5V6X | pdb_00005v6x

Crystal structure of the tRNA binding domain of Pyrrolysyl-tRNA synthetase mutant (32A NTD) bound to tRNA(Pyl)

• PDB DOI: https://doi.org/10.2210/pdb5V6X/pdb
• NAKB: 5V6X

• Classification: LIGASE/RNA
• Organism(s): Methanosarcina mazei Go1
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2017-03-17 Released: 2017-10-11 
• Deposition Author(s): Suzuki, T., Soll, D.
• 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: 2.76 Å
• R-Value Free: 
  0.249 (Depositor), 0.245 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.213 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Literature

Crystal structures reveal an elusive functional domain of pyrrolysyl-tRNA synthetase.

Suzuki, T., Miller, C., Guo, L.T., Ho, J.M.L., Bryson, D.I., Wang, Y.S., Liu, D.R., Soll, D.

(2017) Nat Chem Biol 13: 1261-1266

• PubMed: 29035363 
• DOI: https://doi.org/10.1038/nchembio.2497
• Primary Citation Related Structures: 
  5UD5, 5V6X


• PubMed Abstract: 
  

  Pyrrolysyl-tRNA synthetase (PylRS) is a major tool in genetic code expansion using noncanonical amino acids, yet its structure and function are not completely understood. Here we describe the crystal structure of the previously uncharacterized essential N-terminal domain of this unique enzyme in complex with tRNA ^Pyl . This structure explains why PylRS remains orthogonal in a broad range of organisms, from bacteria to humans. The structure also illustrates why tRNA ^Pyl recognition by PylRS is anticodon independent: the anticodon does not contact the enzyme. Then, using standard microbiological culture equipment, we established a new method for laboratory evolution-a noncontinuous counterpart of the previously developed phage-assisted continuous evolution. With this method, we evolved novel PylRS variants with enhanced activity and amino acid specificity. Finally, we employed an evolved PylRS variant to determine its N-terminal domain structure and show how its mutations improve PylRS activity in the genetic encoding of a noncanonical amino acid.

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Organizational Affiliation: 
• Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA.
Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA.
Howard Hughes Medical Institute, Cambridge, Massachusetts, USA.
Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.
Department of Chemistry, Yale University, New Haven, Connecticut, USA.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly Evidence: native gel electrophoresis

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 71.58 kDa 
• Atom Count: 4,390 
• Modeled Residue Count: 310 
• Deposited Residue Count: 362 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyrrolysine--tRNA ligase	A, B	109	Methanosarcina mazei Go1	Mutation(s): 4  Gene Names: pylS, MM_1445 EC: 6.1.1.26
UniProt
Find proteins for Q8PWY1 (Methanosarcina mazei (strain ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88)) Explore Q8PWY1  Go to UniProtKB:  Q8PWY1

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (70-MER)	C, D	72	Methanosarcina mazei Go1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	E [auth A], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.76 Å
• R-Value Free:  0.249 (Depositor), 0.245 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.213 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.62	α = 90
b = 72.62	β = 90
c = 238.58	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-10-11 
Deposition Author(s): Suzuki, T., Soll, D.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM22854

Revision History  

• Version 1.0: 2017-10-11
  Type: Initial release
  
• Version 1.1: 2017-10-25
  Changes: Database references
• Version 1.2: 2017-11-01
  Changes: Database references
• Version 1.3: 2017-12-06
  Changes: Database references
• Version 1.4: 2020-01-01
  Changes: Author supporting evidence
• Version 1.5: 2024-03-06
  Changes: Data collection, Database references