PDBsum entry 2gbt

Oxidoreductase

PDB id: 2gbt

Contents

Protein chains

152 a.a. *

126 a.a. *

Metals

_ZN ×2

CU1 ×2

Waters ×537

* Residue conservation analysis

PDB id:

2gbt

Name:

Oxidoreductase

Title:

C6a/c111a cuzn superoxide dismutase

Structure:

Superoxide dismutase [cu-zn]. Chain: a, b, c, d. Synonym: cu/zn superoxide dismutase. Engineered: yes. Mutation: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: sod1. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

1.70Å R-factor: 0.204 R-free: 0.230

Authors:

A.Hornberg,D.T.Logan,S.L.Marklund,M.Oliveberg

Key ref:

A.Hörnberg et al. (2007). The coupling between disulphide status, metallation and dimer interface strength in Cu/Zn superoxide dismutase. J Mol Biol, 365, 333-342. PubMed id: 17070542 DOI: 10.1016/j.jmb.2006.09.048

Date:

11-Mar-06 Release date: 02-Jan-07

Protein chains

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

Seq: 154 a.a.

Struc: 152 a.a.*

Protein chains

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

Seq: 154 a.a.

Struc: 126 a.a.*

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

Enzyme reactions

• Enzyme class: Chains A, B, C, D: 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.2006.09.048

J Mol Biol 365:333-342 (2007)

PubMed id: 17070542

The coupling between disulphide status, metallation and dimer interface strength in Cu/Zn superoxide dismutase.

A.Hörnberg, D.T.Logan, S.L.Marklund, M.Oliveberg.

ABSTRACT

The gain of neurotoxic function in amyotrophic lateral sclerosis (ALS) has been linked to misfolding of the homodimeric enzyme Cu/Zn superoxide dismutase (SOD). Here, we present the crystal structure of fully cysteine-depleted human SOD (SOD(CallA)), representing a reduced, marginally stable intermediate on the folding pathway in vivo that has also been implicated as neurotoxic precursor state. A hallmark of this species is that it fails to dimerize and becomes trapped as a monomer in the absence of the active-site metals. The crystallographic data show that removal of the C57-C146 disulphide bond sets free the interface loop IV in the apo protein, whereas the same loop remains unaffected in the holo protein. Thus, the low dimerisation propensity of disulphide-reduced apoSOD seems to be of entropic origin due to increased loop flexibility in the monomeric state: in the disulphide-reduced holo protein this gain in configurational entropy upon splitting of the dimer interface is reduced by the metal coordination.

Selected figure(s)

Figure 3.
Figure 3. Changes of the homodimer interface of the fully cysteine-depleted variant apoSOD^CallA. (a) The apoSOD^CallA dimer. (b) The interface areas of the individual apoSOD^CallA monomers indicating the contacts that are lost, weakened and maintained upon truncation of the C57–C146 disulphide link and movement of loop IV. Figure 3. Changes of the homodimer interface of the fully cysteine-depleted variant apoSOD^CallA. (a) The apoSOD^CallA dimer. (b) The interface areas of the individual apoSOD^CallA monomers indicating the contacts that are lost, weakened and maintained upon truncation of the C57–C146 disulphide link and movement of loop IV.

Figure 4.
Figure 4. Displacement of Arg143 in apoSOD^CallA provides a clue to the structural origin of decreased activity in monomeric and disulphide-reduced protein. Accompanying the structural alteration of loop IV, the catalytically important guanidinium group of R143 moves from its native position and forms new hydrogen bonds with S59, D52 and the water molecules Wat26 and Wat68. (a) The 2F[o]–F[c] electron density map of apoSOD^CallA at 1σ. (b) Schematic representation of the apoSOD^CallA structure illustrating the hydrogen bonding to R143. (c) Comparison of the loop IV conformations and positioning of R143 by superposition of the A monomers of apoSOD^CallA (blue) and holoSOD^CallA (red). Figure 4. Displacement of Arg143 in apoSOD^CallA provides a clue to the structural origin of decreased activity in monomeric and disulphide-reduced protein. Accompanying the structural alteration of loop IV, the catalytically important guanidinium group of R143 moves from its native position and forms new hydrogen bonds with S59, D52 and the water molecules Wat26 and Wat68. (a) The 2F[o]–F[c] electron density map of apoSOD^CallA at 1σ. (b) Schematic representation of the apoSOD^CallA structure illustrating the hydrogen bonding to R143. (c) Comparison of the loop IV conformations and positioning of R143 by superposition of the A monomers of apoSOD^CallA (blue) and holoSOD^CallA (red).

The above figures are reprinted by permission from Elsevier: J Mol Biol (2007, 365, 333-342) copyright 2007.

Figures were selected by an automated process.