1Q0F

Crystal structure of Ni-containing superoxide dismutase with Ni-ligation corresponding to the state after partial x-ray-induced reduction


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.157 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of nickel-containing superoxide dismutase reveals another type of active site

Wuerges, J.Lee, J.-W.Yim, Y.-I.Yim, H.-S.Kang, S.-O.Djinovic Carugo, K.

(2004) Proc.Natl.Acad.Sci.USA 101: 8569-8574

  • DOI: 10.1073/pnas.0308514101
  • Primary Citation of Related Structures:  1Q0D, 1Q0G, 1Q0K, 1Q0M

  • PubMed Abstract: 
  • Superoxide dismutases (SODs, EC 1.15.1.1) are ubiquitous enzymes that efficiently catalyze the dismutation of superoxide radical anions to protect biological molecules from oxidative damage. The crystal structure of nickel-containing SOD (NiSOD) from ...

    Superoxide dismutases (SODs, EC 1.15.1.1) are ubiquitous enzymes that efficiently catalyze the dismutation of superoxide radical anions to protect biological molecules from oxidative damage. The crystal structure of nickel-containing SOD (NiSOD) from Streptomyces seoulensis was determined for the resting, x-ray-reduced, and thiosulfate-reduced enzyme state. NiSOD is a homohexamer consisting of four-helix-bundle subunits. The catalytic center resides in the N-terminal active-site loop, where a Ni(III) ion is coordinated by the amino group of His-1, the amide group of Cys-2, two thiolate groups of Cys-2 and Cys-6, and the imidazolate of His-1 as axial ligand that is lost in the chemically reduced state as well as after x-ray-induced reduction. This structure represents a third class of SODs concerning the catalytic metal species, subunit structure, and oligomeric organization. It adds a member to the small number of Ni-metalloenzymes and contributes with its Ni(III) active site to the general understanding of Ni-related biochemistry. NiSOD is shown to occur also in bacteria other than Streptomyces and is predicted to be present in some cyanobacteria.


    Organizational Affiliation

    International School for Advanced Studies, Via Beirut 2-4, I-34014 Trieste, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Superoxide dismutase [Ni]
A, B, C, D, E, F, G, H, I, J, K, L
117Streptomyces seoulensisGene Names: sodN
EC: 1.15.1.1
Find proteins for P80734 (Streptomyces seoulensis)
Go to UniProtKB:  P80734
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3NI
Query on 3NI

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L
NICKEL (III) ION
Ni
JDRCAGKFDGHRNQ-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.157 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 112.260α = 90.00
b = 113.749β = 90.00
c = 128.618γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
CCP4data scaling
SCALAdata scaling
CNSrefinement
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-05-18
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance