Replication Protein A Interactions with DNA: Differential Binding of the Core Domains and Analysis of the DNA Interaction Surface

Human replication protein A (RPA) is a heterotrimeric (70, 32, and 14 kDa subunits), eukaryotic single-stranded DNA (ssDNA) binding protein required for DNA recombination, repair, and replication. The three subunits of human RPA are composed of six conserved DNA binding domains (DBDs). Deletion and...

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Bibliographic Details
Published in:	Biochemistry (Easton) Vol. 42; no. 44; pp. 12909 - 12918
Main Authors:	Wyka, Iwona M, Dhar, Kajari, Binz, Sara K, Wold, Marc S
Format:	Journal Article
Language:	English
Published:	United States American Chemical Society 11-11-2003
Subjects:	Conserved Sequence - genetics DNA Mutational Analysis DNA, Single-Stranded - chemistry DNA, Single-Stranded - genetics DNA, Single-Stranded - metabolism DNA-Binding Proteins - chemistry DNA-Binding Proteins - genetics DNA-Binding Proteins - metabolism Genetic Vectors Humans Models, Chemical Mutagenesis, Site-Directed Point Mutation Protein Binding - genetics Protein Structure, Tertiary - genetics Protein Subunits - chemistry Protein Subunits - genetics Protein Subunits - metabolism Replication Protein A Surface Properties
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Summary:	Human replication protein A (RPA) is a heterotrimeric (70, 32, and 14 kDa subunits), eukaryotic single-stranded DNA (ssDNA) binding protein required for DNA recombination, repair, and replication. The three subunits of human RPA are composed of six conserved DNA binding domains (DBDs). Deletion and mutational studies have identified a high-affinity DNA binding core in the central region of the 70 kDa subunit, composed of DBDs A and B. To define the roles of each DBD in DNA binding, monomeric and tandem DBD A and B domain chimeras were created and characterized. Individually, DBDs A and B have a very low intrinsic affinity for ssDNA. In contrast, tandem DBDs (AA, AB, BA, and BB) bind ssDNA with moderate to high affinity. The AA chimera had a much higher affinity for ssDNA than did the other tandem DBDs, demonstrating that DBD A has a higher intrinsic affinity for ssDNA than DBD B. The RPA−DNA interface is similar in both DBD A and DBD B. Mutational analysis was carried out to probe the relative contributions of the two domains to DNA binding. Mutation of polar residues in either core DBD resulted in a significant decrease in the affinity of the RPA complex for ssDNA. RPA complexes with pairs of mutated polar residues had lower affinities than those with single mutations. The decrease in affinity observed when polar mutations were combined suggests that multiple polar interactions contribute to the affinity of the RPA core for DNA. These results indicate that RPA−ssDNA interactions are the result of binding of multiple nonequivalent domains. Our data are consistent with a sequential binding model for RPA, in which DBD A is responsible for positioning and initial binding of the RPA complex while DBD A together with DBD B direct stable, high-affinity binding to ssDNA.
Bibliography:	These studies were supported by Grant GM44721 from the General Medicine Institute of the National Institutes of Heath. istex:D460D129D711A393BD99726F0D39ABD7F697F313 ark:/67375/TPS-FL1HT7SW-S ObjectType-Article-2 SourceType-Scholarly Journals-1 ObjectType-Feature-1 content type line 23
ISSN:	0006-2960 1520-4995
DOI:	10.1021/bi034930h