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 

Starting Model: experimental
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This is version 1.4 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: https://doi.org/10.1074/jbc.M108582200
  • Primary Citation of Related Structures:  
    1KEE

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Carbamoyl-phosphate synthetase large chain
A, C, E, G
1,073Escherichia coliMutation(s): 0 
Gene Names: CARB
EC: 6.3.5.5 (PDB Primary Data), 6.3.4.16 (UniProt)
UniProt
Find proteins for P00968 (Escherichia coli (strain K12))
Explore P00968 
Go to UniProtKB:  P00968
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00968
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Carbamoyl-phosphate synthetase small chain
B, D, F, H
382Escherichia coliMutation(s): 1 
Gene Names: CARA
EC: 6.3.5.5
UniProt
Find proteins for P0A6F1 (Escherichia coli (strain K12))
Explore P0A6F1 
Go to UniProtKB:  P0A6F1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A6F1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download Ideal Coordinates CCD File 
KC [auth G]
LC [auth G]
PB [auth E]
QB [auth E]
UA [auth C]
KC [auth G],
LC [auth G],
PB [auth E],
QB [auth E],
UA [auth C],
VA [auth C],
Y [auth A],
Z [auth A]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
ORN
Query on ORN

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AA [auth A],
MC [auth G],
RB [auth E],
WA [auth C]
L-ornithine
C5 H12 N2 O2
AHLPHDHHMVZTML-BYPYZUCNSA-N
NET
Query on NET

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BA [auth A],
NC [auth G],
SB [auth E],
XA [auth C]
TETRAETHYLAMMONIUM ION
C8 H20 N
CBXCPBUEXACCNR-UHFFFAOYSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
JC [auth G],
OB [auth E],
TA [auth C],
X [auth A]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
MN
Query on MN

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AB [auth E]
BB [auth E]
EA [auth C]
EB [auth E]
FA [auth C]
AB [auth E],
BB [auth E],
EA [auth C],
EB [auth E],
FA [auth C],
I [auth A],
IA [auth C],
J [auth A],
M [auth A],
VB [auth G],
WB [auth G],
ZB [auth G]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
K
Query on K

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AC [auth G]
BC [auth G]
CA [auth B]
CB [auth E]
CC [auth G]
AC [auth G],
BC [auth G],
CA [auth B],
CB [auth E],
CC [auth G],
DB [auth E],
DC [auth G],
EC [auth G],
FB [auth E],
GA [auth C],
GB [auth E],
HA [auth C],
HB [auth E],
IB [auth E],
JA [auth C],
JB [auth E],
K [auth A],
KA [auth C],
L [auth A],
LA [auth C],
MA [auth C],
N [auth A],
NA [auth C],
O [auth A],
OC [auth H],
P [auth A],
Q [auth A],
R [auth A],
TB [auth F],
XB [auth G],
YA [auth D],
YB [auth G]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
DA [auth B]
FC [auth G]
GC [auth G]
HC [auth G]
IC [auth G]
DA [auth B],
FC [auth G],
GC [auth G],
HC [auth G],
IC [auth G],
KB [auth E],
LB [auth E],
MB [auth E],
NB [auth E],
OA [auth C],
PA [auth C],
PC [auth H],
QA [auth C],
RA [auth C],
S [auth A],
SA [auth C],
T [auth A],
U [auth A],
UB [auth F],
V [auth A],
W [auth A],
ZA [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
143
Query on 143
B, D, F, H
L-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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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.4: 2023-08-16
    Changes: Data collection, Database references, Derived calculations, Refinement description