PDBsum entry 1ibh

Oxidoreductase

PDB id: 1ibh

Contents

Protein chain

151 a.a. *

Metals

_CU

_ZN

Waters ×73

* Residue conservation analysis

PDB id:

1ibh

Name:

Oxidoreductase

Title:

X-ray 3d structure of p.Leiognathi cu,zn sod mutant m41i

Structure:

Cu,zn superoxide dismutase. Chain: a. Engineered: yes. Mutation: yes

Source:

Photobacterium leiognathi. Organism_taxid: 658. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Dimer (from PDB file)

Resolution:

2.00Å R-factor: 0.229 R-free: 0.287

Authors:

M.E.Stroppolo,A.Pesce,M.D'Orazio,P.O'Neill,D.Bordo,C.Rosano,M.Milani, A.Battistoni,M.Bolognesi,A.Desideri

Key ref:

M.E.Stroppolo et al. (2001). Single mutations at the subunit interface modulate copper reactivity in Photobacterium leiognathi Cu,Zn superoxide dismutase. J Mol Biol, 308, 555-563. PubMed id: 11327787 DOI: 10.1006/jmbi.2001.4606

Date:

28-Mar-01 Release date: 09-May-01

Protein chain

P00446  (SODC_PHOLE) -  Superoxide dismutase [Cu-Zn] from Photobacterium leiognathi

Seq: 173 a.a.

Struc: 151 a.a.*

* PDB and UniProt seqs differ at 2 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: 10.1006/jmbi.2001.4606

J Mol Biol 308:555-563 (2001)

PubMed id: 11327787

Single mutations at the subunit interface modulate copper reactivity in Photobacterium leiognathi Cu,Zn superoxide dismutase.

M.E.Stroppolo, A.Pesce, M.D'Orazio, P.O'Neill, D.Bordo, C.Rosano, M.Milani, A.Battistoni, M.Bolognesi, A.Desideri.

ABSTRACT

The functional properties and X-ray structures of five mutant forms of Photobacterium leiognathi Cu,Zn superoxide dismutase carrying single mutations at residues located at the dimer association interface have been investigated. When compared to the wild-type enzyme, the three-dimensional structures of the mutants show structural perturbations limited to the proximity of the mutation sites and substantial identity of active site geometry. Nonetheless, the catalytic rates of all mutants, measured at neutral pH and low ionic strength by pulse radiolysis, are higher than that of the wild-type protein. Such enzymatic activity increase is paralleled by enhanced active site accessibility to external chelating agents, which, in the mutated enzyme, remove more readily the active site copper ion. It is concluded that mutations at the prokaryotic Cu,Zn superoxide dismutase subunit interface can transduce dynamical perturbation to the active site region, promoting substrate active site accessibility. Such long-range intramolecular communication effects have not been extensively described before within the Cu,Zn superoxide dismutase homology family.

Selected figure(s)

Figure 1.
Figure 1. A schematic view of the PSOD dimer displaying one enzyme subunit as a van der Waals surface (green), the interface trapped water molecules (red spheres) and the second subunit shown as a skeletal C^a trace including the active site Cu,Zn pair (cyan and purple atoms, respectively). Drawn with Dino.[39]

Figure 2.
Figure 2. (a) A stereo view of the subunit interface residues in wild-type PSOD. The blue molecular surface indicating the enzyme association interface hosts the side-chains of residues (skeletal side-chains) building up the subunit contact area. The residues individually mutated in the present study are drawn in purple and specifically labeled. (b) The PSOD subunit interface is portrayed as shown in (a), including five out of the ten interface water molecules (red spheres) buried once the active dimeric enzyme is assembled through crystallographic two-fold symmetry. Drawn with Dino.[39]

The above figures are reprinted by permission from Elsevier: J Mol Biol (2001, 308, 555-563) copyright 2001.

Figures were selected by an automated process.