2H3E | pdb_00002h3e

Structure of wild-type E. coli Aspartate Transcarbamoylase in the presence of N-phosphonacetyl-L-isoasparagine at 2.3A resolution

• PDB DOI: https://doi.org/10.2210/pdb2H3E/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-05-22 Released: 2006-10-17 
• Deposition Author(s): Eldo, J., Cardia, J.P., O'Day, E.M., Xia, J., Tsuruta, H., Kantrowitz, E.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.250 (Depositor) 
• R-Value Work: 
  0.206 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Starting Model: experimental

Literature

N-Phosphonacetyl-l-isoasparagine a Potent and Specific Inhibitor of Escherichia coli Aspartate Transcarbamoylase.

Eldo, J., Cardia, J.P., O'day, E.M., Xia, J., Tsuruta, H., Kantrowitz, E.R.

(2006) J Med Chem 49: 5932-5938

• PubMed: 17004708 
• DOI: https://doi.org/10.1021/jm0607294
• Primary Citation of Related Structures:  
  2H3E


• PubMed Abstract: 
  

  The synthesis of a new inhibitor, N-phosphonacetyl-L-isoasparagine (PALI), of Escherichia coli aspartate transcarbamoylase (ATCase) is reported, as well as structural studies of the enzyme.PALI complex. PALI was synthesized in 7 steps from beta-benzyl L-aspartate. The KD of PALI was 2 microM. Kinetics and small-angle X-ray scattering experiments showed that PALI can induce the cooperative transition of ATCase from the T to the R state. The X-ray structure of the enzyme.PALI complex showed 22 hydrogen-bonding interactions between the enzyme and PALI. The kinetic characterization and crystal structure of the ATCase.PALI complex also provides detailed information regarding the importance of the alpha-carboxylate for the binding of the substrate aspartate.

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Organizational Affiliation: 

Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, Massachussetts 02467-3808, USA.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Hetero 12-mer - A6B6 

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

Macromolecule Content

• Total Structure Weight: 103.6 kDa 
• Atom Count: 7,609 
• Modelled Residue Count: 910 
• Deposited Residue Count: 926 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aspartate carbamoyltransferase catalytic chain	A, C	310	Escherichia coli	Mutation(s): 0  Gene Names: pyrB EC: 2.1.3.2
UniProt
Find proteins for P0A786 (Escherichia coli (strain K12)) Explore P0A786  Go to UniProtKB:  P0A786

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Aspartate carbamoyltransferase regulatory chain	B, D	153	Escherichia coli	Mutation(s): 0  Gene Names: pyrI
UniProt
Find proteins for P0A7F3 (Escherichia coli (strain K12)) Explore P0A7F3  Go to UniProtKB:  P0A7F3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6PR	E [auth A], G [auth C]	(S)-4-AMINO-4-OXO-3-(2-PHOSPHONOACETAMIDO)BUTANOIC ACID C6 H11 N2 O7 P HCFYWDYKLQITSR-VKHMYHEASA-N
ZN	F [auth B], H [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.250 (Depositor) 
• R-Value Work:  0.206 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 3 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.32	α = 90
b = 120.32	β = 90
c = 154.51	γ = 120

Software Package:

Software Name	Purpose
d*TREK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-10-17 
Deposition Author(s): Eldo, J., Cardia, J.P., O'Day, E.M., Xia, J., Tsuruta, H., Kantrowitz, E.R.

Revision History  

• Version 1.0: 2006-10-17
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description