Biological Assembly 1  

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

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 37.00 kDa 
• Atom Count: 2484 
• Modelled Residue Count: 303 
• Deposited Residue Count: 327 
• Unique protein chains: 1

3NH4

Crystal structure of murine aminoacylase 3

• PDB DOI: 10.2210/pdb3NH4/pdb

• Classification: HYDROLASE
• Organism(s): Mus musculus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-06-14 Released: 2010-10-20 
• Deposition Author(s): Hsieh, J.M., Tsirulnikov, K., Sawaya, M.R., Magilnick, N., Abuladze, N., Kurtz, I., Abramson, J., Pushkin, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.207 
• R-Value Work: 0.184 
• R-Value Observed: 0.185 

Literature

Structures of aminoacylase 3 in complex with acetylated substrates.

Hsieh, J.M., Tsirulnikov, K., Sawaya, M.R., Magilnick, N., Abuladze, N., Kurtz, I., Abramson, J., Pushkin, A.

(2010) Proc Natl Acad Sci U S A 107: 17962-17967

• PubMed: 20921362 
• DOI: 10.1073/pnas.1006687107
• Primary Citation of Related Structures:  
  3NFZ, 3NH4, 3NH5, 3NH8


• PubMed Abstract: 
  

Trichloroethylene (TCE) is one of the most widespread environmental contaminants, which is metabolized to N-acetyl-S-1,2-dichlorovinyl-L-cysteine (NA-DCVC) before being excreted in the urine. Alternatively, NA-DCVC can be deacetylated by aminoacylase 3 (AA3), an enzyme that is highly expressed in the kidney, liver, and brain. NA-DCVC deacetylation initiates the transformation into toxic products that ultimately causes acute renal failure. AA3 inhibition is therefore a target of interest to prevent TCE induced nephrotoxicity. Here we report the crystal structure of recombinant mouse AA3 (mAA3) in the presence of its acetate byproduct and two substrates: N(α)-acetyl-L-tyrosine and NA-DCVC. These structures, in conjunction with biochemical data, indicated that AA3 mediates substrate specificity through van der Waals interactions providing a dynamic interaction interface, which facilitates a diverse range of substrates.

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Organizational Affiliation: 

Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aspartoacylase-2	A	327	Mus musculus	Mutation(s): 0  Gene Names: ACY-3, Acy3, Aspa2 EC: 3.5.1 (PDB Primary Data), 3.5.1.114 (UniProt)
UniProt
Find proteins for Q91XE4 (Mus musculus) Explore Q91XE4  Go to UniProtKB:  Q91XE4

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CS	C [auth A], D [auth A]	CESIUM ION Cs NCMHKCKGHRPLCM-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT	G [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
FMT	H [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
CL	E [auth A], F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.207 
• R-Value Work: 0.184 
• R-Value Observed: 0.185 
• Space Group: P 6₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.661	α = 90
b = 93.661	β = 90
c = 97.128	γ = 120

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
BOS	data collection
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-06-14 
• Released Date: 2010-10-20 
Deposition Author(s): Hsieh, J.M., Tsirulnikov, K., Sawaya, M.R., Magilnick, N., Abuladze, N., Kurtz, I., Abramson, J., Pushkin, A.

Revision History  

• Version 1.0: 2010-10-20
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance