3R7L

Crystal Structure of PALA-bound Aspartate Transcarbamoylase from Bacillus subtilis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.585 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystallographic Snapshots of the Complete Catalytic Cycle of the Unregulated Aspartate Transcarbamoylase from Bacillus subtilis.

Harris, K.M.Cockrell, G.M.Puleo, D.E.Kantrowitz, E.R.

(2011) J.Mol.Biol. 411: 190-200

  • DOI: 10.1016/j.jmb.2011.05.036
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Here, we report high-resolution X-ray structures of Bacillus subtilis aspartate transcarbamoylase (ATCase), an enzyme that catalyzes one of the first reactions in pyrimidine nucleotide biosynthesis. Structures of the enzyme have been determined in th ...

    Here, we report high-resolution X-ray structures of Bacillus subtilis aspartate transcarbamoylase (ATCase), an enzyme that catalyzes one of the first reactions in pyrimidine nucleotide biosynthesis. Structures of the enzyme have been determined in the absence of ligands, in the presence of the substrate carbamoyl phosphate, and in the presence of the bisubstrate/transition state analog N-phosphonacetyl-L-aspartate. Combining the structural data with in silico docking and electrostatic calculations, we have been able to visualize each step in the catalytic cycle of ATCase, from the ordered binding of the substrates, to the formation and decomposition of the tetrahedral intermediate, to the ordered release of the products from the active site. Analysis of the conformational changes associated with these steps provides a rationale for the lack of cooperativity in trimeric ATCases that do not possess regulatory subunits.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Aspartate carbamoyltransferase
A, B, C, D, E, F
304Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: pyrB
EC: 2.1.3.2
Find proteins for P05654 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P05654
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
C, D
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
PAL
Query on PAL

Download SDF File 
Download CCD File 
A, B, C, D, E, F
N-(PHOSPHONACETYL)-L-ASPARTIC ACID
C6 H10 N O8 P
ZZKNRXZVGOYGJT-VKHMYHEASA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.585 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.178 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 189.649α = 90.00
b = 141.432β = 109.96
c = 114.829γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-06-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2011-08-10
    Type: Database references
  • Version 1.3: 2017-11-08
    Type: Refinement description