1U0J

Crystal Structure of AAV2 Rep40-ADP complex

Summary for 1U0J

• Entry DOI: 10.2210/pdb1u0j/pdb
• Descriptor: DNA replication protein, ADENOSINE-5'-DIPHOSPHATE (3 entities in total)
• Functional Keywords: aaa+ protein, p-loop atpases, helicase, replication
• Biological source: Adeno-associated virus - 2
• Total number of polymer chains: 1
• Total formula weight: 30554.33

Authors

James, J.A.,Aggarwal, A.K.,Linden, R.M.,Escalante, C.R. (deposition date: 2004-07-13, release date: 2004-08-24, Last modification date: 2023-08-23)

Primary citation

James, J.A.,Aggarwal, A.K.,Linden, R.M.,Escalante, C.R.
Structure of adeno-associated virus type 2 Rep40-ADP complex: Insight into nucleotide recognition and catalysis by superfamily 3 helicases
Proc.Natl.Acad.Sci.USA, 101:12455-12460, 2004

PubMed Abstract: We have determined the structure of adeno-associated virus type 2 (AAV2) Rep40 to 2.1-A resolution with ADP bound at the active site. The complex crystallizes as a monomer with one ADP molecule positioned in an unexpectedly open binding site. The nucleotide-binding pocket consists of the P-loop residues interacting with the phosphates and a loop (nucleoside-binding loop) that emanates from the last strand of the central beta-sheet and interacts with the sugar and base. As a result of the open nature of the binding site, one face of the adenine ring is completely exposed to the solvent, and consequently the number of protein-nucleotide contacts is scarce as compared with other P-loop nucleotide phosphohydrolases. The conformation of the ADP molecule in its binding site bears a resemblance to those found in only three other families of P-loop ATPases: the ATP-binding cassette transporter family, the bacterial RecA proteins, and the type II topoisomerase family. In all these cases, oligomerization is required to attain a competent nucleotide-binding pocket. We propose that this characteristic is native to superfamily 3 helicases and allows for an additional mechanism of regulation by these multifunctional proteins. Furthermore, it explains the strong tendency by members of this family such as simian virus 40 TAg to oligomerize after binding ATP.

PubMed: 15310852
DOI: 10.1073/pnas.0403454101

Experimental method

X-RAY DIFFRACTION (2.1 Å)