Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 18.77 kDa 
• Atom Count: 1704 
• Modelled Residue Count: 164 
• Deposited Residue Count: 164 
• Unique protein chains: 1

1TT8

CHORISMATE LYASE WITH PRODUCT, 1.0 A RESOLUTION

• PDB DOI: 10.2210/pdb1TT8/pdb

• Classification: LYASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 


• 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: 1.00 Å
• R-Value Free: 0.153 
• R-Value Work: 0.123 
• R-Value Observed: 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:  
  1JD3, 1TT8, 1XLR, 2AHC


• 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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chorismate-pyruvate lyase	A	164	Escherichia coli	Mutation(s): 2  Gene Names: ubiC, b4039 EC: 4 (PDB Primary Data), 4.1.3.40 (UniProt)
UniProt
Find proteins for P26602 (Escherichia coli (strain K12)) Explore P26602  Go to UniProtKB:  P26602

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.00 Å
• R-Value Free: 0.153 
• R-Value Work: 0.123 
• R-Value Observed: 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
X-GEN	data scaling
X-GEN	data reduction
SHELX	model building
SHELXL-97	refinement
SHELX	phasing

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
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2021-10-27
  Changes: Database references, Derived calculations