Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 40.01 kDa 
• Atom Count: 2867 
• Modelled Residue Count: 349 
• Deposited Residue Count: 349 
• Unique protein chains: 1

1FKX

MURINE ADENOSINE DEAMINASE (D296A)

• PDB DOI: 10.2210/pdb1FKX/pdb

• Classification: AMINOHYDROLASE
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 1996-02-29 Released: 1996-08-01 
• Deposition Author(s): Wilson, D.K., Quiocho, F.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Work: 0.158 
• R-Value Observed: 0.158 

Literature

Probing the functional role of two conserved active site aspartates in mouse adenosine deaminase.

Sideraki, V., Mohamedali, K.A., Wilson, D.K., Chang, Z., Kellems, R.E., Quiocho, F.A., Rudolph, F.B.

(1996) Biochemistry 35: 7862-7872

• PubMed: 8672487 
• DOI: 10.1021/bi952920d
• Primary Citation of Related Structures:  
  1FKW, 1FKX


• PubMed Abstract: 
  

Two adjacent aspartates, Asp 295 and Asp 296, playing major roles in the reaction catalyzed by mouse adenosine deaminase (mADA) were altered using site-directed mutagenesis. These mutants were expressed and purified from an ADA-deficient bacterial strain and characterized. Circular dichroism spectroscopy shows the mutants to have unperturbed secondary structure. Their zinc content compares well to that of wild-type enzyme. Changing Asp 295 to a glutamate decreases the kcat but does not alter the Km for adenosine, confirming the importance of this residue in the catalytic process and its minimal role in substrate binding. The crystal structure of the D295E mutant reveals a displacement of the catalytic water from the active site due to the longer glutamate side chain, resulting in the mutant's inability to turn over the substrate. In contrast, Asp 296 mutants exhibit markedly increased Km values, establishing this residue's critical role in substrate binding. The Asp 296->Ala mutation causes a 70-fold increase in the Km for adenosine and retains 0.001% of the wild-type kcat/Km value, whereas the ASP 296->Asn mutant has a 10-fold higher Km and retains 1% of the wild-type kcat/Km value. The structure of the D296A mutant shows that the impaired binding of substrate is caused by the loss of a single hydrogen bond between a carboxylate oxygen and N7 of the purine ring. These results and others discussed below are in agreement with the postulated role of the adjacent aspartates in the catalytic mechanism for mADA.

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Related Citations: 

• 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

• 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

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Organizational Affiliation: 

Department of Biochemistry and Cell Biology, Rice University, Houston, Texas 77005, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ADENOSINE DEAMINASE	A	349	Mus musculus	Mutation(s): 1  Gene Names: Ada EC: 3.5.4.4
UniProt
Find proteins for P03958 (Mus musculus) Explore P03958  Go to UniProtKB:  P03958

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PRH	C [auth A]	6-HYDROXY-1,6-DIHYDRO PURINE NUCLEOSIDE C10 H15 N4 O5 WGRXVKRHIMUTPD-YOHZANMFSA-O
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
PRH	Binding MOAD:  1FKX	Ki: 6.00e+6 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Work: 0.158 
• R-Value Observed: 0.158 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.71	α = 90
b = 94.07	β = 127.27
c = 73.08	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
SDMS	data reduction
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1996-02-29 
• Released Date: 1996-08-01 
Deposition Author(s): Wilson, D.K., Quiocho, F.A.

Revision History  

• Version 1.0: 1996-08-01
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-11-03
  Changes: Database references, Derived calculations, Other