6AT1

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Work: 0.160 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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-A resolution.

Stevens, R.C.Gouaux, J.E.Lipscomb, W.N.

(1990) Biochemistry 29: 7691-7701

  • Primary Citation of Related Structures:  4AT1, 5AT1

  • PubMed Abstract: 
  • The crystal structure of Escherichia coli aspartate carbamoyltransferase complexed with adenosine 5'-triphosphate (ATP) has been solved by molecular replacement and has been refined to a crystallographic residual of 0.17 at 2.6-A resolution by using ...

    The crystal structure of Escherichia coli aspartate carbamoyltransferase complexed with adenosine 5'-triphosphate (ATP) has been solved by molecular replacement and has been refined to a crystallographic residual of 0.17 at 2.6-A resolution by using the computer program X-PLOR. The unit cell dimensions of this crystal form are a = b = 122.2 A and c = 143.3 A and the space group is P321. Although the c-axis unit cell dimension is approximately 1 A longer than the corresponding dimension of the CTP-ligated P321 crystal form (c = 142.2 A), the ATP-ligated enzyme adopts a T-like quaternary structure. The base moiety of ATP interacts with residues Glu10, Ile12, and Lys60 while the ribose is near Asp19 and Lys60; the triphosphate entity is bound to Lys94, although His20 and Arg96 are nearby. We observe a higher occupancy for ATP in the allosteric site of the R1 regulatory chain in comparison to the occupancy of the R6 allosteric site. These crystallographically independent sites are related by a molecular 2-fold axis. There are other violations of the noncrystallographic symmetry that are similar to those observed in the refined CTP-ligated aspartate carbamoyltransferase structure. These infringements on the molecular symmetry might be the result of intermolecular interactions in the crystal. To ensure the most meaningful comparison with the ATP-ligated structure, we refined the previously reported CTP-bound and unligated structures to crystallographic residuals between 0.17 and 0.18 using X-PLOR. These X-PLOR refined structures are not significantly different from the initial structures that had been crystallographically refined by a restrained least-squares method. After making all possible comparisons between the CTP- and ATP-ligated and the unligated T-state structures, we find that the most significant differences are located at the allosteric sites and in small changes in the quaternary structures. At the allosteric site, the binding of CTP and ATP successively enlarges the nucleotide binding cavity, particularly in the vicinity of the base. The changes in the quaternary structure can be characterized by an increase in the separation of the catalytic trimers by approximately 0.5 A as ATP binds to the unligated T structure. On the basis of these structural studies, we discuss the relationships between the conformational differences in the allosteric site and the small changes in the quaternary structure within the T form to the possible mechanisms for CTP inhibition and ATP activation.


