4F04

A Second Allosteric site in E. coli Aspartate Transcarbamoylase: R-state ATCase with UTP bound

• PDB DOI: https://doi.org/10.2210/pdb4F04/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-05-03 Released: 2012-07-11 
• Deposition Author(s): Peterson, A.W., Cockrell, G.M., Kantrowitz, E.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.207 
• R-Value Work: 0.173 
• R-Value Observed: 0.175 

Literature

A second allosteric site in Escherichia coli aspartate transcarbamoylase.

Peterson, A.W., Cockrell, G.M., Kantrowitz, E.R.

(2012) Biochemistry 51: 4776-4778

• PubMed: 22667327 
• DOI: https://doi.org/10.1021/bi3006219
• Primary Citation of Related Structures:  
  4F04


• PubMed Abstract: 
  

  Escherichia coli aspartate transcarbamoylase is feedback inhibited by CTP and UTP in the presence of CTP. Here, we show by X-ray crystallography that UTP binds to a unique site on each regulatory chain of the enzyme that is near but not overlapping with the known CTP site. These results bring into question all of the previously proposed mechanisms of allosteric regulation in aspartate transcarbamoylase.

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Organizational Affiliation: 

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

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 104.57 kDa 
• Atom Count: 7,448 
• Modelled Residue Count: 906 
• Deposited Residue Count: 926 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aspartate carbamoyltransferase catalytic chain	A, C	310	Escherichia coli K-12	Mutation(s): 0  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	B, D	153	Escherichia coli K-12	Mutation(s): 0  Gene Names: b4244, JW4203, pyrI EC: 2.1.3.2
UniProt
Find proteins for P0A7F3 (Escherichia coli (strain K12)) Explore P0A7F3  Go to UniProtKB:  P0A7F3

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UTP	G [auth B], J [auth D]	URIDINE 5'-TRIPHOSPHATE C9 H15 N2 O15 P3 PGAVKCOVUIYSFO-XVFCMESISA-N
PAL	E [auth A], H [auth C]	N-(PHOSPHONACETYL)-L-ASPARTIC ACID C6 H10 N O8 P ZZKNRXZVGOYGJT-VKHMYHEASA-N
ZN	F [auth B], I [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.207 
• R-Value Work: 0.173 
• R-Value Observed: 0.175 
• Space Group: P 3 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.277	α = 90
b = 121.277	β = 90
c = 155.109	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-07-11 
Deposition Author(s): Peterson, A.W., Cockrell, G.M., Kantrowitz, E.R.

Revision History  

• Version 1.0: 2012-07-11
  Type: Initial release
  
• Version 1.1: 2013-06-26
  Changes: Database references
• Version 1.2: 2017-11-15
  Changes: Refinement description
• Version 1.3: 2024-02-28
  Changes: Data collection, Database references, Derived calculations