2AT1

CRYSTAL STRUCTURES OF PHOSPHONOACETAMIDE LIGATED T AND PHOSPHONOACETAMIDE AND MALONATE LIGATED R STATES OF ASPARTATE CARBAMOYLTRANSFERASE AT 2.8-ANGSTROMS RESOLUTION AND NEUTRAL PH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Work: 0.170 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Crystal structures of phosphonoacetamide ligated T and phosphonoacetamide and malonate ligated R states of aspartate carbamoyltransferase at 2.8-A resolution and neutral pH.

Gouaux, J.E.Lipscomb, W.N.

(1990) Biochemistry 29: 389-402

  • DOI: 10.1021/bi00454a013
  • Primary Citation of Related Structures:  
    3AT1, 2AT1, 1AT1

  • PubMed Abstract: 
  • The T----R transition of the cooperative enzyme aspartate carbamoyltransferase occurs at pH 7 in single crystals without visibly cracking many of the crystals and leaving those uncracked suitable for single-crystal X-ray analysis. To promote the T----R transition, we employ the competitive inhibitors of carbamoyl phosphate and aspartate, which are phosphonoacetamide (PAM) and malonate, respectively ...

    The T----R transition of the cooperative enzyme aspartate carbamoyltransferase occurs at pH 7 in single crystals without visibly cracking many of the crystals and leaving those uncracked suitable for single-crystal X-ray analysis. To promote the T----R transition, we employ the competitive inhibitors of carbamoyl phosphate and aspartate, which are phosphonoacetamide (PAM) and malonate, respectively. In response to PAM binding to the T-state crystals, residues Thr 53-Thr 55 and Pro 266-Pro 268 move to their R-state positions to bind to the phosphonate and amino group of PAM. These changes induce a conformation that can bind tightly the aspartate analogue malonate, which thereby effects the allosteric transition. We prove this by showing that PAM-ligated T-state crystals (Tpam), space group P321 (a = 122.2 A, c = 142.2 A), when transferred to a solution containing 20 mM PAM and 8 mM malonate at pH 7, isomerize to R-state crystals (Rpam,mal,soak), space group also P321 (a = 122.2 A, c = 156.4 A). The R-state structure in which the T----R transition occurs within the crystal at pH 7 compares very well (rms = 0.19 A for all atoms) with an R-state structure determined at pH 7 in which the crystals were initially grown in a solution of PAM and malonate at pH 5.9 and subsequently transferred to a buffer containing the ligands at pH 7 (Rpam,mal,crys). In fact, both of the PAM and malonate ligated R-state structures are very similar to both the carbamoyl phosphate and succinate or the N-(phosphonoacetyl)-L-aspartate ligated structures, even though the R-state structures reported here were determined at pH 7. Crystallographic residuals refined to 0.16-0.18 at 2.8-A resolution for the three structures.


    Related Citations: 
    • 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
    • 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
    • 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
    • Structural Transitions in Crystals of Native Aspartate Carbamoyltransferase
      Gouaux, J.E., Lipscomb, W.N.
      (1989) Proc Natl Acad Sci U S A 86: 845
    • 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
    • Escherichia Coli Aspartate Transcarbamylase. The Relation between Structure and Function
      Kantrowitz, E.R., Lipscomb, W.N.
      (1988) Science 241: 669
    • Three-Dimensional Structure of Carbamoyl Phosphate and Succinate Bound to Aspartate Carbamoyltransferase
      Gouaux, J.E., Lipscomb, W.N.
      (1988) Proc Natl Acad Sci U S A 85: 4205
    • 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
    • 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
    • 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 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 U S A 82: 1643
    • 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 U S A 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
    • 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
    • Interactions of Metal-Nucleotide Complexes with Aspartate Carbamoyltransferase in the Crystalline State
      Honzatko, R.B., Lipscomb, W.N.
      (1982) Proc Natl Acad Sci U S A 79: 7171
    • 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 U S A 79: 3125
    • 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 U S A 76: 5105
    • 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 U S A 75: 5276
    • 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
    • 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 U S A 70: 1117

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ASPARTATE CARBAMOYLTRANSFERASE (R STATE), CATALYTIC CHAINA, C310Escherichia coliMutation(s): 0 
EC: 2.1.3.2
UniProt
Find proteins for P0A786 (Escherichia coli (strain K12))
Explore P0A786 
Go to UniProtKB:  P0A786
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ASPARTATE CARBAMOYLTRANSFERASE REGULATORY CHAINB, D153Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7F3 (Escherichia coli (strain K12))
Explore P0A7F3 
Go to UniProtKB:  P0A7F3
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranoseE, F2N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G07411ON
GlyCosmos:  G07411ON
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PCT
Query on PCT

Download Ideal Coordinates CCD File 
G [auth A], I [auth C]PHOSPHONOACETAMIDE
C2 H6 N O4 P
AKVIWWJLBFWFLM-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
H [auth B], J [auth D]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 3
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900001
Query on PRD_900001
E, Falpha-maltoseOligosaccharide /  Nutrient Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Work: 0.170 
  • Space Group: P 3 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.2α = 90
b = 122.2β = 90
c = 156.6γ = 120
Software Package:
Software NamePurpose
X-PLORrefinement

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1990-10-15
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-11-29
    Changes: Advisory, Derived calculations, Other
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary