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Catalytic Site Atlas

CSA LITERATURE entry for 1d8t

E.C. nameELONGATION FACTOR TU
SpeciesEscherichia coli (Bacteria)
E.C. Number (IntEnz) -.-.-.-
CSA Homologues of 1d8tThere are 269 Homologs
CSA Entries With UniProtID
CSA Entries With EC Number -.-.-.-
PDBe Entry 1d8t
PDBSum Entry 1d8t
MACiE Entry 1d8t

Literature Report

IntroductionElongation factor Tu hydrolyses GTP to give GDP and Pi, thus providing the free energy that the ribosome needs to incorporate amino acids into the growing polypeptide. As such, it shows homology to other GTP binding proteins such as the oncogene ras, but may show a different mechanism of GTP hydrolysis. Many antibiotics are able to inhibit EFTu, making study of its mechanism particularly useful in view of the possibility of synthesising new antibiotics.
MechansimThe reaction, unlike those commonly seen with GTPases, is most likely to proceed via a dissociative mechanism. This means that a general acid Asp 21 protonates the gamma phosphate causing it to leave the molecule before the water molecule attacks the beta phosphate. Thus the reaction proceeds via a trigonal planar transition state rather than the pentavalent phosphate transition state normally observed for nucleotide hydrolysis.

Catalytic Sites for 1d8t

Annotated By Reference To The Literature - Site 1 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
AspA2122macie:sideChainDonates a proton to the gamma phosphate of GTP to allow it to act as a leaving group resulting in the trigonal planar intermediate which is subsequently attacked by a nucleophilic water molecule to give GDP.

Annotated By Reference To The Literature - Site 2 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
AspB2122macie:sideChainDonates a proton to the gamma phosphate of GTP to allow it to act as a leaving group resulting in the trigonal planar intermediate which is subsequently attacked by a nucleophilic water molecule to give GDP.

Literature References

Notes:Although the authors of the main evidence source for this annotation favour a dissociative mechanism it is not possible to rule out the alternative associative (SN2) reaction with Arg 59 acting as the transition state stabiliser, even though a large conformational change on binding would be necessary for this reaction to occur.
Geggier P
Conformational sampling of aminoacyl-tRNA during selection on the bacterial ribosome.
J Mol Biol 2010 399 576-595
PubMed: 20434456
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