Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 72.12 kDa 
• Atom Count: 4939 
• Residue Count: 602 
• Unique protein chains: 1

2O4H

Human brain aspartoacylase complex with intermediate analog (N-phosphonomethyl-L-aspartate)

• DOI: 10.2210/pdb2O4H/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2006-12-04 Released: 2007-11-06 
• Deposition Author(s): Le Coq, J., Pavlovsky, A., Sanishvili, R., Viola, R.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.271 
• R-Value Work: 0.202 
• R-Value Observed: 0.205 

Literature

Examination of the Mechanism of Human Brain Aspartoacylase through the Binding of an Intermediate Analogue.

Le Coq, J., Pavlovsky, A., Malik, R., Sanishvili, R., Xu, C., Viola, R.E.

(2008) Biochemistry 47: 3484-3492

• PubMed: 18293939 
• DOI: 10.1021/bi702400x
• Primary Citation of Related Structures:  
  2O4H, 2O53


• PubMed Abstract: 
  

Canavan disease is a fatal neurological disorder caused by the malfunctioning of a single metabolic enzyme, aspartoacylase, that catalyzes the deacetylation of N-acetyl-L-aspartate to produce L-aspartate and acetate. The structure of human brain aspartoacylase has been determined in complex with a stable tetrahedral intermediate analogue, N-phosphonomethyl-L-aspartate. This potent inhibitor forms multiple interactions between each of its heteroatoms and the substrate binding groups arrayed within the active site. The binding of the catalytic intermediate analogue induces the conformational ordering of several substrate binding groups, thereby setting up the active site for catalysis. The highly ordered binding of this inhibitor has allowed assignments to be made for substrate binding groups and provides strong support for a carboxypeptidase-type mechanism for the hydrolysis of the amide bond of the substrate, N-acetyl- l-aspartate.

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Organizational Affiliation: 

Department of Chemistry, University of Toledo, Toledo, Ohio 43606, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aspartoacylase	A, B	313	Homo sapiens	Mutation(s): 0  Gene Names: ASPA, ACY2, ASP EC: 3.5.1.15
Find proteins for P45381 (Homo sapiens) Explore P45381  Go to UniProtKB:  P45381
NIH Common Fund Data Resources
PHAROS:  P45381 GTEx:  ENSG00000108381

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AS9	A, B	N-[HYDROXY(METHYL)PHOSPHORYL]-L-ASPARTIC ACID C5 H10 N O6 P GKKRPYJQMIDFSC-VKHMYHEASA-N
ZN	A, B	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
AS9	Ki :  300   nM  PDBBind

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.271 
• R-Value Work: 0.202 
• R-Value Observed: 0.205 
• Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 143.081	α = 90
b = 143.081	β = 90
c = 104.604	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345dtb	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-12-04 
• Released Date: 2007-11-06 
Deposition Author(s): Le Coq, J., Pavlovsky, A., Sanishvili, R., Viola, R.E.

Revision History 

• Version 1.0: 2007-11-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance