Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 646617.75 
• Atom Count: 44850 
• 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 (strain K12)
• Expression System: Escherichia coli BL21, Escherichia coli
• Mutation(s): 1 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.1 Å
• R-Value Free: 0.209 
• R-Value Work: 0.176 

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


• 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.

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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Carbamoyl-phosphate synthase large chain	A, C, E, G	1073	Escherichia 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
Molecule	Chains	Sequence Length	Organism	Details
Carbamoyl-phosphate synthase small chain	B, D, F, H	382	Escherichia 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 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
K	A, B, C, D, E, F, G, H	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
MN	A, C, E, G	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
PO4	A, C, E, G	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
ADP	A, C, E, G	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
CL	A, C, D, E, F, G, H	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
U	A, C, E, G	URIDINE-5'-MONOPHOSPHATE C9 H13 N2 O9 P DJJCXFVJDGTHFX-XVFCMESISA-N
NET	A, C, E, G	TETRAETHYLAMMONIUM ION C8 H20 N CBXCPBUEXACCNR-UHFFFAOYSA-N
ORN	A, C, E, G	L-ornithine C5 H12 N2 O2 AHLPHDHHMVZTML-BYPYZUCNSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.1 Å
• R-Value Free: 0.209 
• R-Value Work: 0.176 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 152.500	α = 90.00
b = 164.900	β = 90.00
c = 333.100	γ = 90.00

Software Package:

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

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
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Non-polymer description, Version format compliance