4WJ4 | pdb_00004wj4

Crystal structure of non-discriminating aspartyl-tRNA synthetase from Pseudomonas aeruginosa complexed with tRNA(Asn) and aspartic acid

• PDB DOI: https://doi.org/10.2210/pdb4WJ4/pdb
• NAKB: 4WJ4

• Classification: LIGASE/RNA
• Organism(s): Pseudomonas aeruginosa PAO1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-09-29 Released: 2014-12-31 
• Deposition Author(s): Suzuki, T., Nakamura, A., Kato, K., Tanaka, I., Yao, M.
• Funding Organization(s): Ministry of Education, Culture, Sports, Science and Technology of Japan

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.29 Å
• R-Value Free: 
  0.224 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Literature

Structure of the Pseudomonas aeruginosa transamidosome reveals unique aspects of bacterial tRNA-dependent asparagine biosynthesis

Suzuki, T., Nakamura, A., Kato, K., Soll, D., Tanaka, I., Sheppard, K., Yao, M.

(2015) Proc Natl Acad Sci U S A 112: 382-387

• PubMed: 25548166 
• DOI: https://doi.org/10.1073/pnas.1423314112
• Primary Citation of Related Structures:  
  4WJ3, 4WJ4


• PubMed Abstract: 
  

  Many prokaryotes lack a tRNA synthetase to attach asparagine to its cognate tRNA(Asn), and instead synthesize asparagine from tRNA(Asn)-bound aspartate. This conversion involves two enzymes: a nondiscriminating aspartyl-tRNA synthetase (ND-AspRS) that forms Asp-tRNA(Asn), and a heterotrimeric amidotransferase GatCAB that amidates Asp-tRNA(Asn) to form Asn-tRNA(Asn) for use in protein synthesis. ND-AspRS, GatCAB, and tRNA(Asn) may assemble in an ∼400-kDa complex, known as the Asn-transamidosome, which couples the two steps of asparagine biosynthesis in space and time to yield Asn-tRNA(Asn). We report the 3.7-Å resolution crystal structure of the Pseudomonas aeruginosa Asn-transamidosome, which represents the most common machinery for asparagine biosynthesis in bacteria. We show that, in contrast to a previously described archaeal-type transamidosome, a bacteria-specific GAD domain of ND-AspRS provokes a principally new architecture of the complex. Both tRNA(Asn) molecules in the transamidosome simultaneously serve as substrates and scaffolds for the complex assembly. This architecture rationalizes an elevated dynamic and a greater turnover of ND-AspRS within bacterial-type transamidosomes, and possibly may explain a different evolutionary pathway of GatCAB in organisms with bacterial-type vs. archaeal-type Asn-transamidosomes. Importantly, because the two-step pathway for Asn-tRNA(Asn) formation evolutionarily preceded the direct attachment of Asn to tRNA(Asn), our structure also may reflect the mechanism by which asparagine was initially added to the genetic code.

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Organizational Affiliation: 
• Graduate School of Life Science and.
Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan; Department of Molecular Biophysics and Biochemistry and Department of Chemistry, Yale University, New Haven, CT 06520; and.
Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan;
Department of Molecular Biophysics and Biochemistry and Department of Chemistry, Yale University, New Haven, CT 06520; and [e-mail] [e-mail].
Department of Chemistry, Skidmore College, Saratoga Springs, NY 12866.
Graduate School of Life Science and Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan; [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: 91.92 kDa 
• Atom Count: 6,245 
• Modeled Residue Count: 661 
• Deposited Residue Count: 675 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aspartate--tRNA(Asp/Asn) ligase	A	599	Pseudomonas aeruginosa PAO1	Mutation(s): 0  Gene Names: aspS, PA0963 EC: 6.1.1.23
UniProt
Find proteins for Q51422 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q51422  Go to UniProtKB:  Q51422

Entity ID: 2
Molecule	Chains	Length	Organism	Image
76mer-tRNA	B	76	Pseudomonas aeruginosa PAO1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ASP	C [auth A]	ASPARTIC ACID C4 H7 N O4 CKLJMWTZIZZHCS-REOHCLBHSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.29 Å
• R-Value Free:  0.224 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 157.913	α = 90
b = 157.913	β = 90
c = 146.26	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2014-12-31 
Deposition Author(s): Suzuki, T., Nakamura, A., Kato, K., Tanaka, I., Yao, M.

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Funding Organization	Location	Grant Number
Ministry of Education, Culture, Sports, Science and Technology of Japan	Japan	21370041

Revision History  

• Version 1.0: 2014-12-31
  Type: Initial release
  
• Version 1.1: 2015-01-14
  Changes: Database references, Structure summary
• Version 1.2: 2015-01-28
  Changes: Database references
• Version 1.3: 2020-02-05
  Changes: Data collection, Database references, Derived calculations, Source and taxonomy
• Version 1.4: 2024-03-20
  Changes: Data collection, Database references