    Related Citations: 
    • Three-Dimensional Structures of Aspartate Carbamoyltransferase from Escherichia Coli and of its Complex with Cytidine Triphosphate
      Monaco, H.L.,Crawford, J.L.,Lipscomb, W.N.
      (1978) Proc.Natl.Acad.Sci.USA 75: 5276
    • The Catalytic Mechanism of Escherichia Coli Aspartate Carbamoyltransferase. A Molecular Modelling Study
      Gouaux, J.E.,Krause, K.L.,Lipscomb, W.N.
      (1987) Biochem.Biophys.Res.Commun. 142: 893
    • Crystal and Molecular Structures of Native and Ctp-Liganded Aspartate Carbamoyltransferase from Escherichia Coli
      Honzatko, R.B.,Crawford, J.L.,Monaco, H.L.,Ladner, J.E.,Edwards, B.F.P.,Evans, D.R.,Warren, S.G.,Wiley, D.C.,Ladner, R.C.,Lipscomb, W.N.
      (1982) J.Mol.Biol. 160: 219
    • Structure at 2.9-Angstroms Resolution of Aspartate Carbamoyltransferase Complexed with the Bisubstrate Analogue N-(Phosphonacetyl)-L-Aspartate
      Krause, K.L.,Volz, K.W.,Lipscomb, W.N.
      (1985) Proc.Natl.Acad.Sci.USA 82: 1643
    • Structural Asymmetry in the Ctp-Liganded Form of Aspartate Carbamoyltransferase from Escherichia Coli
      Kim, K.H.,Pan, Z.,Honzatko, R.B.,Ke, H.,Lipscomb, W.N.
      (1987) J.Mol.Biol. 196: 853
    • Gross Quaternary Changes in Aspartate Carbamoyltransferase are Induced by the Binding of N-(Phosphonacetyl)-L-Aspartate. A 3.5-Angstroms Resolution Study
      Ladner, J.E.,Kitchell, J.P.,Honzatko, R.B.,Ke, H.M.,Volz, K.W.,Kalb(Gilboa), A.J.,Ladner, R.C.,Lipscomb, W.N.
      (1982) Proc.Natl.Acad.Sci.USA 79: 3125
    • Escherichia Coli Aspartate Transcarbamylase. The Relation between Structure and Function
      Kantrowitz, E.R.,Lipscomb, W.N.
      (1988) Science 241: 669
    • Interactions of Phosphate Ligands with Escherichia Coli Aspartate Carbamoyltransferase in the Crystalline State
      Honzatko, R.B.,Lipscomb, W.N.
      (1982) J.Mol.Biol. 160: 265
    • Aspartate Transcarbamoylase from Escherichia Coli. Electron Density at 5.5 Angstroms Resolution
      Warren, S.G.,Edwards, B.F.P.,Evans, D.R.,Wiley, D.C.,Lipscomb, W.N.
      (1973) Proc.Natl.Acad.Sci.USA 70: 1117
    • 2.5 Angstroms Structure of Aspartate Carbamoyltransferase Complexed with the Bisubstrate Analog N-(Phosphonacetyl)-L-Aspartate
      Krause, K.L.,Volz, K.W.,Lipscomb, W.N.
      (1987) J.Mol.Biol. 193: 527
    • Structural Transitions in Crystals of Native Aspartate Carbamoyltransferase
      Gouaux, J.E.,Lipscomb, W.N.
      (1989) Proc.Natl.Acad.Sci.USA 86: 845
    • Crystal Structures of Aspartate Carbamoyltransferase Ligated with Phosphonoacetamide, Malonate, and Ctp or ATP at 2.8-Angstroms Resolution and Neutral Ph
      Gouaux, J.E.,Stevens, R.C.,Lipscomb, W.N.
      (1990) Biochemistry 29: 7702
    • Interactions of Metal-Nucleotide Complexes with Aspartate Carbamoyltransferase in the Crystalline State
      Honzatko, R.B.,Lipscomb, W.N.
      (1982) Proc.Natl.Acad.Sci.USA 79: 7171
    • A 3.0-Angstroms Resolution Study of Nucleotide Complexes with Aspartate Carbamoyltransferase
      Honzatko, R.B.,Monaco, H.L.,Lipscomb, W.N.
      (1979) Proc.Natl.Acad.Sci.USA 76: 5105
    • Binding Site at 5.5 Angstroms Resolution of Cytidine Triphosphate, the Allosteric Inhibitor of Aspartate Transcarbamylase from Escherichia Coli. Relation to Mechanisms of Control
      Lipscomb, W.N.,Edwards, B.F.P.,Evans, D.R.,Pastra-Landis, S.C.
      (1975) STRUCTURE AND CONFORMATION OF NUCLEIC ACIDS AND PROTEIN-NUCLEIC ACID INTERACTIONS : PROCEEDINGS OF THE FOURTH ANNUAL HARRY STEENBOCK SYMPOSIUM, JUNE 16-19, 1974, MADISON, WISCONSIN --: 333
    • Crystal Structures of Phosphonoacetamide Ligated T and Phosphonoacetamide and Malonate Ligated R States of Aspartate Carbamoyltransferase at 2.8-Angstroms Resolution and Neutral Ph
      Gouaux, J.E.,Lipscomb, W.N.
      (1990) Biochemistry 29: 389
    • Complex of N-Phosphonacetyl-L-Aspartate with Aspartate Carbamoyltransferase. X-Ray Refinement, Analysis of Conformational Changes and Catalytic and Allosteric Mechanisms
      Ke, H.,Lipscomb, W.N.,Cho, Y.,Honzatko, R.B.
      (1988) J.Mol.Biol. 204: 725
    • Three-Dimensional Structure of Carbamoyl Phosphate and Succinate Bound to Aspartate Carbamoyltransferase
      Gouaux, J.E.,Lipscomb, W.N.
      (1988) Proc.Natl.Acad.Sci.USA 85: 4205
    • Structure of a Single Amino Acid Mutant of Aspartate Carbamoyltransferase at 2.5-Angstroms Resolution. Implications for the Cooperative Mechanism
      Gouaux, J.E.,Lipscomb, W.N.,Middleton, S.A.,Kantrowitz, E.R.
      (1989) Biochemistry 28: 1798
    • Structure of Unligated Aspartate Carbamoyltransferase of Escherichia Coli at 2.6-Angstroms Resolution
      Ke, H.,Honzatko, R.B.,Lipscomb, W.N.
      (1984) Proc.Natl.Acad.Sci.USA 81: 4037


    Organizational Affiliation

    Gibbs Chemical Laboratory, Harvard University, Cambridge, Massachusetts 02138.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ASPARTATE CARBAMOYLTRANSFERASE (T STATE), CATALYTIC CHAIN
A, C
310Escherichia coli (strain K12)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)Gene Names: pyrI
Find proteins for P0A7F3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7F3
Small Molecules
Ligands 1 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Work: 0.160 
  • Space Group: P 3 2 1
Unit Cell:
Length (Å)Angle (°)
a = 122.000α = 90.00
b = 122.000β = 90.00
c = 142.000γ = 120.00
Software Package:
Software NamePurpose
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1990-10-15
    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: 2017-11-29
    Type: Derived calculations, Other