Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 18773.68 
• Atom Count: 1333 
• Residue Count: 164 
• Unique protein chains: 1

1TT8

CHORISMATE LYASE WITH PRODUCT, 1.0 A RESOLUTION

• DOI: 10.2210/pdb1TT8/pdb

• Classification: LYASE
• Organism(s): Escherichia coli (strain K12)
• Expression System: Escherichia coli
• Mutation(s): 2 


• Deposited: 2004-06-22 Released: 2004-12-28 
• Deposition Author(s): Gallagher, D.T., Mayhew, M., Holden, M.J., Vilker, V., Howard, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1 Å
• R-Value Free: 0.153 
• R-Value Work: 0.123 

Literature

Structural analysis of ligand binding and catalysis in chorismate lyase.

Smith, N., Roitberg, A.E., Rivera, E., Howard, A., Holden, M.J., Mayhew, M., Kaistha, S., Gallagher, D.T.

(2006) Arch.Biochem.Biophys. 445: 72-80

• PubMed: 16343413 
• DOI: 10.1016/j.abb.2005.10.026
• Primary Citation of Related Structures:  
  2AHC, 1XLR, 1JD3


• PubMed Abstract: 
  

Chorismate lyase (CL) removes the pyruvyl group from chorismate to provide 4-hydroxybenzoate (4HB) for the ubiquinone pathway. We previously reported the crystal structure at 1.4A resolution of the Escherichia coli CL with bound 4HB product, showing that the product is bound in an internal cavity behind two flaps. To provide a more complete basis for understanding CL's unusual ligand-binding properties and mechanism of action, we now report four crystal structures of CL mutants and inhibitor complexes, together with binding and activity measurements and molecular dynamics simulations. First, an ultrahigh resolution (1.0A) crystal structure of the CL*product complex reveals details of a substrate-sized internal cavity, also behind the flaps, near the product site. Second, a 2.4A structure of CL complexed with the inhibitor vanillate shows the flaps partly opened relative to their product-bound positions. Third, a 2.0A structure of the G90A mutant with bound product reveals the basis for tighter product binding and kinetic effects of this active site mutation. Fourth, the combination of the G90A mutation with the vanillate inhibitor produces a 1.9A structure containing two inhibitor molecules, one in the product site and the other in the adjacent cavity. The two sites are connected by a short tunnel that is partly open at each end, suggesting that CL may operate via a 2-site or tunnel mechanism.

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Organizational Affiliation: 

University of Maryland Biotechnology Institute, Rockville, MD 20850, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Chorismate-pyruvate lyase	A	164	Escherichia coli (strain K12)	Mutations: S14C, S81C Gene Names: ubiC EC: 4.1.3.40
Find proteins for P26602 (Escherichia coli (strain K12)) Go to UniProtKB:  P26602

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
PHB	A	P-HYDROXYBENZOIC ACID C7 H6 O3 FJKROLUGYXJWQN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1 Å
• R-Value Free: 0.153 
• R-Value Work: 0.123 
• Space Group: P 1

Unit Cell:

Length (Å)	Angle (°)
a = 31.315	α = 67.57
b = 33.849	β = 87.83
c = 39.776	γ = 65.66

Software Package:

Software Name	Purpose
SHELXL-97	refinement
X-GEN	data reduction
SHELX	phasing
SHELX	model building
X-GEN	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-06-22 
• Released Date: 2004-12-28 
• Deposition Author(s): Gallagher, D.T., Mayhew, M., Holden, M.J., Vilker, V., Howard, A.

Revision History 

• Version 1.0: 2004-12-28
  Type: Initial release
• Version 1.1: 2008-04-30
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance
• Version 1.3: 2017-10-11
  Type: Refinement description