2HDN

Trypsin-modified Elongation Factor Tu in complex with tetracycline at 2.8 Angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.180 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history


Literature

Molecular complementarity between tetracycline and the GTPase active site of elongation factor Tu.

Heffron, S.E.Mui, S.Aorora, A.Abel, K.Bergmann, E.Jurnak, F.

(2006) Acta Crystallogr D Biol Crystallogr 62: 1392-1400

  • DOI: https://doi.org/10.1107/S0907444906035426
  • Primary Citation of Related Structures:  
    2HCJ, 2HDN

  • PubMed Abstract: 

    Two crystal forms of a complex between trypsin-modified elongation factor Tu-MgGDP from Escherichia coli and the antibiotic tetracycline have been solved by X-ray diffraction analysis to resolutions of 2.8 and 2.1 A, respectively. In the P2(1) form, cocrystals were grown from a solution mixture of the protein and tetracycline. Six copies of the trypsin-modified EF-Tu-MgGDP-tetracycline complex are arranged as three sets of dimers in the asymmetric unit. In the second crystal form, tetracycline was diffused into P4(3)2(1)2 crystals, resulting in a monomeric complex in the asymmetric unit. Atomic coordinates have been refined to crystallographic R factors of 18.0% for the P2(1) form and 20.0% for the P4(3)2(1)2 form. In both complexes, tetracycline makes significant interactions with the GTPase active site of EF-Tu. The phenoldiketone moiety of tetracycline interacts directly with the Mg(2+), the alpha-phosphate group of GDP and two amino acids, Thr25 and Asp80, which are conserved in the GX(4)GKS/T and DX(2)G sequence motifs found in all GTPases and many ATPases. The molecular complementarity, previously unrecognized between invariant groups present in all GTPase/ATPases and the active moiety of tetracycline, may have wide-ranging implications for all drugs containing the phenoldiketone moiety as well as for the design of new compounds targeted against a broad range of GTPases or ATPases.


  • Organizational Affiliation

    Department of Physiology and Biophysics, 346-D Med Sci I, University of California, Irvine, CA 92697-4560, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Elongation factor EF-Tu
A, C, E, G, I
A, C, E, G, I, K
37Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0CE47 (Escherichia coli (strain K12))
Explore P0CE47 
Go to UniProtKB:  P0CE47
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CE47
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Elongation factor EF-Tu
B, D, F, H, J
B, D, F, H, J, L
335Escherichia coliMutation(s): 1 
UniProt
Find proteins for P0CE47 (Escherichia coli (strain K12))
Explore P0CE47 
Go to UniProtKB:  P0CE47
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CE47
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TAC
Query on TAC

Download Ideal Coordinates CCD File 
AA [auth J]
DA [auth L]
O [auth B]
R [auth D]
U [auth F]
AA [auth J],
DA [auth L],
O [auth B],
R [auth D],
U [auth F],
X [auth H]
TETRACYCLINE
C22 H24 N2 O8
OFVLGDICTFRJMM-WESIUVDSSA-N
GDP
Query on GDP

Download Ideal Coordinates CCD File 
CA [auth L]
N [auth B]
Q [auth D]
T [auth F]
W [auth H]
CA [auth L],
N [auth B],
Q [auth D],
T [auth F],
W [auth H],
Z [auth J]
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
BA [auth K]
M [auth A]
P [auth C]
S [auth E]
V [auth G]
BA [auth K],
M [auth A],
P [auth C],
S [auth E],
V [auth G],
Y [auth I]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.180 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.71α = 90
b = 156.06β = 95.38
c = 134.83γ = 90
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
MERLOTphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-10-31
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations
  • Version 1.4: 2024-04-03
    Changes: Refinement description