1KEE

Inactivation of the Amidotransferase Activity of Carbamoyl Phosphate Synthetase by the Antibiotic Acivicin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Inactivation of the amidotransferase activity of carbamoyl phosphate synthetase by the antibiotic acivicin.

Miles, B.W.Thoden, J.B.Holden, H.M.Raushel, F.M.

(2002) J Biol Chem 277: 4368-4373

  • DOI: 10.1074/jbc.M108582200
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Carbamoyl phosphate synthetase (CPS) from Escherichia coli catalyzes the formation of carbamoyl phosphate from 2 mol of ATP, bicarbonate, and glutamine. CPS was inactivated by the glutamine analog, acivicin. In the presence of ATP and bicarbonate the ...

    Carbamoyl phosphate synthetase (CPS) from Escherichia coli catalyzes the formation of carbamoyl phosphate from 2 mol of ATP, bicarbonate, and glutamine. CPS was inactivated by the glutamine analog, acivicin. In the presence of ATP and bicarbonate the second-order rate constant for the inactivation of the glutamine-dependent activities was 4.0 x 10(4) m(-1) s(-1). In the absence of ATP and bicarbonate the second-order rate constant for inactivation of CPS was reduced by a factor of 200. The enzyme was protected against inactivation by the inclusion of glutamine in the reaction mixture. The ammonia-dependent activities were unaffected by the incubation of CPS with acivicin. These results are consistent with the covalent labeling of the glutamine-binding site located within the small amidotransferase subunit. The binding of ATP and bicarbonate to the large subunit of CPS must also induce a conformational change within the amidotransferase domain of the small subunit that enhances the nucleophilic character of the thiol group required for glutamine hydrolysis. The acivicin-inhibited enzyme was crystallized, and the three-dimensional structure was determined by x-ray diffraction techniques. The thiol group of Cys-269 was covalently attached to the dihydroisoxazole ring of acivicin with the displacement of a chloride ion.


    Organizational Affiliation

    Department of Chemistry, Texas A & M University, College Station, Texas 77842-3012, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Carbamoyl-phosphate synthetase small chainB, D, F, H382Escherichia coliMutation(s): 1 
Gene Names: carA
EC: 6.3.5.5
Find proteins for P0A6F1 (Escherichia coli (strain K12))
Explore P0A6F1 
Go to UniProtKB:  P0A6F1
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Carbamoyl-phosphate synthetase large chainA, C, E, G1073Escherichia coliMutation(s): 0 
Gene Names: carB
EC: 6.3.5.5
Find proteins for P00968 (Escherichia coli (strain K12))
Explore P00968 
Go to UniProtKB:  P00968
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download CCD File 
A, C, E, G
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
ORN
Query on ORN

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A, C, E, G
L-ornithine
C5 H12 N2 O2
AHLPHDHHMVZTML-BYPYZUCNSA-N
 Ligand Interaction
NET
Query on NET

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A, C, E, G
TETRAETHYLAMMONIUM ION
C8 H20 N
CBXCPBUEXACCNR-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

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A, C, E, G
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
MN
Query on MN

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A, C, E, G
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

Download CCD File 
A, B, C, D, E, F, G, H
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A, B, C, D, E, F, G, H
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
143
Query on 143
B,D,F,HL-PEPTIDE LINKINGC8 H13 N3 O5 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.187 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 152.4α = 90
b = 164.4β = 90
c = 333.2γ = 90
Software Package:
Software NamePurpose
TNTrefinement
MAR345data collection
SCALEPACKdata scaling
TNTphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-12-21
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2019-11-20
    Changes: Advisory, Database references, Derived calculations, Refinement description