3AK1

Superoxide dismutase from Aeropyrum pernix K1, apo-form

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Crystal structure of the cambialistic superoxide dismutase from Aeropyrum pernix K1 - insights into the enzyme mechanism and stability

Nakamura, T., Torikai, K., Uegaki, K., Morita, J., Machida, K., Suzuki, A., Kawata, Y.

(2011) FEBS J 278: 598-609

  • DOI: https://doi.org/10.1111/j.1742-4658.2010.07977.x
  • Primary Citation of Related Structures:  
    3AK1, 3AK2, 3AK3

  • PubMed Abstract: 

    • Aeropyrum pernix K1, an aerobic hyperthermophilic archaeon, produces a cambialistic superoxide dismutase that is active in the presence of either of Mn or Fe. The crystal structures of the superoxide dismutase from A. pernix in the apo, Mn-bound and Fe-bound forms were determined at resolutions of 1 ...

    Aeropyrum pernix K1, an aerobic hyperthermophilic archaeon, produces a cambialistic superoxide dismutase that is active in the presence of either of Mn or Fe. The crystal structures of the superoxide dismutase from A. pernix in the apo, Mn-bound and Fe-bound forms were determined at resolutions of 1.56, 1.35 and 1.48 Å, respectively. The overall structure consisted of a compact homotetramer. Analytical ultracentrifugation was used to confirm the tetrameric association in solution. In the Mn-bound form, the metal was in trigonal bipyramidal coordination with five ligands: four side chain atoms and a water oxygen. One aspartate and two histidine side chains ligated to the central metal on the equatorial plane. In the Fe-bound form, an additional water molecule was observed between the two histidines on the equatorial plane and the metal was in octahedral coordination with six ligands. The additional water occupied the postulated superoxide binding site. The thermal stability of the enzyme was compared with superoxide dismutase from Thermus thermophilus, a thermophilic bacterium, which contained fewer ion pairs. In aqueous solution, the stabilities of the two enzymes were almost identical but, when the solution contained ethylene glycol or ethanol, the A. pernix enzyme had significantly higher thermal stability than the enzyme from T. thermophilus. This suggests that dominant ion pairs make A. pernix superoxide dismutase tolerant to organic media.

    Organizational Affiliation: 

    National Institute of Advanced Industrial Science and Technology, Ikeda, Osaka, Japan. nakamura-t@aist.go.jp



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Superoxide dismutase [Mn/Fe]
A, B, C, D
214Aeropyrum pernix K1Mutation(s): 0 
Gene Names: APE0741, sod, APE_0741
EC: 1.15.1.1
UniProt
Find proteins for Q9Y8H8 (Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1))
Explore Q9Y8H8 
Go to UniProtKB:  Q9Y8H8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y8H8
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO
Download Ideal Coordinates CCD File 
AA [auth D]
BA [auth D]
CA [auth D]
DA [auth D]
E [auth A]
AA [auth D],
BA [auth D],
CA [auth D],
DA [auth D],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
S [auth B],
T [auth C],
U [auth C],
V [auth C],
W [auth C],
X [auth C],
Y [auth D],
Z [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.26α = 90
b = 72.251β = 90.99
c = 76.652γ = 90
Software Package:
Software NamePurpose
BSSdata collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-02-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance