2HDN image
Deposition Date 2006-06-20
Release Date 2006-10-31
Last Version Date 2024-04-03
Entry Detail
PDB ID:
2HDN
Keywords:
Title:
Trypsin-modified Elongation Factor Tu in complex with tetracycline at 2.8 Angstrom resolution
Biological Source:
Source Organism:
Escherichia coli (Taxon ID: 562)
Method Details:
Experimental Method:
Resolution:
2.80 Å
R-Value Free:
0.22
R-Value Work:
0.18
Space Group:
P 1 21 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Elongation factor EF-Tu
Chain IDs:A, C, E, G, I, K
Chain Length:37
Number of Molecules:6
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Elongation factor EF-Tu
Chain IDs:B, D, F, H, J, L
Chain Length:335
Number of Molecules:6
Biological Source:Escherichia coli
Primary Citation
Molecular complementarity between tetracycline and the GTPase active site of elongation factor Tu.
Acta Crystallogr.,Sect.D 62 1392 1400 (2006)
PMID: 17057344 DOI: 10.1107/S0907444906035426

Abstact

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.

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