1OBC

LEUCYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS COMPLEXED WITH A POST-TRANSFER EDITING SUBSTRATE ANALOGUE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.193 

wwPDB Validation   3D Report Full Report


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: 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
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
LEUCYL-TRNA SYNTHETASEA878Thermus thermophilus HB27Mutation(s): 0 
Gene Names: leuSTT_C1825
EC: 6.1.1.4
Find proteins for Q72GM3 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Explore Q72GM3 
Go to UniProtKB:  Q72GM3
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LMS
Query on LMS

Download Ideal Coordinates CCD File 
G [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
2AD
Query on 2AD

Download Ideal Coordinates CCD File 
F [auth A]2'-AMINO-2'-DEOXYADENOSINE
C10 H14 N6 O3
CQKMBZHLOYVGHW-QYYRPYCUSA-N
 Ligand Interaction
LEU
Query on LEU

Download Ideal Coordinates CCD File 
B [auth A]LEUCINE
C6 H13 N O2
ROHFNLRQFUQHCH-YFKPBYRVSA-N
 Ligand Interaction
NVA
Query on NVA

Download Ideal Coordinates CCD File 
E [auth A]NORVALINE
C5 H11 N O2
SNDPXSYFESPGGJ-BYPYZUCNSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A], D [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.193 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.896α = 90
b = 154.81β = 90
c = 175.118γ = 90
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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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