1RAD

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


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

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

  • DOI: 10.1002/prot.340150206
  • Primary Citation of Related Structures:  

  • 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 ide ...

    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.


    Related Citations: 
    • 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
    • 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
    • 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
    • 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
    • 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


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Aspartate carbamoyltransferase catalytic chain
A, C
310Escherichia 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
MoleculeChainsSequence LengthOrganismDetails
Aspartate carbamoyltransferase regulatory chain
B, D
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
ZN
Query on ZN

Download SDF File 
Download CCD File 
B, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CTP
Query on CTP

Download SDF File 
Download CCD File 
B, D
CYTIDINE-5'-TRIPHOSPHATE
C9 H16 N3 O14 P3
PCDQPRRSZKQHHS-XVFCMESISA-N
 Ligand Interaction
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 = 122.130α = 90.00
b = 122.130β = 90.00
c = 142.510γ = 120.00
Software Package:
Software NamePurpose
X-PLORphasing
X-PLORrefinement
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

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