Evolutionary clues to eukaryotic DNA clamp-loading mechanisms: analysis of the functional constraints imposed on replication factor C AAA+ ATPases

Neuwald, Andrew F. (2005) Evolutionary clues to eukaryotic DNA clamp-loading mechanisms: analysis of the functional constraints imposed on replication factor C AAA+ ATPases. Nucleic Acids Res, 33 (11). pp. 3614-28. ISSN 1362-4962 (Electronic)

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URL: http://nar.oxfordjournals.org/content/33/11/3614
DOI: 10.1093/nar/gki674

Abstract

Ring-shaped sliding clamps encircle DNA and bind to DNA polymerase, thereby preventing it from falling off during DNA replication. In eukaryotes, sliding clamps are loaded onto DNA by the replication factor C (RFC) complex, which consists of five distinct subunits (A-E), each of which contains an AAA+ module composed of a RecA-like alpha/beta ATPase domain followed by a helical domain. AAA+ ATPases mediate chaperone-like protein remodeling. Despite remarkable progress in our understanding of clamp loaders, it is still unclear how recognition of primed DNA by RFC triggers ATP hydrolysis and how hydrolysis leads to conformational changes that can load the clamp onto DNA. While these questions can, of course, only be resolved experimentally, the design of such experiments is itself non-trivial and requires that one first formulate the right hypotheses based on preliminary observations. The functional constraints imposed on protein sequences during evolution are potential sources of information in this regard, inasmuch as these presumably are due to and thus reflect underlying mechanisms. Here, rigorous statistical procedures are used to measure and compare the constraints imposed on various RFC clamp-loader subunits, each of which performs a related but somewhat different, specialized function. Visualization of these constraints, within the context of the RFC structure, provides clues regarding clamp-loader mechanisms--suggesting, for example, that RFC-A possesses a triggering component for DNA-dependent ATP hydrolysis. It also suggests that, starting with RFC-A, four RFC subunits (A-D) are sequentially activated through a propagated switching mechanism in which a conserved arginine swings away from a position that disrupts the catalytic Walker B region and into contact with DNA thread through the center of the RFC/clamp complex. Strong constraints near regions of interaction between subunits and with the clamp likewise provide clues regarding possible coupling of hydrolysis-driven conformational changes to the clamp's release and loading onto DNA.

Item Type: Paper
Uncontrolled Keywords: Adenosinetriphosphatase chemistry Amino Acid Sequence sliding clamps replication factor C DNA Replication DNA-Binding Proteins chemistry Data Interpretation Statistical Eukaryotic Cells metabolism Evolution Molecular Models Molecular Molecular Sequence Data Proliferating Cell Nuclear Antigen chemistry Replication Factor A Replication Factor C Sequence Alignment
Subjects: bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > DNA replication
CSHL Authors:
Depositing User: CSHL Librarian
Date: 2005
Date Deposited: 06 Jan 2012 19:41
Last Modified: 06 Jan 2012 19:41
URI: http://repository.cshl.edu/id/eprint/22665

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