7AT1

CRYSTAL STRUCTURES OF ASPARTATE CARBAMOYLTRANSFERASE LIGATED WITH PHOSPHONOACETAMIDE, MALONATE, AND CTP OR ATP AT 2.8-ANGSTROMS RESOLUTION AND NEUTRAL P*H


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structures of aspartate carbamoyltransferase ligated with phosphonoacetamide, malonate, and CTP or ATP at 2.8-A resolution and neutral pH.

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

(1990) Biochemistry 29: 7702-7715

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The R-state structures of the ATP and CTP complexes of aspartate carbamoyltransferase ligated with phosphonoacetamide and malonate have been determined at 2.8-A resolution and neutral pH. These structures were solved by the method of molecular replac ...

    The R-state structures of the ATP and CTP complexes of aspartate carbamoyltransferase ligated with phosphonoacetamide and malonate have been determined at 2.8-A resolution and neutral pH. These structures were solved by the method of molecular replacement and were refined to crystallographic residuals between 0.167 and 0.182. The triphosphate, the ribose, and the purine and pyrimidine moieties of ATP and CTP interact with similar regions of the allosteric domain of the regulatory dimer. ATP and CTP relatively increase and decrease the size of the allosteric site in the vicinity of the base, respectively. For both CTP and ATP at pH 7, the gamma-phosphates are bound to His20 and are also near Lys94, while the alpha-phosphates interact exclusively with Lys94. The 2'-hydroxyls of both CTP and ATP are near the amino group of Lys60. The pyrimidine ring of CTP makes specific hydrogen bonds at the allosteric site: the NH2 group donates hydrogen bonds to the main-chain carbonyls of Ile12 and Tyr89 and the pyrimidine ring carbonyl oxygen accepts a hydrogen bond from the amino group of Lys60; the nitrogen at position 3 in the pyrimidine ring is hydrogen bonded to a main-chain NH group of Ile12. The purine ring of ATP also makes numerous interactions with residues at the allosteric site: the purine NH2 (analogous to the amino group of CTP) donates a hydrogen bond to the main-chain carbonyl oxygen of Ile12, the N3 nitrogen interacts with the amino group of Lys60, and the N1 nitrogen hydrogen bonds to the NH group of Ile12. The binding of CTP and ATP to the allosteric site in the presence of phosphonoacetamide and malonate does not dramatically alter the structure of the allosteric binding site or of the allosteric domain. Nonetheless, in the CTP-ligated structure, the average separation between the catalytic trimers decreases by approximately 0.5 A, indicating a small shift of the quaternary structure toward the T state. In the CTP- and ATP-ligated R-state structures, the binding and occupancy of phosphonoacetamide and malonate are similar and the structures of the active sites are similar at the current resolution of 2.8 A.


    Related Citations: 
    • 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
    • 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
    • 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
    • Escherichia Coli Aspartate Transcarbamylase. The Relation between Structure and Function
      Kantrowitz, E.R.,Lipscomb, W.N.
      (1988) Science 241: 669
    • 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
    • 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
    • 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
    • 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
    • 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
    • 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
    • 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
    • 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
    • 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
    • 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
    • Structural Transitions in Crystals of Native Aspartate Carbamoyltransferase
      Gouaux, J.E.,Lipscomb, W.N.
      (1989) Proc.Natl.Acad.Sci.USA 86: 845
    • 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
    • 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
    • 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
    • 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


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ASPARTATE CARBAMOYLTRANSFERASE (R STATE), 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 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download SDF File 
Download CCD File 
B
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
MAL
Query on MAL

Download SDF File 
Download CCD File 
A, C
MALTOSE
C12 H22 O11
GUBGYTABKSRVRQ-ASMJPISFSA-N
 Ligand Interaction
ZN
Query on ZN

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

Download SDF File 
Download CCD File 
A, C
PHOSPHONOACETAMIDE
C2 H6 N O4 P
AKVIWWJLBFWFLM-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Work: 0.183 
  • Space Group: P 3 2 1
Unit Cell:
Length (Å)Angle (°)
a = 122.500α = 90.00
b = 122.500β = 90.00
c = 156.500γ = 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: Advisory, Derived calculations, Other