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PDBsum entry 1q0k

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Oxidoreductase PDB id
1q0k
Jmol
Contents
Protein chains
(+ 6 more) 117 a.a. *
Ligands
SO4 ×12
THJ ×12
Metals
_NI ×12
Waters ×504
* Residue conservation analysis

References listed in PDB file
Key reference
Title Crystal structure of nickel-Containing superoxide dismutase reveals another type of active site.
Authors J.Wuerges, J.W.Lee, Y.I.Yim, H.S.Yim, S.O.Kang, K.D.Carugo.
Ref. Proc Natl Acad Sci U S A, 2004, 101, 8569-8574. [DOI no: 10.1073/pnas.0308514101]
PubMed id 15173586
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.
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.
PROCHECK
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