2BYT

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.243 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


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
LEUCYL-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 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HG
Query on HG

Download Ideal Coordinates CCD File 
H [auth A],
U [auth D]
MERCURY (II) ION
Hg
BQPIGGFYSBELGY-UHFFFAOYSA-N
 Ligand Interaction
LEU
Query on LEU

Download Ideal Coordinates CCD File 
E [auth A],
R [auth D]
LEUCINE
C6 H13 N O2
ROHFNLRQFUQHCH-YFKPBYRVSA-N
 Ligand Interaction
SO4
Query on SO4

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AA [auth D],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
AA [auth D],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
V [auth D],
W [auth D],
X [auth D],
Y [auth D],
Z [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ZN
Query on ZN

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F [auth A],
G [auth A],
S [auth D],
T [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.243 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 203.869α = 90
b = 125.578β = 118.44
c = 172.979γ = 90
Software Package:
Software NamePurpose
CNSrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

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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