PDBsum entry 1u3n

Unknown function

PDB id: 1u3n

Contents

Protein chain

162 a.a. *

* Residue conservation analysis

PDB id:

1u3n

Name:

Unknown function

Title:

A sod-like protein from b. Subtilis, unstructured in solution, becomes ordered in the crystal: implications for function and for fibrillogenesis

Structure:

Hypothetical superoxide dismutase-like protein yojm. Chain: a. Fragment: sod-like. Engineered: yes

Source:

Bacillus subtilis. Organism_taxid: 1423. Gene: yojm, bsu19400. Expressed in: escherichia coli. Expression_system_taxid: 562.

NMR struc:

30 models

Authors:

L.Banci,I.Bertini,V.Calderone,F.Cramaro,R.Del Conte,A.Fantoni, S.Mangani,A.Quattrone,M.S.Viezzoli

Key ref:

L.Banci et al. (2005). A prokaryotic superoxide dismutase paralog lacking two Cu ligands: from largely unstructured in solution to ordered in the crystal. Proc Natl Acad Sci U S A, 102, 7541-7546. PubMed id: 15897454 DOI: 10.1073/pnas.0502450102

Date:

22-Jul-04 Release date: 03-May-05

Protein chain

O31851  (YOJM_BACSU) -  Superoxide dismutase-like protein YojM from Bacillus subtilis (strain 168)

Seq: 196 a.a.

Struc: 162 a.a.

DOI no: 10.1073/pnas.0502450102

Proc Natl Acad Sci U S A 102:7541-7546 (2005)

PubMed id: 15897454

A prokaryotic superoxide dismutase paralog lacking two Cu ligands: from largely unstructured in solution to ordered in the crystal.

L.Banci, I.Bertini, V.Calderone, F.Cramaro, R.Del Conte, A.Fantoni, S.Mangani, A.Quattrone, M.S.Viezzoli.

ABSTRACT

Little is known about prokaryotic homologs of Cu,Zn superoxide dismutase (SOD), an enzyme highly conserved among eukaryotic species. In 138 Archaea and Bacteria genomes, 57 of these putative homologs were found, 11 of which lack at least one of the metal ligands. Both the solution and the crystal structures of the SOD-like protein from Bacillus subtilis, lacking two Cu ligands and found to be enzymatically inactive, were determined. In solution, the protein is monomeric. The available nuclear Overhauser effects, together with chemical-shift index values, allowed us to define and to recognize the typical Cu,Zn SOD Greek beta-barrel but with largely unstructured loops (which, therefore, sample a wide range of conformations). On the contrary, in the crystal structure (obtained in the presence of slight excess of Zn), the protein is well structured and organized in covalent dimers held by a symmetric bridge consisting of a Zn ion bound to an Asp-His dyad in a tetrahedral geometry. Couples of dimers held by hydrophobic interactions and H bonds are further organized in long chains. The order/disorder transition is discussed in terms of metal binding and physical state.

Selected figure(s)

Figure 2.
Fig. 2. Quaternary structure of BsSOD in the crystal. The Zn ions are shown as red spheres, and Cl ions are shown as yellow spheres. The view is approximately down the noncrystallographic twofold axis passing through the exogenous Zn.

Figure 4.
Fig. 4. Comparison between BsSOD and HSOD structures. (A) The native metal-binding sites of BsSOD (green) and HSOD (red). Only the BsSOD residues are labeled. The Cl anion is shown as a yellow sphere. (B) BsSOD (green) and HSOD (red) monomers, highlighting the conformational differences present in the loop, are compared. The Zn ions and the Cl anion bound are shown as red and yellow spheres, respectively.

Figures were selected by an automated process.