1Q0K

Crystal structure of Ni-containing superoxide dismutase with Ni-ligation corresponding to the thiosulfate-reduced state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.204 

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 U S A 101: 8569-8574

  • DOI: 10.1073/pnas.0308514101
  • Primary Citation of Related Structures:  
    1Q0D, 1Q0F, 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 Streptomyces seoulensis was determined for the resting, x-ray-reduced, and thiosulfate-reduced enzyme state ...

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Superoxide dismutase [Ni]
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H, I, J, K, L
117Streptomyces seoulensisMutation(s): 0 
Gene Names: sodN
EC: 1.15.1.1
UniProt
Find proteins for P80734 (Streptomyces seoulensis)
Explore P80734 
Go to UniProtKB:  P80734
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
THJ
Query on THJ

Download Ideal Coordinates CCD File 
GA [auth G] , JA [auth H] , KA [auth H] , NA [auth I] , O [auth A] , R [auth B] , S [auth B] , UA [auth L] , 
GA [auth G], JA [auth H], KA [auth H], NA [auth I], O [auth A], R [auth B], S [auth B], UA [auth L], V [auth C], VA [auth L], Y [auth D], Z [auth D]
THIOSULFATE
O3 S2
DHCDFWKWKRSZHF-UHFFFAOYSA-L
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
BA [auth E] , DA [auth F] , FA [auth G] , IA [auth H] , MA [auth I] , N [auth A] , PA [auth J] , Q [auth B] , 
BA [auth E], DA [auth F], FA [auth G], IA [auth H], MA [auth I], N [auth A], PA [auth J], Q [auth B], RA [auth K], TA [auth L], U [auth C], X [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
NI
Query on NI

Download Ideal Coordinates CCD File 
AA [auth E] , CA [auth F] , EA [auth G] , HA [auth H] , LA [auth I] , M [auth A] , OA [auth J] , P [auth B] , 
AA [auth E], CA [auth F], EA [auth G], HA [auth H], LA [auth I], M [auth A], OA [auth J], P [auth B], QA [auth K], SA [auth L], T [auth C], W [auth D]
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.204 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.635α = 90
b = 113.651β = 90
c = 129.356γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
CCP4data scaling
CNSphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

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