Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 104058.59 
• Atom Count: 7282 
• Residue Count: 926 
• Unique protein chains: 2

1RAE

CRYSTAL STRUCTURE OF CTP-LIGATED T STATE ASPARTATE TRANSCARBAMOYLASE AT 2.5 ANGSTROMS RESOLUTION: IMPLICATIONS FOR ATCASE MUTANTS AND THE MECHANISM OF NEGATIVE COOPERATIVITY

• DOI: 10.2210/pdb1RAE/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli (strain K12)


• Deposited: 1992-08-14 Released: 1994-01-31 
• Deposition Author(s): Kosman, R.P., Gouaux, J.E., Lipscomb, W.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.5 Å
• R-Value Work: 0.189 

Literature

Crystal structure of CTP-ligated T state aspartate transcarbamoylase at 2.5 A resolution: implications for ATCase mutants and the mechanism of negative cooperativity.

Kosman, R.P., Gouaux, J.E., Lipscomb, W.N.

(1993) Proteins 15: 147-176

• PubMed: 8441751 
• DOI: 10.1002/prot.340150206
• Primary Citation of Related Structures:  
  1RAI, 1RAH, 1RAG, 1RAF, 1RAD, 1RAC, 1RAB, 1RAA


• PubMed Abstract: 
  

The X-ray crystal structure of CTP-ligated T state aspartate transcarbamoylase has been refined to an R factor of 0.182 at 2.5 A resolution using the computer program X-PLOR. The structure contains 81 sites for solvent and has rms deviations from ideality in bond lengths and bond angles of 0.018 A and 3.722 degrees, respectively. The cytosine base of CTP interacts with the main chain carbonyl oxygens of rTyr-89 and rIle-12, the main chain NH of rIle-12, and the amino group of rLys-60. The ribose hydroxyls form polar contacts with the amino group of rLys-60, a carboxylate oxygen of rAsp-19, and the main chain carbonyl oxygen of rVal-9. The phosphate oxygens of CTP interact with the amino group of rLys-94, the hydroxyl of rThr-82, and an imidazole nitrogen of rHis-20. Recent mutagenesis experiments evaluated in parallel with the structure reported here indicate that alterations in the hydrogen bonding environment of the side chain of rAsn-111 may be responsible for the homotropic behavior of the pAR5 mutant of ATCase. The location of the first seven residues of the regulatory chain has been identified for the first time in a refined ATCase crystal structure, and the proximity of this portion of the regulatory chain to the allosteric site suggests a potential role for these residues in nucleotide binding to the enzyme. Finally, a series of amino acid side chain rearrangements leading from the R1 CTP allosteric to the R6 CTP allosteric site has been identified which may constitute the molecular mechanism of distinct CTP binding sites on ATCase.

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Related Citations: 

• Nucleotide Sequence of the Structural Gene (Pyrb) that Encodes the Catalytic Polypeptide of Aspartate Transcarbamoylase of Escherichia Coli
  Hoover, T.A.,Roof, W.D.,Foltermann, K.F.,O'Donovan, G.A.,Bencini, D.A.,Wild, J.R.
  (1983) Proc.Natl.Acad.Sci.USA 80: 2462
• Structural Consequences of Effector Binding to the T State of Aspartate Carbamoyltransferase: Crystal Structures of the Unligated and ATP-and Ctp-Complexed Enzymes at 2.6 Angstroms Resolution
  Stevens, R.C.,Gouaux, J.E.,Lipscomb, W.N.
  (1990) Biochemistry 29: 7691
• Structural Asymmetry in the Ctp-Liganded Form of Aspartate Carbamoyltransferase from Escherichia Coli
  Kim, K.H.,Pan, Z.,Honzatko, R.B.,Ke, H.-M.,Lipscomb, W.N.
  (1987) J.Mol.Biol. 196: 853
• Amino Acid Sequence of the Catalytic Subunit of Aspartate Transcarbamoylase from Escherichia Coli
  Konigsberg, W.H.,Henderson, L.
  (1983) Proc.Natl.Acad.Sci.USA 80: 2467
• Location of Amino Acid Alterations in Mutants of Aspartate Transcarbamoylase: Structural Aspects of Interallelic Complementation
  Schachman, H.K.,Pauza, C.D.,Navre, M.,Karels, M.J.,Wu, L.,Yang, Y.R.
  (1984) Proc.Natl.Acad.Sci.USA 81: 115




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Organizational Affiliation: 

Department of Chemistry, Gibbs Chemical Laboratory, Harvard University, Cambridge, Massachusetts 02138.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Aspartate carbamoyltransferase catalytic chain	A, C	310	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: pyrB EC: 2.1.3.2
Find proteins for P0A786 (Escherichia coli (strain K12)) Go to UniProtKB:  P0A786

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Aspartate carbamoyltransferase regulatory chain	B, D	153	Escherichia 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
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	B, D	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CTP	B, D	CYTIDINE-5'-TRIPHOSPHATE C9 H16 N3 O14 P3 PCDQPRRSZKQHHS-XVFCMESISA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.5 Å
• R-Value Work: 0.189 
• Space Group: P 3 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 122.130	α = 90.00
b = 122.130	β = 90.00
c = 142.510	γ = 120.00

Software Package:

Software Name	Purpose
X-PLOR	phasing
X-PLOR	model building
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1992-08-14 
• Released Date: 1994-01-31 
• Deposition Author(s): Kosman, R.P., Gouaux, J.E., Lipscomb, W.N.

Revision History 

• Version 1.0: 1994-01-31
  Type: Initial release
• Version 1.1: 2008-03-03
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Derived calculations, Version format compliance
• Version 1.3: 2014-07-02
  Type: Database references, Source and taxonomy
• Version 1.4: 2017-11-29
  Type: Derived calculations, Other