 3f7k 3f7l
  19193992 H.L.Pedersen, N.P.Willassen, and I.Leiros (2009).
The first structure of a cold-adapted superoxide dismutase (SOD): biochemical and structural characterization of iron SOD from Aliivibrio salmonicida.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 84-92.
PDB code: 2w7w
19384994 J.F.Bachega, M.V.Navarro, L.Bleicher, R.K.Bortoleto-Bugs, D.Dive, P.Hoffmann, E.Viscogliosi, and R.C.Garratt (2009).
Systematic structural studies of iron superoxide dismutases from human parasites and a statistical coupling analysis of metal binding specificity.
  Proteins, 77, 26-37.
PDB codes: 2goj 2gpc 3esf
19265433 J.J.Perry, A.S.Hearn, D.E.Cabelli, H.S.Nick, J.A.Tainer, and D.N.Silverman (2009).
Contribution of human manganese superoxide dismutase tyrosine 34 to structure and catalysis.
  Biochemistry, 48, 3417-3424.
PDB codes: 1zsp 1zte 1zuq 2p4k
19894770 J.Shearer, K.P.Neupane, and P.E.Callan (2009).
Metallopeptide based mimics with substituted histidines approximate a key hydrogen bonding network in the metalloenzyme nickel superoxide dismutase.
  Inorg Chem, 48, 10560-10571.  
19572492 R.M.Jenkins, M.L.Singleton, E.Almaraz, J.H.Reibenspies, and M.Y.Darensbourg (2009).
Imidazole-containing (N3S)-Ni(II) complexes relating to nickel containing biomolecules.
  Inorg Chem, 48, 7280-7293.  
19363030 S.W.Ragsdale (2009).
Nickel-based Enzyme Systems.
  J Biol Chem, 284, 18571-18575.  
17951444 C.L.Dupont, K.Barbeau, and B.Palenik (2008).
Ni uptake and limitation in marine Synechococcus strains.
  Appl Environ Microbiol, 74, 23-31.  
18412551 C.L.Dupont, K.Neupane, J.Shearer, and B.Palenik (2008).
Diversity, function and evolution of genes coding for putative Ni-containing superoxide dismutases.
  Environ Microbiol, 10, 1831-1843.  
18505253 J.S.Iwig, S.Leitch, R.W.Herbst, M.J.Maroney, and P.T.Chivers (2008).
Ni(II) and Co(II) sensing by Escherichia coli RcnR.
  J Am Chem Soc, 130, 7592-7606.  
18690655 M.Schmidt, S.Zahn, M.Carella, O.Ohlenschläger, M.Görlach, E.Kothe, and J.Weston (2008).
Solution structure of a functional biomimetic and mechanistic implications for nickel superoxide dismutases.
  Chembiochem, 9, 2135-2146.  
17912757 R.Wintjens, D.Gilis, and M.Rooman (2008).
Mn/Fe superoxide dismutase interaction fingerprints and prediction of oligomerization and metal cofactor from sequence.
  Proteins, 70, 1564-1577.  
17304620 A.Schmidt, A.Schmidt, G.Haferburg, and E.Kothe (2007).
Superoxide dismutases of heavy metal resistant streptomycetes.
  J Basic Microbiol, 47, 56-62.  
18042279 B.Priya, J.Premanandh, R.T.Dhanalakshmi, T.Seethalakshmi, L.Uma, D.Prabaharan, and G.Subramanian (2007).
Comparative analysis of cyanobacterial superoxide dismutases to discriminate canonical forms.
  BMC Genomics, 8, 435.  
17637984 D.P.Giedroc, and A.I.Arunkumar (2007).
Metal sensor proteins: nature's metalloregulated allosteric switches.
  Dalton Trans, (), 3107-3120.  
17522887 Z.Su, M.F.Chai, P.L.Lu, R.An, J.Chen, and X.C.Wang (2007).
AtMTM1, a novel mitochondrial protein, may be involved in activation of the manganese-containing superoxide dismutase in Arabidopsis.
  Planta, 226, 1031-1039.  
16724228 C.S.Mullins, C.A.Grapperhaus, and P.M.Kozlowski (2006).
Density functional theory investigations of NiN2S2 reactivity as a function of nitrogen donor type and N-H...S hydrogen bonding inspired by nickel-containing superoxide dismutase.
  J Biol Inorg Chem, 11, 617-625.  
16932945 I.A.Kaltashov, M.Zhang, S.J.Eyles, and R.R.Abzalimov (2006).
Investigation of structure, dynamics and function of metalloproteins with electrospray ionization mass spectrometry.
  Anal Bioanal Chem, 386, 472-481.  
16830148 L.Noodleman, and W.G.Han (2006).
Structure, redox, pKa, spin. A golden tetrad for understanding metalloenzyme energetics and reaction pathways.
  J Biol Inorg Chem, 11, 674-694.  
16802319 L.Rulísek, K.P.Jensen, K.Lundgren, and U.Ryde (2006).
The reaction mechanism of iron and manganese superoxide dismutases studied by theoretical calculations.
  J Comput Chem, 27, 1398-1414.  
16804959 R.Prabhakar, K.Morokuma, and D.G.Musaev (2006).
A DFT study of the mechanism of Ni superoxide dismutase (NiSOD): role of the active site cysteine-6 residue in the oxidative half-reaction.
  J Comput Chem, 27, 1438-1445.  
16828895 V.C.Culotta, M.Yang, and T.V.O'Halloran (2006).
Activation of superoxide dismutases: putting the metal to the pedal.
  Biochim Biophys Acta, 1763, 747-758.  
15817398 O.Carugo, and K.Djinović Carugo (2005).
When X-rays modify the protein structure: radiation damage at work.
  Trends Biochem Sci, 30, 213-219.  
15674245 R.L.Lieberman, and A.C.Rosenzweig (2005).
Crystal structure of a membrane-bound metalloenzyme that catalyses the biological oxidation of methane.
  Nature, 434, 177-182.
PDB code: 1yew
16158232 T.Eitinger, J.Suhr, L.Moore, and J.A.Smith (2005).
Secondary transporters for nickel and cobalt ions: theme and variations.
  Biometals, 18, 399-405.  
15516600 T.Eitinger (2004).
In vivo production of active nickel superoxide dismutase from Prochlorococcus marinus MIT9313 is dependent on its cognate peptidase.
  J Bacteriol, 186, 7821-7825.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.