1WB7

Iron Superoxide Dismutase (Fe-SOD) From The Hyperthermophile Sulfolobus Solfataricus. Crystal Structure of the Y41F mutant.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

The Role of Tyr41 and His155 in the Functional Properties of Superoxide Dismutase from the Archaeon Sulfolobus Solfataricus

Gogliettino, M.A.Tanfani, F.Scire, A.Ursby, T.Adinolfi, B.S.Cacciamani, T.De Vendittis, E.

(2004) Biochemistry 43: 2199

  • DOI: 10.1021/bi035661y

  • PubMed Abstract: 
  • We have examined and compared the effects of mutating Y41 and H155 in the iron superoxide dismutase (SOD) from the archaeon Sulfolobus solfataricus (Ss). These two neighboring residues in the active site are known to have crucial functions in structu ...

    We have examined and compared the effects of mutating Y41 and H155 in the iron superoxide dismutase (SOD) from the archaeon Sulfolobus solfataricus (Ss). These two neighboring residues in the active site are known to have crucial functions in structurally related SODs from different sources. The metal analysis indicates a slightly lower iron content after either Y41F or H155Q replacement, without any significant substitution of iron for manganese. The specific activity of SsSOD referred to the iron content is 17-fold reduced in the Y41F mutant, whereas it is less than 2-fold reduced by the H155Q mutation. The noticeable pH dependence of the activity of SsSOD and H155Q-SsSOD, due to the ionization of Y41 (pK 8.4), is lost in Y41F-SsSOD. After H155Q and even more after the Y41F substitution, the archaeal enzyme acquires a moderate sensitivity to sodium azide inhibition. The hydrogen peroxide inactivation of SsSOD is significantly increased after H155Q replacement; however, both mutants are insensitive to the modification of residue 41 by phenylmethanesulfonyl fluoride. Heat inactivation studies showed that the high stability of SsSOD is reduced by the H155Q mutation; however, upon the addition of SDS, a much faster inactivation kinetics is observed both with wild-type and mutant SsSOD forms. The detergent is also required to follow thermal denaturation of the archaeal enzyme by Fourier transform infrared spectroscopy; these studies gave information about the effect of mutations and modification on flexibility and compactness of the protein structure. The crystal structure of Y41F mutant revealed an uninterrupted hydrogen bond network including three solvent molecules connecting the iron-ligating hydroxide ion via H155 with F41 and H37, which is not present in structures of the corresponding mutant SODs from other sources. These data suggest that Y41 and H155 are important for the structural and functional properties of SsSOD; in particular, Y41 seems to be a powerful regulator of the activity of SsSOD, whereas H155 is apparently involved in the organization of the active site of the enzyme.


    Related Citations: 
    • Phenylmethanesulfonyl Fluoride Inactivates an Archaeal Superoxide Dismutase by Chemical Modification of a Specific Tyrosine Residue
      De Vendittis, E.,Ursby, T.,Rullo, R.,Gogliettino, M.A.,Masullo, M.,Bocchini, V.
      (2001) Eur.J.Biochem. 268: 1794
    • Iron Superoxide Dismutase from the Archaeon Sulfolobus Solfataricus: Analysis of Structure and Thermostability
      Ursby, T.,Adinolfi, B.S.,Al-Karadaghi, S.,De Vendittis, E.,Bocchini, V.
      (1999) J.Mol.Biol. 286: 189


    Organizational Affiliation

    Dipartimento di Biochimica e Biotecnologie Mediche, Università di Napoli Federico II, Via S. Pansini, 5, I-80131 Naples, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SUPEROXIDE DISMUTASE [FE]
A, B
210Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)Mutation(s): 1 
Gene Names: sod
EC: 1.15.1.1
Find proteins for P80857 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
Go to UniProtKB:  P80857
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FE
Query on FE

Download SDF File 
Download CCD File 
A, B
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.181 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 75.188α = 90.00
b = 121.753β = 128.74
c = 59.420γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
CNSrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-11-08
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-01-17
    Type: Data collection
  • Version 1.4: 2019-05-08
    Type: Data collection, Experimental preparation