1A4M

ADA STRUCTURE COMPLEXED WITH PURINE RIBOSIDE AT PH 7.0


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 8314-8324

  • DOI: 10.1021/bi980324o
  • Primary Citation of Related Structures:  1A4L
  • Also Cited By: 3MVI, 3MVT

  • PubMed Abstract: 
  • Adenosine deaminase, which catalyzes the irreversible hydrolytic deamination of adenosine nucleosides to inosine nucleosides and ammonia, is a key enzyme in purine metabolism and lymphoid development. The X-ray structures of murine adenosine deaminas ...

    Adenosine deaminase, which catalyzes the irreversible hydrolytic deamination of adenosine nucleosides to inosine nucleosides and ammonia, is a key enzyme in purine metabolism and lymphoid development. The X-ray structures of murine adenosine deaminase with bound potent inhibitors (Ki values approximately 10(-13) M) (8R)-hydroxyl-2'-deoxycoformycin (pentostatin), a transition state analogue, and (6S)-hydroxyl-1,6-dihydropurine riboside, a reaction coordinate analogue, have been determined and refined to resolutions of 2.6 and 1.95 A, respectively. Crystals of both complexes were obtained at pH 7, where the enzyme is fully active, in an identical space group with the asymmetric unit containing four molecules. In addition to the very high degree of similarity between the four independent molecules in each complex structure, there is also considerable structural similarity of the complex with the dihydropurine riboside with that of an identical complex previously determined at pH 4.2 where the enzyme is 20% active. The interactions between the enzyme and the two analogues are extremely similar. These include the coordination of the 8R- or 6S-hydroxyl group of the analogues to the Zn2+ which mainly contributes to the strong potency and very high degree of stereospecificity of inhibition by these analogues. The interactions are further indicative of the structural and chemical requirements of substrates. These structures and recent site-directed mutagenesis have further shed light on the catalytic mechanism of the enzyme.


    Related Citations: 
    • Atomic Structure of Adenosine Deaminase Complexed with a Transition-State Analog: Understanding Catalysis and Immunodeficiency Mutations
      Wilson, D.K.,Rudolph, F.B.,Quiocho, F.A.
      (1991) Science 252: 1278
    • A Pre-Transition-State Mimic of an Enzyme: X-Ray Structure of Adenosine Deaminase with Bound 1-Deazaadenosine and Zinc-Activated Water
      Wilson, D.K.,Quiocho, F.A.
      (1993) Biochemistry 32: 1689
    • Refined 2.5 A Structure of Murine Adenosine Deaminase at Ph 6.0
      Sharff, A.J.,Wilson, D.K.,Chang, Z.,Quiocho, F.A.
      (1992) J.Mol.Biol. 226: 917


    Organizational Affiliation

    Structural and Computational Biology and Molecular Biophysics Program, Howard Hughes Medical Institute, Baylor College of Medicine, Houston, Texas 77030, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ADENOSINE DEAMINASE
A, B, C, D
349Mus musculusGene 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
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
PRH
Query on PRH

Download SDF File 
Download CCD File 
A, B, C, D
6-HYDROXY-1,6-DIHYDRO PURINE NUCLEOSIDE
C10 H15 N4 O5
WGRXVKRHIMUTPD-YOHZANMFSA-O
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PRHKi: 0.00016 nM BINDINGMOAD
PRHKi: ~0.0001 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.193 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 88.693α = 90.00
b = 93.644β = 102.84
c = 102.177γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
DENZOdata reduction
X-PLORmodel building
X-PLORphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-10-14
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance