4R1J | pdb_00004r1j

Crystal structure of Arc1p-C

• PDB DOI: https://doi.org/10.2210/pdb4R1J/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-08-06 Released: 2015-02-18 
• Deposition Author(s): Altegoer, F., Bange, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.201 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.178 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

Starting Model: experimental

Literature

A Synthetic Adenylation-Domain-Based tRNA-Aminoacylation Catalyst.

Giessen, T.W., Altegoer, F., Nebel, A.J., Steinbach, R.M., Bange, G., Marahiel, M.A.

(2015) Angew Chem Int Ed Engl 54: 2492-2496

• PubMed: 25583137 
• DOI: https://doi.org/10.1002/anie.201410047
• Primary Citation Related Structures: 
  4R1J


• PubMed Abstract: 
  

  The incorporation of non-proteinogenic amino acids represents a major challenge for the creation of functionalized proteins. The ribosomal pathway is limited to the 20-22 proteinogenic amino acids while nonribosomal peptide synthetases (NRPSs) are able to select from hundreds of different monomers. Introduced herein is a fusion-protein-based design for synthetic tRNA-aminoacylation catalysts based on combining NRPS adenylation domains and a small eukaryotic tRNA-binding domain (Arc1p-C). Using rational design, guided by structural insights and molecular modeling, the adenylation domain PheA was fused with Arc1p-C using flexible linkers and achieved tRNA-aminoacylation with both proteinogenic and non-proteinogenic amino acids. The resulting aminoacyl-tRNAs were functionally validated and the catalysts showed broad substrate specificity towards the acceptor tRNA. Our strategy shows how functional tRNA-aminoacylation catalysts can be created for bridging the ribosomal and nonribosomal worlds. This opens up new avenues for the aminoacylation of tRNAs with functional non-proteinogenic amino acids.

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Organizational Affiliation: 
• Department of Chemistry, Philipps-University Marburg, Hans-Meerwein-Strasse 4, 35032 Marburg (Germany); LOEWE Center for Synthetic Microbiology (Synmikro), Philipps-University Marburg, Hans-Meerwein-Strasse, 35032 Marburg (Germany). [e-mail].

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 22.15 kDa 
• Atom Count: 1,652 
• Modeled Residue Count: 174 
• Deposited Residue Count: 197 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GU4 nucleic-binding protein 1	A	197	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: ARC1, G4P1, YGL105W, G3085 EC: 3.1.1
UniProt
Find proteins for P46672 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P46672  Go to UniProtKB:  P46672

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.201 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.178 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.658	α = 90
b = 49.961	β = 90
c = 82.941	γ = 90

Software Package:

Software Name	Purpose
DNA	data collection
PHASER	phasing
PHENIX	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-02-18 
Deposition Author(s): Altegoer, F., Bange, G.

Revision History  

• Version 1.0: 2015-02-18
  Type: Initial release
  
• Version 1.1: 2015-03-11
  Changes: Database references
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description