The essential GTPase YphC displays a major domain rearrangement associated with nucleotide binding
Open Access
- 15 August 2006
- journal article
- research article
- Published by Proceedings of the National Academy of Sciences in Proceedings of the National Academy of Sciences
- Vol. 103 (33) , 12359-12364
- https://doi.org/10.1073/pnas.0602585103
Abstract
The structure of a Bacillus subtilis YphC/GDP complex shows that it contains two GTPase domains that pack against a central domain whose fold resembles that of an RNA binding KH-domain. Comparisons of this structure to that of a homologue in Thermotoga maritima reveals a dramatic rearrangement in the position of the N-terminal GTPase domain with a shift of up to 60 Å and the formation of a totally different interface to the central domain. This rearrangement appears to be triggered by conformational changes of the switch II region in this domain in response to nucleotide binding. Modeling studies suggest that this motion represents transitions between the “on” and “off” states of the GTPase, the effect of which is to alternately expose and bury a positively charged face of the central domain that we suggest is involved in RNA recognition as part of the possible role of this enzyme in ribosome binding.Keywords
This publication has 26 references indexed in Scilit:
- Cloning, purification and preliminary crystallographic analysis of theBacillus subtilisGTPase YphC–GDP complexActa Crystallographica Section F Structural Biology and Crystallization Communications, 2006
- Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensionsActa Crystallographica Section D-Biological Crystallography, 2004
- Domain Arrangement of Der, a Switch Protein Containing Two GTPase DomainsStructure, 2002
- Classification and evolution of P-loop GTPases and related ATPasesJournal of Molecular Biology, 2002
- The Guanine Nucleotide-Binding Switch in Three DimensionsScience, 2001
- Structure of the C-terminal RNA-binding domain of hnRNP D0 (AUF1), its interactions with RNA and DNA, and change in backbone dynamics upon complex formation with DNAJournal of Molecular Biology, 2001
- An Essential GTPase, Der, Containing Double GTP-binding Domains from Escherichia coli and Thermotoga maritimaPublished by Elsevier ,2001
- The Importance of Structural Transitions of the Switch II Region for the Functions of Elongation Factor Tu on the RibosomeJournal of Biological Chemistry, 2001
- Refinement of Macromolecular Structures by the Maximum-Likelihood MethodActa Crystallographica Section D-Biological Crystallography, 1997
- The GTPase superfamily: conserved structure and molecular mechanismNature, 1991