2ADA

ATOMIC STRUCTURE OF ADENOSINE DEAMINASE COMPLEXED WITH A TRANSITION-STATE ANALOG: UNDERSTANDING CATALYSIS AND IMMUNODEFICIENCY MUTATIONS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 1278-1284


  • PubMed Abstract: 
  • The crystal structure of a murine adenosine deaminase complexed with 6-hydroxyl-1,6-dihydropurine ribonucleoside, a nearly ideal transition-state analog, has been determined and refined at 2.4 angstrom resolution. The structure is folded as an eight- ...

    The crystal structure of a murine adenosine deaminase complexed with 6-hydroxyl-1,6-dihydropurine ribonucleoside, a nearly ideal transition-state analog, has been determined and refined at 2.4 angstrom resolution. The structure is folded as an eight-stranded parallel alpha/beta barrel with a deep pocket at the beta-barrel COOH-terminal end wherein the inhibitor and a zinc are bound and completely sequestered. The presence of the zinc cofactor and the precise structure of the bound analog were not previously known. The 6R isomer of the analog is very tightly held in place by the coordination of the 6-hydroxyl to the zinc and the formation of nine hydrogen bonds. On the basis of the structure of the complex a stereoselective addition-elimination or SN2 mechanism of the enzyme is proposed with the zinc atom and the Glu and Asp residues playing key roles. A molecular explanation of a hereditary disease caused by several point mutations of an enzyme is also presented.


    Related Citations: 
    • Crystallographic Observation of a Trapped Tetrahedral Intermediate in a Metalloenzyme
      Wilson, D.K.,Quiocho, F.A.
      (1994) Nat.Struct.Mol.Biol. 1: 691
    • Preliminary X-Ray Analysis of Crystals of Murine Adenosine Deaminase
      Wilson, D.K.,Rudolph, F.B.,Harrison, M.L.,Kellems, R.E.,Quiocho, F.A.
      (1988) J.Mol.Biol. 200: 613
    • A Pre-Transition-State Mimic of an Enzyme: X-Ray Structure of Adenosine Deaminase with Bound 1-Deazaadenosine
      Wilson, D.K.,Quiocho, F.A.
      (1993) Biochemistry 32: 1689
    • Refined 2.5 Angstroms Structure of the Murine Adenosine Deaminase at Ph 6.0
      Sharff, A.J.,Wilson, D.K.,Chang, Z.
      (1992) J.Mol.Biol. 226: 917


    Organizational Affiliation

    Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ADENOSINE DEAMINASE
A
352Mus 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
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
HPR
Query on HPR

Download SDF File 
Download CCD File 
A
6-HYDROXY-7,8-DIHYDRO PURINE NUCLEOSIDE
C10 H14 N4 O5
ZWTNXGIZBOQCAJ-KQYNXXCUSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
HPRKi: ~0.0001 nM BINDINGMOAD
HPRKi: 0.0001 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Work: 0.195 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 102.360α = 90.00
b = 94.110β = 127.19
c = 72.930γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORphasing
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1995-03-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance