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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glutamyl-tRNA(Gln) amidotransferase subunit AA, D, G, J484Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: gatAPA4483
EC: 6.3.5.7
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
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit BB, E, H, K481Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: gatBPA4484
EC: 6.3.5
Find proteins for Q9HVT7 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
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Go to UniProtKB:  Q9HVT7
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Glutamyl-tRNA(Gln) amidotransferase subunit CC, F, I, L104Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: gatCPA4482
EC: 6.3.5
Find proteins for Q9HVT9 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
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Go to UniProtKB:  Q9HVT9
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Aspartate--tRNA(Asp/Asn) ligaseM, N, O, P599Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: aspSPA0963
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))
Explore Q51422 
Go to UniProtKB:  Q51422
Protein Feature View
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsLengthOrganismImage
76mer-tRNAQ, R, S, T76Pseudomonas aeruginosa PAO1
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

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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