3MVT

Crystal structure of apo mADA at 2.2A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The role of Zn2+ on the structure and stability of murine adenosine deaminase.

Niu, W.Shu, Q.Chen, Z.Mathews, S.Di Cera, E.Frieden, C.

(2010) J.Phys.Chem.B 114: 16156-16165

  • DOI: 10.1021/jp106041v
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Adenosine deaminase (ADA) is a key enzyme in purine metabolism and crucial for normal immune competence. It is a 40 kDa monomeric TIM-barrel protein containing a tightly bound Zn(2+), which is required for activity. In this study, we have investigate ...

    Adenosine deaminase (ADA) is a key enzyme in purine metabolism and crucial for normal immune competence. It is a 40 kDa monomeric TIM-barrel protein containing a tightly bound Zn(2+), which is required for activity. In this study, we have investigated the role of Zn(2+) with respect to ADA structure and stability. After removing Zn(2+), the crystallographic structure of the protein remains highly ordered and similar to that of the holo protein with structural changes limited to regions capping the active site pocket. The stability of the protein, however, is decreased significantly in the absence of Zn(2+). Denaturation with urea shows the midpoint to be about 3.5 M for the apo enzyme, compared with 6.4 M for the holo enzyme. ADA contains four tryptophan residues distant from the Zn(2+) site. (19)F NMR studies in the presence and absence of Zn(2+) were carried out after incorporation of 6-(19)F-tryptophan. Chemical shift differences were observed for three of the four tryptophan residues, suggesting that, in contrast to the X-ray data, Zn(2+)-induced structural changes are propagated throughout the protein. Changes throughout the structure as suggested by the NMR data may explain the lower stability of the Zn(2+)-free protein. Real-time (19)F NMR spectroscopy measuring the loss of Zn(2+) showed that structural changes correlated with the loss of enzymatic activity.


    Related Citations: 
    • Complexes of Adenosine Deaminase with Two Potent Inhibitors: X-ray Structures in Four Independent Molecules at pH of Maximum Activity
      Wang, Z.,Quiocho, F.A.
      (1998) Biochemistry 37: 8314


    Organizational Affiliation

    Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri 63104, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Adenosine deaminase
A, C
349Mus musculusMutation(s): 0 
Gene Names: Ada
EC: 3.5.4.4
Find proteins for P03958 (Mus musculus)
Go to UniProtKB:  P03958
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
C
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.187 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 98.833α = 90.00
b = 93.827β = 96.76
c = 86.180γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
MOLREPphasing
HKL-2000data collection
REFMACrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-10-13
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance