6IA6 | pdb_00006ia6

Crystal structure of the bacterial Dehalococcoides mccartyi Elp3 with desulfo-CoA

• PDB DOI: https://doi.org/10.2210/pdb6IA6/pdb

• Classification: TRANSFERASE
• Organism(s): Dehalococcoides mccartyi BTF08
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2018-11-26 Released: 2019-02-20 
• Deposition Author(s): Lin, T.Y., Glatt, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.269 (Depositor), 0.272 (DCC) 
• R-Value Work: 
  0.223 (Depositor), 0.231 (DCC) 
• R-Value Observed: 
  0.225 (Depositor) 

Starting Model: experimental

Literature

The Elongator subunit Elp3 is a non-canonical tRNA acetyltransferase.

Lin, T.Y., Abbassi, N.E.H., Zakrzewski, K., Chramiec-Glabik, A., Jemiola-Rzeminska, M., Rozycki, J., Glatt, S.

(2019) Nat Commun 10: 625-625

• PubMed: 30733442 
• DOI: https://doi.org/10.1038/s41467-019-08579-2
• Primary Citation Related Structures: 
  6IA6, 6IA8, 6IAD, 6IAZ


• PubMed Abstract: 
  

  The Elongator complex catalyzes posttranscriptional tRNA modifications by attaching carboxy-methyl (cm ⁵ ) moieties to uridine bases located in the wobble position. The catalytic subunit Elp3 is highly conserved and harbors two individual subdomains, a radical S-adenosyl methionine (rSAM) and a lysine acetyltransferase (KAT) domain. The details of its modification reaction cycle and particularly the substrate specificity of its KAT domain remain elusive. Here, we present the co-crystal structure of bacterial Elp3 (DmcElp3) bound to an acetyl-CoA analog and compare it to the structure of a monomeric archaeal Elp3 from Methanocaldococcus infernus (MinElp3). Furthermore, we identify crucial active site residues, confirm the importance of the extended N-terminus for substrate recognition and uncover the specific induction of acetyl-CoA hydrolysis by different tRNA species. In summary, our results establish the clinically relevant Elongator subunit as a non-canonical acetyltransferase and genuine tRNA modification enzyme.

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Organizational Affiliation: 
• Max Planck Laboratory, Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow, 30-387, Poland.
Postgraduate School of Molecular Medicine, Warsaw, 02-091, Poland.
Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, 30-387, Poland.
Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow, 30-387, Poland.
Bionanoscience and Biochemistry Laboratory, Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow, 30-387, Poland.
Max Planck Laboratory, Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow, 30-387, Poland. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 50.95 kDa 
• Atom Count: 2,999 
• Modeled Residue Count: 388 
• Deposited Residue Count: 450 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ELP3 family, ELP3 family	A	450	Dehalococcoides mccartyi BTF08	Mutation(s): 0  Gene Names: btf_573 EC: 2.3.1.311
UniProt
Find proteins for A0A1C7D1B7 (Dehalococcoides mccartyi (strain CBDB1)) Explore A0A1C7D1B7  Go to UniProtKB:  A0A1C7D1B7

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DCA	B [auth A]	DESULFO-COENZYME A C21 H36 N7 O16 P3 ILWZMFJBPIYQKW-IBOSZNHHSA-N
FES	C [auth A]	FE2/S2 (INORGANIC) CLUSTER Fe2 S2 NIXDOXVAJZFRNF-UHFFFAOYSA-N
PO4	D [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.269 (Depositor), 0.272 (DCC) 
• R-Value Work:  0.223 (Depositor), 0.231 (DCC) 
• R-Value Observed: 0.225 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.54	α = 90
b = 160.74	β = 90
c = 92.99	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-02-20 
Deposition Author(s): Lin, T.Y., Glatt, S.

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Funding Organization	Location	Grant Number
	Poland	Homing/2016-2/14
	Poland	UMO-2015/19/B/NZ1/00343

Revision History  

• Version 1.0: 2019-02-20
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description