PDBsum entry: 1sdy

Oxidoreductase(superoxide acceptor)

PDB id: 1sdy

Contents

Protein chains

153 a.a. *

Metals

_ZN ×4

_CU ×4

Waters ×513

* Residue conservation analysis

PDB id:

1sdy

Name:

Oxidoreductase(superoxide acceptor)

Title:

Structure solution and molecular dynamics refinement of the yeast cu,zn enzyme superoxide dismutase

Structure:

Copper,zinc superoxide dismutase. Chain: a, b, c, d. Engineered: yes

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932

Biol. unit:

Tetramer (from PQS)

Resolution:

2.50Å R-factor: 0.158

Authors:

K.Djinovic,G.Gatti,A.Coda,L.Antolini,G.Pelosi,A.Desideri, M.Falconi,F.Marmocchi,G.Rotilio,M.Bolognesi

Key ref:

K.Djinović et al. (1991). Structure solution and molecular dynamics refinement of the yeast Cu,Zn enzyme superoxide dismutase. Acta Crystallogr B, 47, 918-927. PubMed id: 1772629 DOI: 10.1107/S0108768191004949

Date:

14-Jun-91 Release date: 31-Jan-94

Protein chains

P00445  (SODC_YEAST) -  Superoxide dismutase [Cu-Zn]

Seq: 154 a.a.

Struc: 153 a.a.

Enzyme reactions

• Enzyme class: E.C.1.15.1.1 - Superoxide dismutase.
• Reaction: 2 superoxide + 2 H⁺ = O₂ + H₂O₂
• Cofactor: Iron or manganese or (zinc and copper)

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

 Gene Ontology (GO) functional annotation 

• Cellular component: cytoplasm (5 terms)
• Biological process: oxidation reduction (7 terms)
• Biochemical function: antioxidant activity (4 terms)

Added reference

DOI no: 10.1107/S0108768191004949

Acta Crystallogr B 47:918-927 (1991)

PubMed id: 1772629

Structure solution and molecular dynamics refinement of the yeast Cu,Zn enzyme superoxide dismutase.

K.Djinović, G.Gatti, A.Coda, L.Antolini, G.Pelosi, A.Desideri, M.Falconi, F.Marmocchi, G.Rolilio, M.Bolognesi.

ABSTRACT

Cu,Zn yeast superoxide dismutase was crystallized from polyethylene glycol solutions. The crystals belong to the P2(1)2(1)2 space group, with cell dimensions a = 105.3, b = 143.0, c = 62.1 A; two dimers of Mr = 32,000 each are contained in the asymmetric unit. Diffraction data at 2.5 A resolution were collected with the image-plate system at the EMBL synchrotron radiation facility in Hamburg. The structure was determined by molecular replacement using as a search model the 'blue-green' dimer of the bovine Cu,Zn superoxide dismutase. The crystallographic refinement of the molecular replacement solution was performed by means of molecular dynamics techniques and resulted in an R factor of 0.268 for the data between 6.0 and 2.5 A. The model was subsequently subjected to conventional restrained crystallographic refinement of the coordinates and temperature factors. The current R value for the data between 6.0 and 2.5 A is 0.220. Owing to the large radius of convergence of the molecular dynamics-crystallographic refinement, the convergence of the refinement process was reached after 18.1 ps of simulation time. The geometry of the active site of the enzyme appears essentially preserved compared with the bovine superoxide dismutase. The beta-barrel structure in the yeast enzyme is closed at the upper part by an efficient hydrogen-bonding scheme.