4TQD | pdb_00004tqd

Crystal Structure of the C-terminal domain of IFRS bound with 3-iodo-L-Phe and ATP

• PDB DOI: https://doi.org/10.2210/pdb4TQD/pdb

• Classification: LIGASE
• Organism(s): Methanosarcina mazei Go1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2014-06-11 Released: 2014-11-12 
• Deposition Author(s): Nakamura, A., O'Donoghue, P., Soll, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.14 Å
• R-Value Free: 
  0.193 (Depositor), 0.191 (DCC) 
• R-Value Work: 
  0.155 (Depositor) 
• R-Value Observed: 
  0.159 (Depositor) 

Starting Model: experimental

Literature

Polyspecific pyrrolysyl-tRNA synthetases from directed evolution.

Guo, L.T., Wang, Y.S., Nakamura, A., Eiler, D., Kavran, J.M., Wong, M., Kiessling, L.L., Steitz, T.A., O'Donoghue, P., Soll, D.

(2014) Proc Natl Acad Sci U S A 111: 16724-16729

• PubMed: 25385624 
• DOI: https://doi.org/10.1073/pnas.1419737111
• Primary Citation Related Structures: 
  4Q6G, 4TQD, 4TQF


• PubMed Abstract: 
  

  Pyrrolysyl-tRNA synthetase (PylRS) and its cognate tRNA(Pyl) have emerged as ideal translation components for genetic code innovation. Variants of the enzyme facilitate the incorporation >100 noncanonical amino acids (ncAAs) into proteins. PylRS variants were previously selected to acylate N(ε)-acetyl-Lys (AcK) onto tRNA(Pyl). Here, we examine an N(ε)-acetyl-lysyl-tRNA synthetase (AcKRS), which is polyspecific (i.e., active with a broad range of ncAAs) and 30-fold more efficient with Phe derivatives than it is with AcK. Structural and biochemical data reveal the molecular basis of polyspecificity in AcKRS and in a PylRS variant [iodo-phenylalanyl-tRNA synthetase (IFRS)] that displays both enhanced activity and substrate promiscuity over a chemical library of 313 ncAAs. IFRS, a product of directed evolution, has distinct binding modes for different ncAAs. These data indicate that in vivo selections do not produce optimally specific tRNA synthetases and suggest that translation fidelity will become an increasingly dominant factor in expanding the genetic code far beyond 20 amino acids.

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Organizational Affiliation: 
• Departments of Molecular Biophysics & Biochemistry and.
Departments of Molecular Biophysics & Biochemistry and Chemistry, and.
Novartis Institutes of Biomedical Research, Cambridge, MA 02139;
Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706; and.
Departments of Molecular Biophysics & Biochemistry and Chemistry, and Howard Hughes Medical Institute, Yale University, New Haven, CT 06510;
Departments of Biochemistry and Chemistry, The University of Western Ontario, London, ON, Canada N6A 5C1 [e-mail] [e-mail].
Departments of Molecular Biophysics & Biochemistry and Chemistry, and [e-mail] [e-mail].

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)

Macromolecule Content 

• Total Structure Weight: 34.7 kDa 
• Atom Count: 2,327 
• Modeled Residue Count: 258 
• Deposited Residue Count: 291 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyrrolysine--tRNA ligase	A	291	Methanosarcina mazei Go1	Mutation(s): 2  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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	E [auth A]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
33S	F [auth A]	3-iodo-L-phenylalanine C9 H10 I N O2 BABTYIKKTLTNRX-QMMMGPOBSA-N
EDO	G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG	B [auth A], C [auth A], D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.14 Å
• R-Value Free:  0.193 (Depositor), 0.191 (DCC) 
• R-Value Work:  0.155 (Depositor) 
• R-Value Observed: 0.159 (Depositor) 

Space Group: P 6₄

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.7	α = 90
b = 104.7	β = 90
c = 70.66	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-11-12 
Deposition Author(s): Nakamura, A., O'Donoghue, P., Soll, D.

Revision History  

• Version 1.0: 2014-11-12
  Type: Initial release
  
• Version 1.1: 2014-11-26
  Changes: Database references
• Version 1.2: 2014-12-03
  Changes: Database references
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Source and taxonomy
• Version 1.4: 2023-11-15
  Changes: Data collection