1ADD

A PRE-TRANSITION STATE MIMIC OF AN ENZYME: X-RAY STRUCTURE OF ADENOSINE DEAMINASE WITH BOUND 1-DEAZA-ADENOSINE AND ZINC-ACTIVATED WATER


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 1689-1694


  • PubMed Abstract: 
  • The refined 2.4-A structure of adenosine deaminase, recently discovered to be a zinc metalloenzyme [Wilson, D. K., Rudolph, F. B., & Quiocho, F. A. (1991) Science 252, 1278-1284], complexed with the ground-state analog 1-deazaadenosine shows the mode ...

    The refined 2.4-A structure of adenosine deaminase, recently discovered to be a zinc metalloenzyme [Wilson, D. K., Rudolph, F. B., & Quiocho, F. A. (1991) Science 252, 1278-1284], complexed with the ground-state analog 1-deazaadenosine shows the mode of binding of the analog and, unexpectedly, a zinc-activated water (hydroxide). This structure of a pre-transition-state mimic, combined with that previously determined for the complex with 6(R)-hydroxy-1,6-dihydropurine ribonucleoside, a nearly ideal transition-state analog, sheds new understanding of the precise stereospecificity and hydrolytic catalysis of an important and well-characterized member of a large group of zinc metalloenzymes. As both of these excellent mimics were generated in the active site, they demonstrate a powerful means of dissecting the course of an enzymatic reaction by direct crystallographic analysis.


    Related Citations: 
    • Atomic Structure of Adenosine Deaminase Complexed with a Transition Analog: Understanding Catalysis and Immunodeficiency Mutations
      Wilson, D.K.,Rudolph, F.B.,Quiocho, F.A.
      (1991) Science 252: 1278
    • Preliminary X-Ray Analysis 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


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ADENOSINE DEAMINASE
A
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
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
1DA
Query on 1DA

Download SDF File 
Download CCD File 
A
1-DEAZA-ADENOSINE
C11 H14 N4 O4
NVUDDRWKCUAERS-PNHWDRBUSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1DAKi: 180 nM (85) BINDINGDB
1DAKi: 180 nM BINDINGMOAD
1DAKi: 180 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Work: 0.181 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 102.390α = 90.00
b = 94.280β = 127.05
c = 73.020γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORphasing
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-01-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance