5L7L

Crystal Structure of Elp3 from Dehalococcoides mccartyi (390-407 GSGSG)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.593 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


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

Literature

Structural basis for tRNA modification by Elp3 from Dehalococcoides mccartyi.

Glatt, S., Zabel, R., Kolaj-Robin, O., Onuma, O.F., Baudin, F., Graziadei, A., Taverniti, V., Lin, T.Y., Baymann, F., Seraphin, B., Breunig, K.D., Muller, C.W.

(2016) Nat.Struct.Mol.Biol. 23: 794-802

  • DOI: 10.1038/nsmb.3265
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • During translation elongation, decoding is based on the recognition of codons by corresponding tRNA anticodon triplets. Molecular mechanisms that regulate global protein synthesis via specific base modifications in tRNA anticodons are receiving incre ...

    During translation elongation, decoding is based on the recognition of codons by corresponding tRNA anticodon triplets. Molecular mechanisms that regulate global protein synthesis via specific base modifications in tRNA anticodons are receiving increasing attention. The conserved eukaryotic Elongator complex specifically modifies uridines located in the wobble base position of tRNAs. Mutations in Elongator subunits are associated with certain neurodegenerative diseases and cancer. Here we present the crystal structure of D. mccartyi Elp3 (DmcElp3) at 2.15-Å resolution. Our results reveal an unexpected arrangement of Elp3 lysine acetyltransferase (KAT) and radical S-adenosyl methionine (SAM) domains, which share a large interface and form a composite active site and tRNA-binding pocket, with an iron-sulfur cluster located in the dimerization interface of two DmcElp3 molecules. Structure-guided mutagenesis studies of yeast Elp3 confirmed the relevance of our findings for eukaryotic Elp3s and should aid in understanding the cellular functions and pathophysiological roles of Elongator.

    Organizational Affiliation: 

    European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ELP3 family, ELP3 family
A
446N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
FES
Query on FES
Download SDF File 
Download CCD File 
A
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.593 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.182 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 73.760α = 90.00
b = 161.410β = 90.00
c = 93.220γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
XSCALEdata scaling
XDSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-08-03
    Type: Initial release
  • Version 1.1: 2016-08-10
    Type: Database references
  • Version 1.2: 2016-09-21
    Type: Database references