3MPU

Crystal structure of the C47A/A241C disulfide-linked E. coli Aspartate Transcarbamoylase holoenzyme


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.855 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The Pathway of Product Release from the R State of Aspartate Transcarbamoylase.

Mendes, K.R.Kantrowitz, E.R.

(2010) J.Mol.Biol. 401: 940-948

  • DOI: 10.1016/j.jmb.2010.07.003

  • PubMed Abstract: 
  • The pathway of product release from the R state of aspartate transcarbamoylase (ATCase; EC 2.1.3.2, aspartate carbamoyltransferase) has been determined here by solving the crystal structure of Escherichia coli ATCase locked in the R quaternary struct ...

    The pathway of product release from the R state of aspartate transcarbamoylase (ATCase; EC 2.1.3.2, aspartate carbamoyltransferase) has been determined here by solving the crystal structure of Escherichia coli ATCase locked in the R quaternary structure by specific introduction of disulfide bonds. ATCase displays ordered substrate binding and product release, remaining in the R state until substrates are exhausted. The structure reported here represents ATCase in the R state bound to the final product molecule, phosphate. This structure has been difficult to obtain previously because the enzyme relaxes back to the T state after the substrates are exhausted. Hence, cocrystallizing the wild-type enzyme with phosphate results in a T-state structure. In this structure of the enzyme trapped in the R state with specific disulfide bonds, we observe two phosphate molecules per active site. The position of the first phosphate corresponds to the position of the phosphate of carbamoyl phosphate (CP) and the position of the phosphonate of N-phosphonacetyl-l-aspartate. However, the second, more weakly bound phosphate is bound in a positively charged pocket that is more accessible to the surface than the other phosphate. The second phosphate appears to be on the path that phosphate would have to take to exit the active site. Our results suggest that phosphate dissociation and CP binding can occur simultaneously and that the dissociation of phosphate may actually promote the binding of CP for more efficient catalysis.


    Organizational Affiliation

    Department of Chemistry, Boston College, Merkert Chemistry Center, Chestnut Hill, MA 02467-3807, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Aspartate carbamoyltransferase catalytic chain
A, C, E
310Escherichia coli (strain K12)Mutation(s): 2 
Gene Names: pyrB
EC: 2.1.3.2
Find proteins for P0A786 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A786
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Aspartate carbamoyltransferase regulatory chain
B, D, F
153Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: pyrI
Find proteins for P0A7F3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7F3
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, C, E
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
B, D, F
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.855 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.173 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 120.711α = 90.00
b = 120.711β = 90.00
c = 692.471γ = 120.00
Software Package:
Software NamePurpose
PHENIXmodel building
HKL-2000data scaling
ADSCdata collection
PHENIXrefinement
PHENIXphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-07-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance