PDBsum entry 2r27

Oxidoreductase

PDB id: 2r27

Contents

Protein chain

134 a.a. *

Ligands

_CU ×2

Waters ×190

* Residue conservation analysis

PDB id:

2r27

Name:

Oxidoreductase

Title:

Constitutively zinc-deficient mutant of human superoxide dismutase (sod), c6a, h80s, h83s, c111s

Structure:

Superoxide dismutase [cu-zn]. Chain: a, b. Engineered: yes. Mutation: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: sod1. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

2.00Å R-factor: 0.184 R-free: 0.246

Authors:

B.R.Roberts,E.D.Getzoff,P.A.Karplus,J.S.Beckman,J.A.Tainer

Key ref:

B.R.Roberts et al. (2007). Structural characterization of zinc-deficient human superoxide dismutase and implications for ALS. J Mol Biol, 373, 877-890. PubMed id: 17888947 DOI: 10.1016/j.jmb.2007.07.043

Date:

24-Aug-07 Release date: 11-Dec-07

Protein chains

P00441  (SODC_HUMAN) -  Superoxide dismutase [Cu-Zn] from Homo sapiens

Seq: 154 a.a.

Struc: 134 a.a.*

* PDB and UniProt seqs differ at 4 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.1.15.1.1 - superoxide dismutase.
• Reaction: 2 superoxide + 2 H⁺ = H2O2 + O2
• Cofactor: Fe cation or Mn(2+) or (Zn(2+) and Cu cation)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1016/j.jmb.2007.07.043

J Mol Biol 373:877-890 (2007)

PubMed id: 17888947

Structural characterization of zinc-deficient human superoxide dismutase and implications for ALS.

B.R.Roberts, J.A.Tainer, E.D.Getzoff, D.A.Malencik, S.R.Anderson, V.C.Bomben, K.R.Meyers, P.A.Karplus, J.S.Beckman.

ABSTRACT

Over 130 mutations to copper, zinc superoxide dismutase (SOD) are implicated in the selective death of motor neurons found in 25% of patients with familial amyotrophic lateral sclerosis (ALS). Despite their widespread distribution, ALS mutations appear positioned to cause structural and misfolding defects. Such defects decrease SOD's affinity for zinc, and loss of zinc from SOD is sufficient to induce apoptosis in motor neurons in vitro. To examine the importance of the zinc site in the structure and pathogenesis of human SOD, we determined the 2.0-A-resolution crystal structure of a designed zinc-deficient human SOD, in which two zinc-binding ligands have been mutated to hydrogen-bonding serine residues. This structure revealed a 9 degrees twist of the subunits, which opens the SOD dimer interface and represents the largest intersubunit rotational shift observed for a human SOD variant. Furthermore, the electrostatic loop and zinc-binding subloop were partly disordered, the catalytically important Arg143 was rotated away from the active site, and the normally rigid intramolecular Cys57-Cys146 disulfide bridge assumed two conformations. Together, these changes allow small molecules greater access to the catalytic copper, consistent with the observed increased redox activity of zinc-deficient SOD. Moreover, the dimer interface is weakened and the Cys57-Cys146 disulfide is more labile, as demonstrated by the increased aggregation of zinc-deficient SOD in the presence of a thiol reductant. However, equimolar Cu,Zn SOD rapidly forms heterodimers with zinc-deficient SOD (t1/2 approximately 15 min) and prevents aggregation. The stabilization of zinc-deficient SOD as a heterodimer with Cu,Zn SOD may contribute to the dominant inheritance of ALS mutations. These results have general implications for the importance of framework stability on normal metalloenzyme function and specific implications for the role of zinc ion in the fatal neuropathology associated with SOD mutations.

Selected figure(s)

Figure 1.
Fig. 1. Key structural features of wild-type Cu,Zn SOD. (a) In the right-hand subunit (chain A), copper (orange) and zinc (grey) are shown as spheres. Loop IV is divided into three sections: the dimerization subloop (residues 50–54, yellow) creates part of the dimer interface, the disulfide subloop (residues 55–61, raspberry) covalently attaches to the β-barrel via the Cys57–Cys146 disulfide, and the zinc-binding region (residues 62–83, blue) contains His63, His71, His80, and Asp83 (shown as sticks). Copper is coordinated by residues His63, His46, His48, and His120 (orange sticks). (b) Surface buried upon dimerization is shown for chain A. The vert, similar 1400-Å^2 area is divided into three regions: the area contributed by the dimerization subloop (yellow), the area buried by the interaction with the dimerization subloop of chain B (cyan with yellow ribbon showing chain B segment), and the area from the β-barrel interaction (light grey). The dimerization subloop is involved in vert, similar 75% of the total surface area buried by the dimer.

Figure 3.
Fig. 3. Increased copper accessibility in zinc-deficient SOD. (a) Access to the active-site copper (orange) of wild-type Cu,Zn SOD (green) is limited by the electrostatic and zinc-binding loops. The red dashes illustrate the dimensions of the active-site channel, which narrows from vert, similar 12 Å to vert, similar 4 Å. (b) The active site of zinc-deficient SOD (blue) is more open and accessible due to the disorder of the electrostatic and zinc-binding loops. Although the disordered residues in these loops may transiently restrict the active-site channel, their flexibility allows small molecules greater access to the copper.

The above figures are reprinted from an Open Access publication published by Elsevier: J Mol Biol (2007, 373, 877-890) copyright 2007.

Figures were selected by the author.