Structural stabilization of GTP-binding domains in circularly permuted GTPases: implications for RNA binding.

Nucleic Acids Research
Baskaran AnandBalaji Prakash

Abstract

GTP hydrolysis by GTPases requires crucial residues embedded in a conserved G-domain as sequence motifs G1-G5. However, in some of the recently identified GTPases, the motif order is circularly permuted. All possible circular permutations were identified after artificially permuting the classical GTPases and subjecting them to profile Hidden Markov Model searches. This revealed G4-G5-G1-G2-G3 as the only possible circular permutation that can exist in nature. It was also possible to recognize a structural rationale for the absence of other permutations, which either destabilize the invariant GTPase fold or disrupt regions that provide critical residues for GTP binding and hydrolysis, such as Switch-I and Switch-II. The circular permutation relocates Switch-II to the C-terminus and leaves it unfastened, thus affecting GTP binding and hydrolysis. Stabilizing this region would require the presence of an additional domain following Switch-II. Circularly permuted GTPases (cpGTPases) conform to such a requirement and always possess an 'anchoring' C-terminal domain. There are four sub-families of cpGTPases, of which three possess an additional domain N-terminal to the G-domain. The biochemical function of these domains, based on avail...Continue Reading

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Citations

Jul 27, 2011·Proceedings of the National Academy of Sciences of the United States of America·Qiang GuoNing Gao
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Methods Mentioned

BETA
GTPases
GTPase

Software Mentioned

cpGTPases
Coffee
PHYLIP
PSI
BLAST
VIMSS operon prediction server
protdist
JPRED
Seaview
Treepuzzle

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