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: 2.40 Å
  • R-Value Work: 0.181 
  • R-Value Observed: 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

  • DOI: 10.1021/bi00058a001
  • Primary Citation of Related Structures:  
    1ADD

  • 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 of binding of the analog and, unexpectedly, a zinc-activated water (hydroxide) ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ADENOSINE DEAMINASEA349Mus musculusMutation(s): 0 
Gene Names: Ada
EC: 3.5.4.4
UniProt
Find proteins for P03958 (Mus musculus)
Explore P03958 
Go to UniProtKB:  P03958
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1DA (Subject of Investigation/LOI)
Query on 1DA

Download Ideal Coordinates CCD File 
C [auth A]1-DEAZA-ADENOSINE
C11 H14 N4 O4
NVUDDRWKCUAERS-PNHWDRBUSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
1DA Binding MOAD:  1ADD Ki: 180 (nM) from 1 assay(s)
PDBBind:  1ADD Ki: 180 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Work: 0.181 
  • R-Value Observed: 0.181 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.39α = 90
b = 94.28β = 127.05
c = 73.02γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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