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PDBsum entry 1q0f

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protein ligands metals Protein-protein interface(s) links
Oxidoreductase PDB id
1q0f
Jmol
Contents
Protein chains
(+ 6 more) 117 a.a. *
Ligands
SO4 ×16
Metals
3NI ×12
Waters ×1538
* Residue conservation analysis
PDB id:
1q0f
Name: Oxidoreductase
Title: Crystal structure of ni-containing superoxide dismutase with ni-ligation corresponding to the state after partial x-ray-induced reduction
Structure: Superoxide dismutase [ni]. Chain: a, b, c, d, e, f, g, h, i, j, k, l. Synonym: nickel-containing superoxide dismutase. Nisod. Ni- containing superoxide dismutase. Other_details: the asymmetric unit contains two hexamers
Source: Streptomyces seoulensis. Organism_taxid: 73044
Biol. unit: Hexamer (from PQS)
Resolution:
2.20Å     R-factor:   0.157     R-free:   0.167
Authors: J.Wuerges,J.-W.Lee,Y.-I.Yim,H.-S.Yim,S.-O.Kang,K.Djinovic Carugo
Key ref:
J.Wuerges et al. (2004). Crystal structure of nickel-containing superoxide dismutase reveals another type of active site. Proc Natl Acad Sci U S A, 101, 8569-8574. PubMed id: 15173586 DOI: 10.1073/pnas.0308514101
Date:
16-Jul-03     Release date:   18-May-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P80734  (SODN_STRSO) -  Superoxide dismutase [Ni]
Seq:
Struc:
131 a.a.
117 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 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: 10.1073/pnas.0308514101 Proc Natl Acad Sci U S A 101:8569-8574 (2004)
PubMed id: 15173586  
 
 
Crystal structure of nickel-containing superoxide dismutase reveals another type of active site.
J.Wuerges, J.W.Lee, Y.I.Yim, H.S.Yim, S.O.Kang, K.D.Carugo.
 
  ABSTRACT  
 
Superoxide dismutases (SODs, EC 1.15.1.1) are ubiquitous enzymes that efficiently catalyze the dismutation of superoxide radical anions to protect biological molecules from oxidative damage. The crystal structure of nickel-containing SOD (NiSOD) from Streptomyces seoulensis was determined for the resting, x-ray-reduced, and thiosulfate-reduced enzyme state. NiSOD is a homohexamer consisting of four-helix-bundle subunits. The catalytic center resides in the N-terminal active-site loop, where a Ni(III) ion is coordinated by the amino group of His-1, the amide group of Cys-2, two thiolate groups of Cys-2 and Cys-6, and the imidazolate of His-1 as axial ligand that is lost in the chemically reduced state as well as after x-ray-induced reduction. This structure represents a third class of SODs concerning the catalytic metal species, subunit structure, and oligomeric organization. It adds a member to the small number of Ni-metalloenzymes and contributes with its Ni(III) active site to the general understanding of Ni-related biochemistry. NiSOD is shown to occur also in bacteria other than Streptomyces and is predicted to be present in some cyanobacteria.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Overall structure of NiSOD. (A) The solvent-accessible surface of NiSOD viewed along the hexamer's threefold symmetry axis. The outer surface (black mesh) is sliced to allow the view to the inner solvent-filled space (in orange) and the protein backbone trace (chain A, yellow; chain B, blue; chain C, red; chain D, magenta; chain E, cyan; chain F, green; Ni ions, salmon-colored spheres). Arrows indicate the three twofold symmetry axes and the entrance to channels that render the inner space accessible to solvent molecules. (B) Ribbon representation of a NiSOD subunit. The N-terminal loop hosting the Ni ion protrudes from the body of the four-helix bundle. Residues involved in aromatic stacking are shown as a ball-and-stick representation. (C) Residues linking the active-site loop (subunit A) to neighboring chains by polar interactions. His-1 N takes part in a hydrogen-bonding triangle with Glu-17 and Arg-47 of subunit C. Main-chain oxygen atoms of Asp-3 and Leu-4 hydrogen bond to the side chain of Arg-39 in subunit C. The side-chain oxygen atoms of Asp-3 hydrogen bond to the side chains of Lys-52, Ser-86, and Lys-89 of subunit F.
Figure 2.
Fig. 2. [A]-weighted 2 F[o] - F[c] electron density maps of the Ni ion environment. (A-C) Structures of subunit F captured at successively increasing x-ray doses. (A) The fifth ligand His-1 N (2.5 Å distant to Ni here) is revealed at low x-ray exposure (map resolution 2.2 Å, 1.0 contour level). (B) After longer exposure of the same crystal as in A, the imidazolate ligation is disrupted. (C) Map at 1.6-Å resolution obtained from a different crystal as in A and B, applying a maximum total x-ray dose. The ligands show a distorted cis square-planar geometry, equaling the thiosulfate-reduced NiSOD. The average angle between planesdefined by N(His-1)-Ni-N(Cys-2) and S(Cys-2)-Ni-S(Cys-6) is 7.5°.(D) Superposition of models from A in green, B in magenta, and C in gray illustrates the His-1 imidazole rotation upon which N reaches a distance of 2.9 Å to Val-8 O, thereby maintaining the hydrogen-bond triangle of His-1 N to Glu-17 O and Arg-47 N of the adjacent subunit. (E) Electron density map of thiosulfate-reduced NiSOD contoured at 1.1 showing the square-planar Ni(II) coordination. One thiosulfate-ion (S[2]O[3]^2-) per subunit is found 7-8 Å away from each metal center (subunit A). The precise bonding pattern of these ions varies among the 12 subunits in the asymmetric unit, indicating a high degree of disorder or low-binding specificity.
 
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
19699328 J.W.Whittaker (2010).
Metal uptake by manganese superoxide dismutase.
  Biochim Biophys Acta, 1804, 298-307.  
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.  
20433725 M.V.Omelchenko, M.Y.Galperin, Y.I.Wolf, and E.V.Koonin (2010).
Non-homologous isofunctional enzymes: a systematic analysis of alternative solutions in enzyme evolution.
  Biol Direct, 5, 31.  
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.  
  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
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.  
19742126 V.Capozzi, D.Fiocco, M.L.Amodio, A.Gallone, and G.Spano (2009).
Bacterial stressors in minimally processed food.
  Int J Mol Sci, 10, 3076-3105.  
19030615 A.Banerjee, R.Singh, D.Chopra, E.Colacio, and K.K.Rajak (2008).
Mixed bridged dinuclear Ni(II) complexes: synthesis, structure, magnetic properties and DFT study.
  Dalton Trans, (), 6539-6545.  
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.  
19117520 D.Thybert, S.Avner, C.Lucchetti-Miganeh, A.Cheron, and F.Barloy-Hubler (2008).
OxyGene: an innovative platform for investigating oxidative-response genes in whole prokaryotic genomes.
  BMC Genomics, 9, 637.  
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.  
17867686 L.M.Brines, J.Shearer, J.K.Fender, D.Schweitzer, S.C.Shoner, D.Barnhart, W.Kaminsky, S.Lovell, and J.A.Kovacs (2007).
Periodic trends within a series of five-coordinate thiolate-ligated [MII(SMe2N4(tren))]+ (M = Mn, Fe, Co, Ni, Cu, Zn) complexes, including a rare example of a stable CuII-thiolate.
  Inorg Chem, 46, 9267-9277.  
  18084079 P.Liu, H.E.Ewis, Y.J.Huang, C.D.Lu, P.C.Tai, and I.T.Weber (2007).
Structure of Bacillus subtilis superoxide dismutase.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 1003-1007.
PDB code: 2rcv
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.  
16807974 E.I.Solomon, S.I.Gorelsky, and A.Dey (2006).
Metal-thiolate bonds in bioinorganic chemistry.
  J Comput Chem, 27, 1415-1428.  
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.  
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.  
15883191 A.P.Dubnovitsky, R.B.Ravelli, A.N.Popov, and A.C.Papageorgiou (2005).
Strain relief at the active site of phosphoserine aminotransferase induced by radiation damage.
  Protein Sci, 14, 1498-1507.
PDB codes: 2bhx 2bi1 2bi2 2bi3 2bi5 2bi9 2bia 2bie 2big
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.  
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 code is shown on the right.