Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Hetero 8-mer - A4B4 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 646.62 kDa 
• Atom Count: 48757 
• Modelled Residue Count: 5748 
• Deposited Residue Count: 5820 
• Unique protein chains: 2

1T36

Crystal structure of E. coli carbamoyl phosphate synthetase small subunit mutant C248D complexed with uridine 5'-monophosphate

• DOI: 10.2210/pdb1T36/pdb

• Classification: LIGASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21, Escherichia coli
• Mutation(s): Yes 


• Deposited: 2004-04-24 Released: 2004-09-21 
• Deposition Author(s): Thoden, J.B., Huang, X., Raushel, F.M., Holden, H.M.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.209 
• R-Value Work: 0.176 
• R-Value Observed: 0.179 

Literature

Long-range allosteric transitions in carbamoyl phosphate synthetase.

Thoden, J.B., Huang, X., Kim, J., Raushel, F.M., Holden, H.M.

(2004) Protein Sci 13: 2398-2405

• PubMed: 15322282 
• DOI: 10.1110/ps.04822704
• Primary Citation of Related Structures:  
  1T36


• PubMed Abstract: 
  

Carbamoyl phosphate synthetase plays a key role in both pyrimidine and arginine biosynthesis by catalyzing the production of carbamoyl phosphate from one molecule of bicarbonate, two molecules of MgATP, and one molecule of glutamine. The enzyme from Escherichia coli consists of two polypeptide chains referred to as the small and large subunits, which contain a total of three separate active sites that are connected by an intramolecular tunnel. The small subunit harbors one of these active sites and is responsible for the hydrolysis of glutamine to glutamate and ammonia. The large subunit binds the two required molecules of MgATP and is involved in assembling the final product. Compounds such as L-ornithine, UMP, and IMP allosterically regulate the enzyme. Here, we report the three-dimensional structure of a site-directed mutant protein of carbamoyl phosphate synthetase from E. coli, where Cys 248 in the small subunit was changed to an aspartate. This residue was targeted for a structural investigation because previous studies demonstrated that the partial glutaminase activity of the C248D mutant protein was increased 40-fold relative to the wild-type enzyme, whereas the formation of carbamoyl phosphate using glutamine as a nitrogen source was completely abolished. Remarkably, although Cys 248 in the small subunit is located at approximately 100 A from the allosteric binding pocket in the large subunit, the electron density map clearly revealed the presence of UMP, although this ligand was never included in the purification or crystallization schemes. The manner in which UMP binds to carbamoyl phosphate synthetase is described.

---

Organizational Affiliation: 

Department of Biochemistry, University of Wisconsin, Madison, WI, 53706, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbamoyl-phosphate synthase large chain	A, C, E, G	1073	Escherichia coli	Mutation(s): 0  Gene Names: carB, pyrA, b0033 EC: 6.3.5.5
Find proteins for P00968 (Escherichia coli (strain K12)) Explore P00968  Go to UniProtKB:  P00968

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbamoyl-phosphate synthase small chain	B, D, F, H	382	Escherichia coli	Mutation(s): 1  Gene Names: carA, pyrA, b0032, Z0037, ECS0035 EC: 6.3.5.5
Find proteins for P0A6F1 (Escherichia coli (strain K12)) Explore P0A6F1  Go to UniProtKB:  P0A6F1

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	A, C, E, G	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
U	A, C, E, G	URIDINE-5'-MONOPHOSPHATE C9 H13 N2 O9 P DJJCXFVJDGTHFX-XVFCMESISA-N
ORN	A, C, E, G	L-ornithine C5 H12 N2 O2 AHLPHDHHMVZTML-BYPYZUCNSA-N
NET	A, C, E, G	TETRAETHYLAMMONIUM ION C8 H20 N CBXCPBUEXACCNR-UHFFFAOYSA-N
PO4	A, C, E, G	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
MN	A, C, E, G	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
K	A, B, C, D, E, F, G, H	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL	A, C, D, E, F, G, H	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
U	Kd:  9000   nM  Binding MOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.209 
• R-Value Work: 0.176 
• R-Value Observed: 0.179 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 152.5	α = 90
b = 164.9	β = 90
c = 333.1	γ = 90

Software Package:

Software Name	Purpose
d*TREK	data scaling
SCALEPACK	data scaling
TNT	refinement
d*TREK	data reduction
TNT	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-04-24 
• Released Date: 2004-09-21 
Deposition Author(s): Thoden, J.B., Huang, X., Raushel, F.M., Holden, H.M.

Revision History  

• Version 1.0: 2004-09-21
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance