8ATC

COMPLEX OF N-PHOSPHONACETYL-L-ASPARTATE WITH ASPARTATE CARBAMOYLTRANSFERASE. X-RAY REFINEMENT, ANALYSIS OF CONFORMATIONAL CHANGES AND CATALYTIC AND ALLOSTERIC MECHANISMS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Observed: 0.165 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Complex of N-phosphonacetyl-L-aspartate with aspartate carbamoyltransferase. X-ray refinement, analysis of conformational changes and catalytic and allosteric mechanisms.

Ke, H.M.Lipscomb, W.N.Cho, Y.J.Honzatko, R.B.

(1988) J Mol Biol 204: 725-747

  • DOI: 10.1016/0022-2836(88)90365-8
  • Primary Citation of Related Structures:  
    8ATC

  • PubMed Abstract: 
  • The allosteric enzyme aspartate carbamoyltransferase of Escherichia coli consists of six regulatory chains (R) and six catalytic chains (C) in D3 symmetry. The less active T conformation, complexed to the allosteric inhibitor CTP has been refined to 2.6 A (R-factor of 0 ...

    The allosteric enzyme aspartate carbamoyltransferase of Escherichia coli consists of six regulatory chains (R) and six catalytic chains (C) in D3 symmetry. The less active T conformation, complexed to the allosteric inhibitor CTP has been refined to 2.6 A (R-factor of 0.155). We now report refinement of the more active R conformation, complexed to the bisubstrate analog N-phosphonacetyl-L-aspartate (PALA) to 2.4 A (R-factor of 0.165, root-mean-square deviations from ideal bond distances and angles of 0.013 A and 2.2 degrees, respectively). The antiparallel beta-sheet in the revised segment 8-65 of the regulatory chain of the T conformation is confirmed in the R conformation, as is also the interchange of alanine 1 with the side-chain of asparagine 2 in the catalytic chain. The crystallographic asymmetric unit containing one-third of the molecule (C2R2) includes 925 sites for water molecules, and seven side-chains in alternative conformations. The gross conformational changes of the T to R transition are confirmed, including the elongation of the molecule along its threefold axis by 12 A, the relative reorientation of the catalytic trimers C3 by 10 degrees, and the rotation of the regulatory dimers R2 about the molecular twofold axis by 15 degrees. No changes occur in secondary structure. Essentially rigid-body transformations account for the movement of the four domains of each catalytic-regulatory unit; these include the allosteric effector domain, the equatorial (aspartate) domain, and the combination of the polar (carbamyl phosphate) and zinc domain, which moves as a rigid unit. However, interfaces change, for example the interface between the zinc domain of the R chain and the equatorial domain of the C chain, is nearly absent in the T state, but becomes extensive in the R state of the enzyme; also one catalytic-regulatory interface (C1-R4) of the T state disappears in the more active R state of the enzyme. Segments 50-55, 77-86 and 231-246 of the catalytic chain and segments 51-55, 67-72 and 150-153 of the regulatory chain show conformational changes that go beyond the rigid-body movement of their corresponding domains. The localized conformational changes in the catalytic chain all derive from the interactions of the enzyme with the inhibitor PALA; these changes may be important for the catalytic mechanism. The conformation changes in segments 67-72 and 150-153 of the regulatory chain may be important for the allosteric control of substrate binding. On the basis of the conformational differences of the T and R states of the enzyme, we present a plausible scheme for catalysis that assumes the ordered binding of substrates and the ordered release o


    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
    • 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
    • Structural Transitions in Crystals of Native Aspartate Carbamoyltransferase
      Gouaux, J.E., Lipscomb, W.N.
      (1989) Proc Natl Acad Sci U S A 86: 845
    • 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
    • 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

    Chemistry Department, Harvard University, Cambridge, MA 02138.



Macromolecules
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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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A786
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7F3
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PAL
Query on PAL

Download Ideal Coordinates CCD File 
E [auth A],
G [auth C]
N-(PHOSPHONACETYL)-L-ASPARTIC ACID
C6 H10 N O8 P
ZZKNRXZVGOYGJT-VKHMYHEASA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
F [auth B],
H [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Observed: 0.165 
  • Space Group: P 3 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.11α = 90
b = 122.11β = 90
c = 156.17γ = 120
Software Package:
Software NamePurpose
PROLSQrefinement

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: Version format compliance
  • Version 1.3: 2017-11-29
    Changes: Derived calculations, Other