2BTE

Thermus thermophilus Leucyl-tRNA synthetase complexed with a tRNAleu transcript in the post-editing conformation and a post- transfer editing substrate analogue

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.217 

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Literature

The Crystal Structure of Leucyl-tRNA Synthetase Complexed with tRNA(Leu) in the Post-Transfer- Editing Conformation.

Tukalo, M., Yaremchuk, A., Fukunaga, R., Yokoyama, S., Cusack, S.

(2005) Nat Struct Mol Biol 12: 923

  • DOI: 10.1038/nsmb986
  • Primary Citation of Related Structures:  
    2BTE, 2BYT

  • PubMed Abstract: 

    • Leucyl-tRNA synthetase (LeuRS) has a specific post-transfer editing activity directed against mischarged isoleucine and similar noncognate amino acids. We describe the post-transfer-editing and product complexes of Thermus thermophilus LeuRS (LeuRSTT) with tRNA(Leu) at 2 ...

    Leucyl-tRNA synthetase (LeuRS) has a specific post-transfer editing activity directed against mischarged isoleucine and similar noncognate amino acids. We describe the post-transfer-editing and product complexes of Thermus thermophilus LeuRS (LeuRSTT) with tRNA(Leu) at 2.9- to 3.3-A resolution. In the post-transfer-editing configuration, A76 binds in the editing active site exactly as previously found for the adenosine moiety of a small-molecule editing-substrate analog. The 60 C-terminal residues of LeuRSTT, unseen in previous structures, fold into a compact domain flexibly linked to the rest of the molecule and interacting with the G19-C56 tertiary base pair of tRNA(Leu). LeuRS recognition of tRNA(Leu) depends essentially on tRNA shape rather than base-specific interactions. The structures show that considerable domain rotations, notably of the editing domain, accompany the tRNA-3' end dynamics associated successively with aminoacylation, post-transfer editing and product release.

    Organizational Affiliation: 

    European Molecular Biology Laboratory, Grenoble Outstation, c/o Institut Laue-Langevin, 156X, F-38042 Grenoble Cedex 9, France.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
AMINOACYL-TRNA SYNTHETASEA,
C [auth D]		878Thermus thermophilusMutation(s): 0 
Gene Names: leuS
EC: 6.1.1.4
UniProt
Find proteins for Q7SIE4 (Thermus thermophilus)
Explore Q7SIE4 
Go to UniProtKB:  Q7SIE4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7SIE4
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsLengthOrganismImage
TRNALEU TRANSCRIPT WITH ANTICODON CAGB,
D [auth E]		83Thermus thermophilus
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2AD
Query on 2AD
Download Ideal Coordinates CCD File 
OA [auth D],
U [auth A]		2'-AMINO-2'-DEOXYADENOSINE
C10 H14 N6 O3
CQKMBZHLOYVGHW-QYYRPYCUSA-N		 Ligand Interaction
HG
Query on HG
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G [auth A],
Y [auth D]		MERCURY (II) ION
Hg
BQPIGGFYSBELGY-UHFFFAOYSA-N		 Ligand Interaction
LEU
Query on LEU
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MA [auth D],
V [auth A]		LEUCINE
C6 H13 N O2
ROHFNLRQFUQHCH-YFKPBYRVSA-N		 Ligand Interaction
NVA
Query on NVA
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NA [auth D],
T [auth A]		NORVALINE
C5 H11 N O2
SNDPXSYFESPGGJ-BYPYZUCNSA-N		 Ligand Interaction
SO4
Query on SO4
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AA [auth D],
BA [auth D],
CA [auth D],
DA [auth D],
EA [auth D],
AA [auth D],
BA [auth D],
CA [auth D],
DA [auth D],
EA [auth D],
FA [auth D],
GA [auth D],
H [auth A],
HA [auth D],
I [auth A],
IA [auth D],
J [auth A],
JA [auth D],
K [auth A],
KA [auth D],
L [auth A],
LA [auth D],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
Z [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
ZN
Query on ZN
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E [auth A],
F [auth A],
W [auth D],
X [auth D]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.217 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 204.121α = 90
b = 125.705β = 120.86
c = 175.432γ = 90
Software Package:
Software NamePurpose
CNSrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-09-15
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance