4WJ3

Crystal structure of the asparagine transamidosome from Pseudomonas aeruginosa

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.71 Å
  • R-Value Free: 0.329 
  • R-Value Work: 0.292 
  • R-Value Observed: 0.294 

wwPDB Validation   3D Report Full Report


This is version 1.3 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 U S A 112: 382-387

  • DOI: 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 ...

    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; dieter.soll@yale.edu yao@castor.sci.hokudai.ac.jp.



Macromolecules

Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glutamyl-tRNA(Gln) amidotransferase subunit AA, D, G, J484Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: gatA, PA4483
EC: 6.3.5.7
UniProt
Find proteins for Q9HVT8 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9HVT8 
Go to UniProtKB:  Q9HVT8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9HVT8
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit BB, E, H, K481Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: gatB, PA4484
EC: 6.3.5
UniProt
Find proteins for Q9HVT7 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9HVT7 
Go to UniProtKB:  Q9HVT7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9HVT7
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Glutamyl-tRNA(Gln) amidotransferase subunit CC, F, I, L104Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: gatC, PA4482
EC: 6.3.5
UniProt
Find proteins for Q9HVT9 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9HVT9 
Go to UniProtKB:  Q9HVT9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9HVT9
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Aspartate--tRNA(Asp/Asn) ligaseM, N, O, P599Pseudomonas aeruginosa PAO1Mutation(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 Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ51422
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChainsLengthOrganismImage
76mer-tRNAQ, R, S, T76Pseudomonas aeruginosa PAO1
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.71 Å
  • R-Value Free: 0.329 
  • R-Value Work: 0.292 
  • R-Value Observed: 0.294 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.14α = 90
b = 185.675β = 92.98
c = 290.359γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History & Funding Information

Deposition Data

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

Revision History  (Full details and data files)

  • 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