Crystal Structure of CP-bound Aspartate Transcarbamoylase from Bacillus subtilis

Experimental Data Snapshot

  • Resolution: 2.10 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.171 

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This is version 1.4 of the entry. See complete history


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: https://doi.org/10.1016/j.jmb.2011.05.036
  • Primary Citation of Related Structures:  
    3R7D, 3R7F, 3R7L

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aspartate carbamoyltransferase
A, B, C
304Bacillus subtilisMutation(s): 0 
Gene Names: pyrBBSU15490
Find proteins for P05654 (Bacillus subtilis (strain 168))
Explore P05654 
Go to UniProtKB:  P05654
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05654
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on CP

Download Ideal Coordinates CCD File 
D [auth A],
K [auth B],
O [auth B],
P [auth C]
C H4 N O5 P
Query on PO4

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
L [auth B],
M [auth B],
N [auth B],
Q [auth C],
R [auth C],
S [auth C],
T [auth C]
O4 P
Experimental Data & Validation

Experimental Data

  • Resolution: 2.10 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.171 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 251.916α = 90
b = 152.96β = 96.1
c = 51.239γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-06-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-08-10
    Changes: Database references
  • Version 1.3: 2017-11-08
    Changes: Advisory, Refinement description
  • Version 1.4: 2024-02-21
    Changes: Advisory, Data collection, Database references, Derived calculations