1OBH

LEUCYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS COMPLEXED WITH A PRE-TRANSFER EDITING SUBSTRATE ANALOGUE IN BOTH SYNTHETIC ACTIVE SITE AND EDITING SITE

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.213 

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This is version 1.2 of the entry. See complete history. 


Literature

Structural and Mechanistic Basis of Pre- and Posttransfer Editing by Leucyl-tRNA Synthetase

Lincecum, T., Tukalo, M., Yaremchuk, A., Mursinna, R., Williams, A., Sproat, B., Van Den Eynde, W., Link, A., Van Calenbergh, S., Grotli, M., Martinis, S., Cusack, S.

(2003) Mol Cell 11: 951

  • DOI: https://doi.org/10.1016/s1097-2765(03)00098-4
  • Primary Citation of Related Structures:  
    1OBC, 1OBH

  • PubMed Abstract: 

    • The aminoacyl-tRNA synthetases link tRNAs with their cognate amino acid. In some cases, their fidelity relies on hydrolytic editing that destroys incorrectly activated amino acids or mischarged tRNAs. We present structures of leucyl-tRNA synthetase complexed with analogs of the distinct pre- and posttransfer editing substrates ...

    The aminoacyl-tRNA synthetases link tRNAs with their cognate amino acid. In some cases, their fidelity relies on hydrolytic editing that destroys incorrectly activated amino acids or mischarged tRNAs. We present structures of leucyl-tRNA synthetase complexed with analogs of the distinct pre- and posttransfer editing substrates. The editing active site binds the two different substrates using a single amino acid discriminatory pocket while preserving the same mode of adenine recognition. This suggests a similar mechanism of hydrolysis for both editing substrates that depends on a key, completely conserved aspartic acid, which interacts with the alpha-amino group of the noncognate amino acid and positions both substrates for hydrolysis. Our results demonstrate the economy by which a single active site accommodates two distinct substrates in a proofreading process critical to the fidelity of protein synthesis.

    Related Citations: 
    • The 2A Structure of Leucyl-tRNA Synthetase and its Complex with a Leucyl-Adenylate Analogue
      Cusack, S., Yaremchuk, A., Tukalo, M.
      (2000) EMBO J 19: 2351
    • Crystallization and Preliminary Crystallographic Analysis of Thermus Thermophilus Leucyl-tRNA Synthetase and its Complexes with Leucine and a Non-Hydrolysable Leucyl-Adenylate Analogue
      Yaremchuk, A., Cusack, S., Gudzera, O., Grotli, M., Tukalo, M.
      (2000) Acta Crystallogr D Biol Crystallogr 56: 667
    Organizational Affiliation: 

    Department of Biology and Biochemistry, University of Houston, Texas 77204, USA.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
LEUCYL-TRNA SYNTHETASE878Thermus thermophilus HB27Mutation(s): 0 
Gene Names: leuS, TT_C1825
EC: 6.1.1.4
UniProt
Find proteins for Q72GM3 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27))
Explore Q72GM3 
Go to UniProtKB:  Q72GM3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ72GM3
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LMS
Query on LMS
Download Ideal Coordinates CCD File 
J [auth A],
L [auth A]		[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDRO-2-FURANYL]METHYL SULFAMATE
C10 H14 N6 O6 S
GNZLUJQJDPRUTD-KQYNXXCUSA-N		 Ligand Interaction
HG
Query on HG
Download Ideal Coordinates CCD File 
H [auth A]MERCURY (II) ION
Hg
BQPIGGFYSBELGY-UHFFFAOYSA-N		 Ligand Interaction
NVA
Query on NVA
Download Ideal Coordinates CCD File 
I [auth A],
K [auth A]		NORVALINE
C5 H11 N O2
SNDPXSYFESPGGJ-BYPYZUCNSA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
B [auth A]
C [auth A]
D [auth A]
E [auth A]
F [auth A]
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.213 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.515α = 90
b = 152.884β = 90
c = 172.605γ = 90
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
SCALAdata 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: 2003-05-09
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance