The Conformation of a Catalytic Loop Is Central to GTPase Activity on the Ribosome

Åqvist, Johan; Kamerlin, Shina Caroline Lynn

doi:10.1021/bi501373g

Cited by 32 publications

(101 citation statements)

References 65 publications

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“…However, the mutant proteins still show a measurable GTPase activity, which contrasts with the idea that EF‐Tu might behave as a metal ion‐activated GTPase. Furthermore, in the presence of the ribosome, no stimulation by K + ions was observed, in agreement with the notion that the K + ion is easily exchanged by a water molecule or a Mg 2+ ion upon binding to the ribosome, as suggested by structural and theoretical studies …”

Section: The Intrinsic Gtpase Of Ef‐tusupporting

confidence: 87%

“…Recent high‐resolution structures of the ribosome‐bound EF‐G show the side chain of the respective Asp residue coordinating a Mg 2+ ion close to the crucial A2662, indicating that the GTPase‐activated state might also involve a rearrangement of Asp21 . Molecular dynamics and free energy calculations suggested that the opposite charge of the side chain of Asp21 and His84 would effectively “push” the negative charge towards the γ phosphate of GTP . Taken together, these results show that the ribosome accelerates GTP hydrolysis by EF‐Tu by arranging the catalytic site in a productive way.…”

Section: The Ribosome As a Gapmentioning

confidence: 84%

“…Several models have been proposed for the mechanism of GTP hydrolysis by EF-Tu and other GTPases based on structural, theoretical and biochemical studies. 20,[53][54][55][56][57][58][59][60][61][62] In general, the reaction proceeds through a nucleophilic attack of a water molecule on the c-phosphate of GTP. For the reaction to become efficient, the water molecule has to be activated.…”

Section: Multiple Pathways Of Gtp Hydrolysismentioning

confidence: 99%

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Review: Translational GTPases

Maracci

Rodnina

2016

Biopolymers

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Translational GTPases (trGTPases) play key roles in facilitating protein synthesis on the ribosome. Despite the high degree of evolutionary conservation in the sequences of their GTP‐binding domains, the rates of GTP hydrolysis and nucleotide exchange vary broadly between different trGTPases. EF‐Tu, one of the best‐characterized model G proteins, evolved an exceptionally rapid and tightly regulated GTPase activity, which ensures rapid and accurate incorporation of amino acids into the nascent chain. Other trGTPases instead use the energy of GTP hydrolysis to promote movement or to ensure the forward commitment of translation reactions. Recent data suggest the GTPase mechanism of EF‐Tu and provide an insight in the catalysis of GTP hydrolysis by its unusual activator, the ribosome. Here we summarize these advances in understanding the functional cycle and the regulation of trGTPases, stimulated by the elucidation of their structures on the ribosome and the progress in dissecting the reaction mechanism of GTPases. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 463–475, 2016.

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Section: The Intrinsic Gtpase Of Ef‐tusupporting

confidence: 87%

Section: The Ribosome As a Gapmentioning

confidence: 84%

Section: Multiple Pathways Of Gtp Hydrolysismentioning

confidence: 99%

See 1 more Smart Citation

Review: Translational GTPases

Maracci

Rodnina

2016

Biopolymers

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“…Unlike glutamine, the relatively low pKa for histidine (typically near 6) would appear to make it a reasonable candidate for general base catalysis through activation of the nucleophilic water. However, simulations for EF‐Tu in the context of the ribosome suggest that the pK a for the catalytic histidine is several units higher due to nearby counter ions such that the histidine is protonated in the ground state and instead functions in electrostatic compensation of the hydroxide ion generated during transfer of the proton from the nucleophilic water to the γ phosphate . Although it is not clear if the histidine in Sar1 functions in an analogous substrate‐assisted mechanism, the Sar1 GAP (i.e., the Sec23/24 complex) supplies a putative arginine finger that is directed into the hydrolytic site in the crystal structure of the Sar1‐GppNHp complex with Sec23/24 …”

Section: Small Gtpase Architecturementioning

confidence: 99%

Invited review: Small GTPases and their GAPs

Mishra

Lambright

2016

Biopolymers

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Summary Widespread utilization of small GTPases as major regulatory hubs in many different biological systems derives from a conserved conformational switch mechanism that facilitates cycling between GTP-bound active and GDP-bound inactive states under control of guanine nucleotide exchange factors (GEFs) and GTPase activating proteins (GAPs), which accelerate slow intrinsic rates of activation by nucleotide exchange and deactivation by GTP hydrolysis, respectively. Here we review developments leading to current understanding of intrinsic and GAP catalyzed GTP hydrolytic reactions in small GTPases from structural, molecular and chemical mechanistic perspectives. Despite the apparent simplicity of the GTPase cycle, the structural bases underlying the hallmark hydrolytic reaction and catalytic acceleration by GAPs are considerably more diverse than originally anticipated. Even the most fundamental aspects of the reaction mechanism have been challenging to decipher. Through a combination of experimental and in silico approaches, the outlines of a consensus view have begun to emerge for the best studied paradigms. Nevertheless, recent observations indicate that there is still much to be learned.

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“…23,24 Studies of the phosphate transfer from ATP to serine or tyrosine residues in protein kinases have been also widely reported. 3,[25][26][27][28][29][30][31] Thus, a theoretical study in cyclindependent kinase (CDK2) by De Vivo et al 25 proposed that an Asp residue located in the active site would play a structural role whereas the activation of the Ser nucleophile was proposed to be due to a proton transfer to ATP.…”

Section: Introductionmentioning

confidence: 99%

Theoretical Study of the Phosphoryl Transfer Reaction from ATP to Dha Catalyzed by DhaK from Escherichia coli

2017

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Protein kinases, representing one of the largest protein family involved in almost all aspects of cell life, have become one of the most important targets for the development of new drugs to be used in, for instance, cancer treatments. In this paper an exhaustive theoretical study of the phosphoryl transfer reaction from adenosine triphosphate (ATP) to dihydroxyacetone (Dha) catalyzed by DhaK from Escherichia coli (E. coli) is reported. Two different mechanisms, previously proposed for the phosphoryl transfer from ATP to the hydroxyl side chain of specific serine, threonine or tyrosine residues, have been explored based on the generation of free energy surfaces (FES) computed with hybrid QM/MM potentials. The results suggest that the substrate-assisted phosphoryl and proton-transfer mechanism is kinetically more favorable than the mechanism where an aspartate would be activating the Dha. Although the details of the mechanisms appear to be dramatically dependent on the level of theory employed in the calculations (PM3/MM, B3LYP:PM3/MM or B3LYP/MM), the transition states (TSs) for the phosphoryl transfer step appear to be described as a concerted step with different degrees of synchronicity in the breaking and forming bonds process in both explored mechanisms. Residues of the active site belonging to different subunits of the protein such as Gly78B, Thr79A, Ser80A, Arg178B and one Mg 2+ cation would be stabilizing the transferred phosphate in the TS. Asp109A would have a structural role by posing the Dha and other residues of the active site in the proper orientation. The information derived from our calculations not only reveals the role of the enzyme and the particular residues of its active site, but it can assist in the rationally design of new more specific inhibitors.3

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The Conformation of a Catalytic Loop Is Central to GTPase Activity on the Ribosome

Cited by 32 publications

References 65 publications

Review: Translational GTPases

Review: Translational GTPases

Invited review: Small GTPases and their GAPs

Theoretical Study of the Phosphoryl Transfer Reaction from ATP to Dha Catalyzed by DhaK from Escherichia coli

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