1D09

ASPARTATE TRANSCARBAMOYLASE COMPLEXED WITH N-PHOSPHONACETYL-L-ASPARTATE (PALA)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.203 

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This is version 2.1 of the entry. See complete history


Literature

Insights into the mechanisms of catalysis and heterotropic regulation of Escherichia coli aspartate transcarbamoylase based upon a structure of the enzyme complexed with the bisubstrate analogue N-phosphonacetyl-L-aspartate at 2.1 A.

Jin, L.Stec, B.Lipscomb, W.N.Kantrowitz, E.R.

(1999) Proteins 37: 729-742


  • PubMed Abstract: 

    A high-resolution structure of Escherichia coli aspartate transcarbamoylase has been determined to 2.1 A; resolution in the presence of the bisubstrate analog N-phosphonacetyl-L-aspartate (PALA). The structure was refined to a free R-factor of 23.4% and a working R-factor of 20.3%. The PALA molecule is completely saturated with interactions to side chain and backbone groups in the active site, including two interactions that are contributed from the 80s loop of the adjacent catalytic chain. The charge neutralization of the bound PALA molecule (and presumably the substrates as well) induced by the electrostatic field of the highly positively charged active site is an important factor in the high binding affinity of PALA and must be important for catalysis. The higher-resolution structure reported here departs in a number of ways from the previously determined structure at lower resolution. These modifications include alterations in the backbone conformation of the C-terminal of the catalytic chains, the N- and C-termini of the regulatory chains, and two loops of the regulatory chain. The high-resolution of this structure has allowed a more detailed description of the binding of PALA to the active site of the enzyme and has allowed a detailed model of the tetrahedral intermediate to be constructed. This model becomes the basis of a description of the catalytic mechanism of the transcarbamoylase reaction. The R-structural state of the enzyme-PALA complex is an excellent representation of the form of the enzyme that occurs at the moment in the catalytic cycle when the tetrahedral intermediate is formed. Finally, improved electron density in the N-terminal region of the regulatory chain (residues 1 to 7) has allowed tracing of the entire regulatory chain. The N-terminal segments of the R1 and R6 chains are located in close proximity to each other and to the regulatory site. This portion of the molecule may be involved in the observed asymmetry between the regulatory binding sites as well as in the heterotropic response of the enzyme.


  • Organizational Affiliation

    Department of Chemistry, Boston College, Merkert Chemistry Center, Chestnut Hill, Massachusetts 02467, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ASPARTATE CARBAMOYLTRANSFERASE CATALYTIC CHAIN
A, C
310Escherichia coliMutation(s): 0 
Gene Names: NATURAL PYRB PROMOTOR
EC: 2.1.3.2
UniProt
Find proteins for P0A786 (Escherichia coli (strain K12))
Explore P0A786 
Go to UniProtKB:  P0A786
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A786
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ASPARTATE CARBAMOYLTRANSFERASE REGULATORY CHAIN
B, D
153Escherichia coliMutation(s): 0 
Gene Names: PYRI
UniProt
Find proteins for P0A7F3 (Escherichia coli (strain K12))
Explore P0A7F3 
Go to UniProtKB:  P0A7F3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7F3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
PAL PDBBind:  1D09 Ki: 27 (nM) from 1 assay(s)
Binding MOAD:  1D09 Ki: 27 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.203 
  • Space Group: P 3 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.24α = 90
b = 122.24β = 90
c = 156.36γ = 120
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
SDMSdata reduction
SDMSdata scaling
X-PLORphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-01-28
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 2.0: 2024-02-07
    Changes: Atomic model, Data collection, Database references, Derived calculations
  • Version 2.1: 2024-03-13
    Changes: Advisory, Derived calculations, Source and taxonomy, Structure summary