4E2F | pdb_00004e2f

Crystal Structure of E. coli Aspartate Transcarbamoylase K164E/E239K Mutant in an intermediate state

• PDB DOI: https://doi.org/10.2210/pdb4E2F/pdb

• Classification: TRANSFERASE/PROTEIN BINDING
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2012-03-08 Released: 2012-05-02 
• Deposition Author(s): Guo, W., Kantrowitz, E.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.274 (Depositor), 0.268 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.207 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Literature

Trapping and structure determination of an intermediate in the allosteric transition of aspartate transcarbamoylase.

Guo, W., West, J.M., Dutton, A.S., Tsuruta, H., Kantrowitz, E.R.

(2012) Proc Natl Acad Sci U S A 109: 7741-7746

• PubMed: 22547808 
• DOI: https://doi.org/10.1073/pnas.1119683109
• Primary Citation Related Structures: 
  4E2F


• PubMed Abstract: 
  

  X-ray crystallography and small-angle X-ray scattering (SAXS) in solution have been used to show that a mutant aspartate transcarbamoylase exists in an intermediate quaternary structure between the canonical T and R structures. Additionally, the SAXS data indicate a pH-dependent structural alteration consistent with either a pH-induced conformational change or a pH-induced alteration in the T to R equilibrium. These data indicate that this mutant is not a model for the R state, as has been proposed, but rather represents the enzyme trapped along the path of the allosteric transition between the T and R states.

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Organizational Affiliation: 
• Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, MA 02467, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 309.28 kDa 
• Atom Count: 21,764 
• Modeled Residue Count: 2,724 
• Deposited Residue Count: 2,778 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aspartate carbamoyltransferase catalytic chain	A [auth I], B [auth K], C [auth G], D [auth C], E [auth A], H [auth E]	310	Escherichia coli K-12	Mutation(s): 2  Gene Names: b4245, JW4204, 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	F [auth D], G [auth B], I [auth J], J [auth L], K [auth H], L [auth F]	153	Escherichia coli K-12	Mutation(s): 0  Gene Names: b4244, JW4203, pyrI
UniProt
Find proteins for P0A7F3 (Escherichia coli (strain K12)) Explore P0A7F3  Go to UniProtKB:  P0A7F3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	M [auth D], N [auth B], O [auth J], P [auth L], Q [auth H], R [auth F]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.274 (Depositor), 0.268 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.207 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.086	α = 90
b = 144.814	β = 90
c = 203.359	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
MOLREP	phasing
PHENIX	refinement
d*TREK	data reduction
d*TREK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-05-02 
Deposition Author(s): Guo, W., Kantrowitz, E.R.

Revision History  

• Version 1.0: 2012-05-02
  Type: Initial release
  
• Version 1.1: 2012-05-16
  Changes: Database references
• Version 1.2: 2012-05-30
  Changes: Database references
• Version 1.3: 2024-02-28
  Changes: Data collection, Database references, Derived calculations, Refinement description