Related Experiment Video
Updated: May 15, 2026
10:37
Comparing the Affinity of GTPase-binding Proteins using Competition Assays
Published on: October 8, 2015
Structural basis unifying diverse GTP hydrolysis mechanisms.
Baskaran Anand1, Soneya Majumdar, Balaji Prakash
1Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur 208016, India.
Biochemistry
|January 9, 2013
Summary
GTPase regulation is diverse. Steric hindrance in active sites explains varied GTP hydrolysis mechanisms, unifying seemingly unrelated GTPase families and guiding future research.
Area of Science:
- Biochemistry
- Molecular Biology
- Structural Biology
Background:
- GTPases are key regulators of biological processes.
- The canonical GTP hydrolysis mechanism involves a conserved Gln and an arginine finger from a GTPase-activating protein (GAP).
- Structurally similar GTPases exhibit diverse hydrolysis mechanisms, challenging the universal model.
Purpose of the Study:
- To decipher the unifying principles governing diverse GTP hydrolysis mechanisms.
- To understand the evolution of these varied mechanisms.
- To predict novel hydrolysis mechanisms and explain existing observations.
Main Methods:
- Comparative structural analysis of GTPases and their GAPs.
- Identification of steric hindrance as a key factor in mechanism selection.
- Analysis of active site residue compatibility.
Main Results:
- Identified steric hindrance between active site residues as a critical determinant of GTPase hydrolysis mechanism.
- Demonstrated that cation-dependent GTPases (MnmE, dynamin) use alternative catalytic residues and ions (K+, Na+) instead of the canonical Gln and arginine finger.
- Showcased Rab33 as an example where the GAP provides both catalytic Gln and arginine finger.
- The Arf-ArfGAP structure exemplifies steric incompatibility influencing mechanism.
Conclusions:
- Steric hindrance provides a unifying principle for diverse GTP hydrolysis mechanisms.
- This understanding predicts new mechanisms and clarifies existing unexplained observations in GTPase catalysis.
- Valuable for designing experiments targeting GTP hydrolysis or constitutive GTPase activity.
Related Concept Videos
02:14GTPases and their Regulation
Guanine nucleotide-binding proteins (G-proteins), also known as GTPases, are a superfamily of proteins that regulate many cellular processes, such as cell signaling, vesicular transport, and the regulation of cell shape and motility. Mutation or dysfunction of these proteins can lead to disease. There are around 40,000 known G-proteins that can broadly be classified into two groups ‒ small G-proteins consisting of a single domain and large multi-domain G-proteins.
Large G-proteins, also known...
Large G-proteins, also known...
02:14GTPases and their Regulation
Guanine nucleotide-binding proteins (G-proteins), also known as GTPases, are a superfamily of proteins that regulate many cellular processes, such as cell signaling, vesicular transport, and the regulation of cell shape and motility. Mutation or dysfunction of these proteins can lead to disease. There are around 40,000 known G-proteins that can broadly be classified into two groups ‒ small G-proteins consisting of a single domain and large multi-domain G-proteins.
Large G-proteins, also known...
Large G-proteins, also known...
01:22Activation and Inactivation of G Proteins
Heterotrimeric G proteins are guanine nucleotide-binding proteins. As the name suggests, heterotrimeric G proteins are composed of three subunits: alpha, beta, and gamma. They remain GDP-bound or GTP-bound inside the cells and switch between inactive/active states. The Gα subunit possesses the nucleotide-binding pocket that binds guanine nucleotides and switches between GDP or GTP-bound states. In contrast, the Gꞵ and Gγ subunits are always bound together with high affinity and are together...
01:48ATP Synthase: Mechanism
In animals, the mitochondrial F1F0 ATP synthase is the key protein that synthesizes ATP molecules through a complex catalytic mechanism. While the nuclear genome encodes the majority of ATP synthase subunits, the mitochondrial genome encodes some of the enzyme's most critical components. The formation of this multi-subunit enzyme is a complex multi-step process regulated at the level of transcription, translation, and assembly. Defects in one or more of these steps can result in decreased ATP...
01:24Small GTPases - Ras and Rho
Ras and Rho are small monomeric GTPases that act downstream of receptor tyrosine kinase (RTK) and regulate various cellular processes. These GTPases switch between active and inactive states by binding to guanine nucleotides.
Three regulatory proteins control their activity:
Three regulatory proteins control their activity:
01:58Mechanical Protein Functions
Proteins perform many mechanical functions in a cell. These proteins can be classified into two general categories- proteins that generate mechanical forces and proteins that are subjected to mechanical forces. Proteins providing mechanical support to the structure of the cell, such as keratin, are subjected to mechanical force, whereas proteins involved in cell movement and transport of molecules across cell membranes, such as an ion pump, are examples of generating mechanical force.