1ACM

ARGININE 54 IN THE ACTIVE SITE OF ESCHERICHIA COLI ASPARTATE TRANSCARBAMOYLASE IS CRITICAL FOR CATALYSIS: A SITE-SPECIFIC MUTAGENESIS, NMR AND X-RAY CRYSTALLOGRAPHY STUDY


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Arginine 54 in the active site of Escherichia coli aspartate transcarbamoylase is critical for catalysis: a site-specific mutagenesis, NMR, and X-ray crystallographic study.

Stebbins, J.W.Robertson, D.E.Roberts, M.F.Stevens, R.C.Lipscomb, W.N.Kantrowitz, E.R.

(1992) Protein Sci. 1: 1435-1446

  • DOI: 10.1002/pro.5560011105

  • PubMed Abstract: 
  • The replacement of Arg-54 by Ala in the active site of Escherichia coli aspartate transcarbamoylase causes a 17,000-fold loss of activity but does not significantly influence the binding of substrates or substrate analogs (Stebbins, J.W., Xu, W., & K ...

    The replacement of Arg-54 by Ala in the active site of Escherichia coli aspartate transcarbamoylase causes a 17,000-fold loss of activity but does not significantly influence the binding of substrates or substrate analogs (Stebbins, J.W., Xu, W., & Kantrowitz, E.R., 1989, Biochemistry 28, 2592-2600). In the X-ray structure of the wild-type enzyme, Arg-54 interacts with both the anhydride oxygen and a phosphate oxygen of carbamoyl phosphate (CP) (Gouaux, J.E. & Lipscomb, W.N., 1988, Proc. Natl. Acad. Sci. USA 85, 4205-4208). The Arg-54-->Ala enzyme was crystallized in the presence of the transition state analog N-phosphonacetyl-L-aspartate (PALA), data were collected to a resolution limit of 2.8 A, and the structure was solved by molecular replacement. The analysis of the refined structure (R factor = 0.18) indicates that the substitution did not cause any significant alterations to the active site, except that the side chain of the arginine was replaced by two water molecules. 31P-NMR studies indicate that the binding of CP to the wild-type catalytic subunit produces an upfield chemical shift that cannot reflect a significant change in the ionization state of the CP but rather indicates that there are perturbations in the electronic environment around the phosphate moiety when CP binds to the enzyme. The pH dependence of this upfield shift for bound CP indicates that the catalytic subunit undergoes a conformational change with a pKa approximately 7.7 upon CP binding. Furthermore, the linewidth of the 31P signal of CP bound to the Arg-54-->Ala enzyme is significantly narrower than that of CP bound to the wild-type catalytic subunit at any pH, although the change in chemical shift for the CP bound to the mutant enzyme is unaltered. 31P-NMR studies of PALA complexed to the wild-type catalytic subunit indicate that the phosphonate group of the bound PALA exists as the dianion at pH 7.0 and 8.8, whereas in the Arg-54-->Ala catalytic subunit the phosphonate group of the bound PALA exists as the monoanion at pH 7.0 and 8.8. Thus, the side chain of Arg-54 is essential for the proper ionization of the phosphonate group of PALA and by analogy the phosphate group in the transition state. These data support the previously proposed proton transfer mechanism, in which a fully ionized phosphate group in the transition state accepts a proton during catalysis.


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


    Organizational Affiliation

    Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, Massachusetts 02167.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ASPARTATE CARBAMOYLTRANSFERASE, 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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PAL
Query on PAL

Download SDF File 
Download CCD File 
A, C
N-(PHOSPHONACETYL)-L-ASPARTIC ACID
C6 H10 N O8 P
ZZKNRXZVGOYGJT-VKHMYHEASA-N
 Ligand Interaction
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: 2.8 Å
  • R-Value Work: 0.180 
  • Space Group: P 3 2 1
Unit Cell:
Length (Å)Angle (°)
a = 122.200α = 90.00
b = 122.200β = 90.00
c = 156.200γ = 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: 1992-07-15
    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