5L7J | pdb_00005l7j

Crystal Structure of Elp3 from Dehalococcoides mccartyi

• PDB DOI: https://doi.org/10.2210/pdb5L7J/pdb

• Classification: TRANSLATION
• Organism(s): Dehalococcoides mccartyi BTF08
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2016-06-03 Released: 2016-08-03 
• Deposition Author(s): Glatt, S., Mueller, C.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.219 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.206 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

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

• PubMed: 27455459 
• DOI: https://doi.org/10.1038/nsmb.3265
• Primary Citation Related Structures: 
  5L7J, 5L7L


• 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 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.

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Organizational Affiliation: 
• European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany.
Max Planck Research Group at the Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.
Institute of Biology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany.
Université de Strasbourg, IGBMC UMR 7104, Illkirch, France.
CNRS, IGBMC UMR 7104, Illkirch, France.
Inserm, IGBMC U964, Illkirch, France.
Unit of Virus Host-Cell Interactions (UMI 3265), University Grenoble Alpes-CNRS-EMBL, Grenoble, France.
Laboratoire de Bioénergétique et Ingénierie des Protéines, BIP/CNRS, UMR7281, AMU, Marseille, France.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 52.01 kDa 
• Atom Count: 3,216 
• Modeled Residue Count: 406 
• Deposited Residue Count: 459 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ELP3 family	A	459	Dehalococcoides mccartyi BTF08	Mutation(s): 1  Gene Names: btf_573 EC: 2.3.1.311
UniProt
Find proteins for A0A1C7D1B6 (Dehalococcoides mccartyi BTF08) Explore A0A1C7D1B6  Go to UniProtKB:  A0A1C7D1B6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FES	C [auth A]	FE2/S2 (INORGANIC) CLUSTER Fe2 S2 NIXDOXVAJZFRNF-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.219 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.206 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.46	α = 90
b = 158.58	β = 90
c = 93.58	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-08-03 
Deposition Author(s): Glatt, S., Mueller, C.W.

Revision History  

• Version 1.0: 2016-08-03
  Type: Initial release
  
• Version 1.1: 2016-08-10
  Changes: Database references
• Version 1.2: 2016-09-21
  Changes: Database references
• Version 2.0: 2024-11-13
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary