3T8L

Crystal Structure of adenine deaminase with Mn/Fe


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.301 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.181 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The catalase activity of diiron adenine deaminase.

Kamat, S.S.Holmes-Hampton, G.P.Bagaria, A.Kumaran, D.Tichy, S.E.Gheyi, T.Zheng, X.Bain, K.Groshong, C.Emtage, S.Sauder, J.M.Burley, S.K.Swaminathan, S.Lindahl, P.A.Raushel, F.M.

(2011) Protein Sci 20: 2080-2094

  • DOI: 10.1002/pro.748
  • Primary Citation of Related Structures:  
    3T8L

  • PubMed Abstract: 
  • Adenine deaminase (ADE) from the amidohydrolase superfamily (AHS) of enzymes catalyzes the conversion of adenine to hypoxanthine and ammonia. Enzyme isolated from Escherichia coli was largely inactive toward the deamination of adenine. Molecular weight d ...

    Adenine deaminase (ADE) from the amidohydrolase superfamily (AHS) of enzymes catalyzes the conversion of adenine to hypoxanthine and ammonia. Enzyme isolated from Escherichia coli was largely inactive toward the deamination of adenine. Molecular weight determinations by mass spectrometry provided evidence that multiple histidine and methionine residues were oxygenated. When iron was sequestered with a metal chelator and the growth medium supplemented with Mn(2+) before induction, the post-translational modifications disappeared. Enzyme expressed and purified under these conditions was substantially more active for adenine deamination. Apo-enzyme was prepared and reconstituted with two equivalents of FeSO(4). Inductively coupled plasma mass spectrometry and Mössbauer spectroscopy demonstrated that this protein contained two high-spin ferrous ions per monomer of ADE. In addition to the adenine deaminase activity, [Fe(II) /Fe(II) ]-ADE catalyzed the conversion of H(2)O(2) to O(2) and H(2)O. The values of k(cat) and k(cat)/K(m) for the catalase activity are 200 s(-1) and 2.4 × 10(4) M(-1) s(-1), respectively. [Fe(II)/Fe(II)]-ADE underwent more than 100 turnovers with H(2)O(2) before the enzyme was inactivated due to oxygenation of histidine residues critical for metal binding. The iron in the inactive enzyme was high-spin ferric with g(ave) = 4.3 EPR signal and no evidence of anti-ferromagnetic spin-coupling. A model is proposed for the disproportionation of H(2)O(2) by [Fe(II)/Fe(II)]-ADE that involves the cycling of the binuclear metal center between the di-ferric and di-ferrous oxidation states. Oxygenation of active site residues occurs via release of hydroxyl radicals. These findings represent the first report of redox reaction catalysis by any member of the AHS.


    Organizational Affiliation

    Department of Chemistry, Texas A&M University, College Station, Texas 77843-3012, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Adenine deaminase 2 AB608Agrobacterium fabrum str. C58Mutation(s): 0 
Gene Names: ade2adeCAGR_L_883Atu4426
EC: 3.5.4.2
Find proteins for Q7CUX4 (Agrobacterium fabrum (strain C58 / ATCC 33970))
Explore Q7CUX4 
Go to UniProtKB:  Q7CUX4
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.301 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.181 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.543α = 90
b = 131.171β = 97.04
c = 69.284γ = 90
Software Package:
Software NamePurpose
CBASSdata collection
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-11-02
    Type: Initial release
  • Version 1.1: 2013-09-18
    Changes: Database references
  • Version 1.2: 2021-02-10
    Changes: Database references, Derived calculations, Structure summary