2C78

EF-Tu complexed with a GTP analog and the antibiotic pulvomycin

• PDB DOI:  https://doi.org/10.2210/pdb2C78/pdb

• Classification: HYDROLASE
• Organism(s): Thermus thermophilus HB8
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2005-11-18 Released: 2006-03-16 
• Deposition Author(s): Parmeggiani, A., Krab, I.M., Okamura, S., Nielsen, R.C., Nyborg, J., Nissen, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.216 
• R-Value Work: 0.197 
• R-Value Observed: 0.197 

Literature

Structural basis of the action of pulvomycin and GE2270 A on elongation factor Tu.

Parmeggiani, A., Krab, I.M., Okamura, S., Nielsen, R.C., Nyborg, J., Nissen, P.

(2006) Biochemistry 45: 6846-6857

• PubMed: 16734421 
• DOI: https://doi.org/10.1021/bi0525122
• Primary Citation of Related Structures:  
  2C77, 2C78


• PubMed Abstract: 
  

Pulvomycin inhibits protein synthesis by preventing the formation of the ternary complex between elongation factor Tu (EF-Tu) x GTP and aa-tRNA. In this work, the crystal structure of Thermus thermophilus EF-Tu x pulvomycin in complex with the GTP analogue guanylyl imino diphosphate (GDPNP) at 1.4 A resolution reveals an antibiotic binding site extending from the domain 1-3 interface to domain 2, overlapping the domain 1-2-3 junction. Pulvomycin binding interferes with the binding of the 3'-aminoacyl group, the acceptor stem, and 5' end of tRNA. Only part of pulvomycin overlaps the binding site of GE2270 A, a domain 2-bound antibiotic of a structure unrelated to pulvomycin, which also hinders aa-tRNA binding. The structure of the T. thermophilus EF-Tu x GDPNP x GE2270 A complex at 1.6 A resolution shows that GE2270 A interferes with the binding of the 3'-aminoacyl group and part of the acceptor stem of aa-tRNA but not with the 5' end. Both compounds, pulvomycin more markedly, hinder the correct positioning of domain 1 over domains 2 and 3 that characterizes the active form of EF-Tu, while they affect the domain 1 switch regions that control the EF-Tu x GDP/GTP transitions in different ways. This work reveals how two antibiotics with different structures and binding modes can employ a similar mechanism of action.

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Organizational Affiliation: 

Department of Molecular Biology, University of Aarhus, Gustav Wieds Vej 10 C, DK-8000 Aarhus C, Denmark. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 46.07 kDa 
• Atom Count: 3,496 
• Modelled Residue Count: 397 
• Deposited Residue Count: 405 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ELONGATION FACTOR TU-A	A	405	Thermus thermophilus HB8	Mutation(s): 0  Gene Names: tufA, tuf, TTHA1694 EC: 3.1.5.1
UniProt
Find proteins for Q5SHN6 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHN6  Go to UniProtKB:  Q5SHN6

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PUL	D [auth A]	(1S,2S,3E,5E,7E,10S,11S,12S)-12-[(2R,4E,6E,8Z,10R,12E,14E,16Z,18S,19Z)-10,18-DIHYDROXY-12,16,19-TRIMETHYL-11,22-DIOXOOX ACYCLODOCOSA-4,6,8,12,14,16,19-HEPTAEN-2-YL]-2,11-DIHYDROXY-1,10-DIMETHYL-9-OXOTRIDECA-3,5,7-TRIEN-1-YL 6-DEOXY-2,4-DI-O-METHYL-BETA-L-GALACTOPYRANOSIDE C47 H66 O13 FXSFWUNCIOIMAC-VXILMCRLSA-N
GNP	B [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER C10 H17 N6 O13 P3 UQABYHGXWYXDTK-UUOKFMHZSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.216 
• R-Value Work: 0.197 
• R-Value Observed: 0.197 
• Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.686	α = 90
b = 86.686	β = 90
c = 105.514	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-03-16 
Deposition Author(s): Parmeggiani, A., Krab, I.M., Okamura, S., Nielsen, R.C., Nyborg, J., Nissen, P.

Revision History  

• Version 1.0: 2006-03-16
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-03-28
  Changes: Database references, Source and taxonomy
• Version 1.4: 2019-07-24
  Changes: Data collection