Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 130.14 kDa 
• Atom Count: 8761 
• Residue Count: 1174 
• Unique protein chains: 1

3T8L

Crystal Structure of adenine deaminase with Mn/Fe

• DOI: 10.2210/pdb3T8L/pdb

• Classification: HYDROLASE
• Organism(s): Agrobacterium fabrum str. C58
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-08-01 Released: 2011-11-02 
• Deposition Author(s): Bagaria, A., Kumaran, D., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

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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 

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

• PubMed: 21998098 
• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenine deaminase 2	A, B	608	Agrobacterium fabrum str. C58	Mutation(s): 0  Gene Names: ade2, adeC, AGR_L_883, Atu4426 EC: 3.5.4.2
Find proteins for Q7CUX4 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore Q7CUX4  Go to UniProtKB:  Q7CUX4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UNX	A, B	UNKNOWN ATOM OR ION X

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A,B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

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 = 61.543	α = 90
b = 131.171	β = 97.04
c = 69.284	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-08-01 
• Released Date: 2011-11-02 
Deposition Author(s): Bagaria, A., Kumaran, D., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

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