6MTG | pdb_00006mtg

A Single Reactive Noncanonical Amino Acid is Able to Dramatically Stabilize Protein Structure

• PDB DOI: https://doi.org/10.2210/pdb6MTG/pdb

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


• Deposited: 2018-10-19 Released: 2019-06-26 
• Deposition Author(s): Li, J.C., Nasertorabi, F., Xuan, W., Han, G.W., Stevens, R.C., Schultz, P.G.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.218 (Depositor), 0.222 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.179 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

Starting Model: experimental

Literature

A Single Reactive Noncanonical Amino Acid Is Able to Dramatically Stabilize Protein Structure.

Li, J.C., Nastertorabi, F., Xuan, W., Han, G.W., Stevens, R.C., Schultz, P.G.

(2019) ACS Chem Biol 14: 1150-1153

• PubMed: 31181898 
• DOI: https://doi.org/10.1021/acschembio.9b00002
• Primary Citation Related Structures: 
  6MTG


• PubMed Abstract: 
  

  A p-isothiocyanate phenylalanine mutant of the homodimeric protein homoserine o-succinyltransferase (MetA) was isolated in a temperature dependent selection from a library of metA mutants containing noncanonical amino acids. This mutant protein has a dramatic increase of 24 °C in thermal stability compared to the wild type protein. Peptide mapping experiments revealed that the isothiocyanate group forms a thiourea cross-link to the N terminal proline of the other monomer, despite the two positions being >30 Å apart in the X-ray crystal structure of the wild type protein. These results show that an expanded set of building blocks beyond the canonical 20 amino acids can lead to significant changes in the properties of proteins.

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Organizational Affiliation: 
• Department of Chemistry and Skaggs Institute for Chemical Biology , The Scripps Research Institute , La Jolla , California 92037 , United States.
Department of Biological Sciences, Bridge Institute, Michaelson Center for Convergent Bioscience , University of Southern California , 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: mass spectrometry, gel filtration

Macromolecule Content 

• Total Structure Weight: 70.7 kDa 
• Atom Count: 5,388 
• Modeled Residue Count: 583 
• Deposited Residue Count: 604 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Homoserine O-succinyltransferase	A, B	302	Escherichia coli K-12	Mutation(s): 1  Gene Names: metAS, metA, b4013, JW3973 EC: 2.3.1.46
UniProt
Find proteins for P07623 (Escherichia coli (strain K12)) Explore P07623  Go to UniProtKB:  P07623

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	C [auth A], D [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	G [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
FMT	E [auth A], F [auth A], H [auth B], I [auth B], J [auth B]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSD	A, B	L-PEPTIDE LINKING	C3 H7 N O4 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.218 (Depositor), 0.222 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.179 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.948	α = 90
b = 100.036	β = 90
c = 125.218	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-06-26 
Deposition Author(s): Li, J.C., Nasertorabi, F., Xuan, W., Han, G.W., Stevens, R.C., Schultz, P.G.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM062159

Revision History  

• Version 1.0: 2019-06-26
  Type: Initial release
  
• Version 1.1: 2019-07-10
  Changes: Data collection, Database references
• Version 1.2: 2020-01-01
  Changes: Author supporting evidence
• Version 1.3: 2023-10-11
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-11-06
  Changes: Structure summary