1KEE | pdb_00001kee

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 (Depositor) 
  • R-Value Work: 
    0.186 (Depositor), 0.179 (DCC) 
  • R-Value Observed: 
    0.187 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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 Biological Chem 277: 4368-4373

  • DOI: https://doi.org/10.1074/jbc.M108582200
  • Primary Citation 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.

Macromolecule Content 

  • Total Structure Weight: 645.96 kDa 
  • Atom Count: 48,896 
  • Modeled Residue Count: 5,748 
  • Deposited Residue Count: 5,820 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  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:|  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



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
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 (Depositor) 
  • R-Value Work:  0.186 (Depositor), 0.179 (DCC) 
  • R-Value Observed: 0.187 (Depositor) 
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