5VHT | pdb_00005vht

E. coli chorismate mutase with orthogonal interface containing p-benzoyl phenylalanine

• PDB DOI: https://doi.org/10.2210/pdb5VHT/pdb

• Classification: ISOMERASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2017-04-13 Released: 2017-05-10 
• Deposition Author(s): Koh, M., Nasertorabi, F., Han, G.W., Stevens, R.C., Shultz, P.G.
• Funding Organization(s): Department of Energy (DOE, United States), Korean Ministry of Education

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.240 (Depositor), 0.244 (DCC) 
• R-Value Work: 
  0.213 (Depositor), 0.218 (DCC) 
• R-Value Observed: 
  0.215 (Depositor) 

Starting Model: experimental

Literature

Generation of an Orthogonal Protein-Protein Interface with a Noncanonical Amino Acid.

Koh, M., Nasertorabi, F., Han, G.W., Stevens, R.C., Schultz, P.G.

(2017) J Am Chem Soc 139: 5728-5731

• PubMed: 28413876 
• DOI: https://doi.org/10.1021/jacs.7b02273
• Primary Citation Related Structures: 
  5VHT


• PubMed Abstract: 
  

  We have engineered the protein interface of the Escherichia coli chorismate mutase (EcCM) homodimer to be dependent on incorporation of a noncanonical amino acid (ncAA) at residue 72. The large hydrophobic amino acid p-benzoyl phenylalanine (pBzF) was substituted for Tyr72, which led to a catalytically inactive protein. A library of five residues (Leu25', Arg29', Leu76, Ile80' and Asp83') surrounding pBzF72 was generated and subjected to a growth based selection in a chorismate mutase deficient strain. An EcCM variant (Phe25', pBzF72, Thr76, Gly80' and Tyr83') forms a stable homodimer, has catalytic activity similar to the wild type enzyme, and unfolds with a T _m of 53 °C. The X-ray crystal structure reveals a pi-pi stacking and hydrogen bonding interactions that stabilize the new protein interface. The strategy described here should be useful for generating organisms that are dependent on the presence of a ncAA for growth.

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Organizational Affiliation: 
• Department of Chemistry and Skaggs Institute for Chemical Biology, The Scripps Research Institute , 10550 N Torrey Pines Road, La Jolla, California 92037, United States.
Department of Biological Sciences, Bridge Institute, University of Southern California , 3430 S Vermont Avenue, Los Angeles, California 90089, United States.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 23.27 kDa 
• Atom Count: 1,612 
• Modeled Residue Count: 190 
• Deposited Residue Count: 198 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chorismate Mutase	A, B	99	Escherichia coli K-12	Mutation(s): 5  Gene Names: pheA, b2599, JW2580 EC: 5.4.99.5 (PDB Primary Data), 4.2.1.51 (UniProt)
UniProt
Find proteins for P0A9J8 (Escherichia coli (strain K12)) Explore P0A9J8  Go to UniProtKB:  P0A9J8

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PBF	A, B	L-PEPTIDE LINKING	C16 H15 N O3		PHE

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.240 (Depositor), 0.244 (DCC) 
• R-Value Work:  0.213 (Depositor), 0.218 (DCC) 
• R-Value Observed: 0.215 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.861	α = 90
b = 61.27	β = 90
c = 62.848	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data scaling
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-05-10 
Deposition Author(s): Koh, M., Nasertorabi, F., Han, G.W., Stevens, R.C., Shultz, P.G.

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Funding Organization	Location	Grant Number
Department of Energy (DOE, United States)	United States	DE-SC0011787
Korean Ministry of Education	Korea, Republic Of	NRF- 210 2016R1A6A3A03009203

Revision History  

• Version 1.0: 2017-05-10
  Type: Initial release
  
• Version 1.1: 2017-09-27
  Changes: Author supporting evidence, Refinement description
• Version 1.2: 2019-12-04
  Changes: Author supporting evidence
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2023-11-15
  Changes: Data collection