1A9X

CARBAMOYL PHOSPHATE SYNTHETASE: CAUGHT IN THE ACT OF GLUTAMINE HYDROLYSIS

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 

Literature

Carbamoyl phosphate synthetase: caught in the act of glutamine hydrolysis.

Thoden, J.B., Miran, S.G., Phillips, J.C., Howard, A.J., Raushel, F.M., Holden, H.M.

(1998) Biochemistry 37: 8825-8831

  • DOI: 10.1021/bi9807761

  • PubMed Abstract: 

    • Carbamoyl phosphate synthetase from Escherichia coli catalyzes the production of carbamoyl phosphate from two molecules of Mg2+ATP, one molecule of bicarbonate, and one molecule of glutamine. The enzyme consists of two polypeptide chains referred to ...

    Carbamoyl phosphate synthetase from Escherichia coli catalyzes the production of carbamoyl phosphate from two molecules of Mg2+ATP, one molecule of bicarbonate, and one molecule of glutamine. The enzyme consists of two polypeptide chains referred to as the large and small subunits. While the large subunit provides the active sites responsible for the binding of nucleotides and other effector ligands, the small subunit contains those amino acid residues that catalyze the hydrolysis of glutamine to glutamate and ammonia. From both amino acid sequence analyses and structural studies it is now known that the small subunit belongs to the class I amidotransferase family of enzymes. Numerous biochemical studies have suggested that the reaction mechanism of the small subunit proceeds through the formation of the glutamyl thioester intermediate and that both Cys 269 and His 353 are critical for catalysis. Here we describe the X-ray crystallographic structure of carbamoyl phosphate synthetase from E. coli in which His 353 has been replaced with an asparagine residue. Crystals employed in the investigation were grown in the presence of glutamine, and the model has been refined to a crystallographic R-factor of 19.1% for all measured X-ray data from 30 to 1.8 A resolution. The active site of the small subunit clearly contains a covalently bound thioester intermediate at Cys 269, and indeed, this investigation provides the first direct structural observation of an enzyme intermediate in the amidotransferase family.

    Organizational Affiliation: 

    Institute for Enzyme Research, The Graduate School, University of Wisconsin-Madison 53705, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CARBAMOYL PHOSPHATE SYNTHETASE (LARGE CHAIN)
A, C, E, G
1073Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: carB (pyrA)
EC: 6.3.5.5
Find proteins for P00968 (Escherichia coli (strain K12))
Go to UniProtKB:  P00968
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CARBAMOYL PHOSPHATE SYNTHETASE (SMALL CHAIN)
B, D, F, H
379Escherichia coli (strain K12)Mutation(s): 1 
Gene Names: carA (pyrA)
EC: 6.3.5.5
Find proteins for P0A6F1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A6F1
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K
Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
MN
Query on MN
Download SDF File 
Download CCD File 
A, C, E, G
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4
Download SDF File 
Download CCD File 
A, C, E, G
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
ADP
Query on ADP
Download SDF File 
Download CCD File 
A, C, E, G
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
CL
Query on CL
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Download CCD File 
A, B, C, D, E, F, G, H
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NET
Query on NET
Download SDF File 
Download CCD File 
A, C, E, G
TETRAETHYLAMMONIUM ION
C8 H20 N
CBXCPBUEXACCNR-UHFFFAOYSA-N
 Ligand Interaction
ORN
Query on ORN
Download SDF File 
Download CCD File 
A, C, E, G
L-ornithine
C5 H12 N2 O2
AHLPHDHHMVZTML-BYPYZUCNSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CYG
Query on CYG
B, D, F, H
L-PEPTIDE LINKINGC8 H14 N2 O5 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 152.100α = 90.00
b = 164.400β = 90.00
c = 332.300γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
XCALIBREdata scaling
TNTrefinement
SAINTdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 1998-04-14 
  • Released Date: 1998-10-21 
  • Deposition Author(s): Thoden, J., Holden, H.

Revision History 

  • Version 1.0: 1998-10-21
    Type: Initial release
  • Version 1.1: 2008-03-10
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2018-03-14
    Type: Database references