4WJ4

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.294 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

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.USA 112: 382-387

  • DOI: 10.1073/pnas.1423314112
  • Primary Citation of Related Structures:  

  • 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) tha ...

    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.


    Organizational Affiliation

    Graduate School of Life Science and.,Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan;,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.,Graduate School of Life Science and Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan; dieter.soll@yale.edu yao@castor.sci.hokudai.ac.jp.,Department of Molecular Biophysics and Biochemistry and Department of Chemistry, Yale University, New Haven, CT 06520; and dieter.soll@yale.edu yao@castor.sci.hokudai.ac.jp.,Department of Chemistry, Skidmore College, Saratoga Springs, NY 12866.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Aspartate--tRNA(Asp/Asn) ligase
A
599Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)Mutation(s): 0 
Gene Names: aspS
EC: 6.1.1.23
Find proteins for Q51422 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Go to UniProtKB:  Q51422
Entity ID: 2
MoleculeChainsLengthOrganism
76mer-tRNAB76Pseudomonas aeruginosa PAO1
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ASP
Query on ASP

Download SDF File 
Download CCD File 
A
ASPARTIC ACID
C4 H7 N O4
CKLJMWTZIZZHCS-REOHCLBHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.294 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.189 
  • Space Group: P 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 157.913α = 90.00
b = 157.913β = 90.00
c = 146.260γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education, Culture, Sports, Science and Technology of JapanJapan21370041

Revision History 

  • Version 1.0: 2014-12-31
    Type: Initial release
  • Version 1.1: 2015-01-14
    Type: Database references, Structure summary
  • Version 1.2: 2015-01-28
    Type: Database references