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Domain-level rocking motion within a polymerase that translocates on single-stranded nucleic acid.
- Source :
-
Acta crystallographica. Section D, Biological crystallography [Acta Crystallogr D Biol Crystallogr] 2013 Apr; Vol. 69 (Pt 4), pp. 617-24. Date of Electronic Publication: 2013 Mar 14. - Publication Year :
- 2013
-
Abstract
- Vaccinia virus poly(A) polymerase (VP55) is the only known polymerase that can translocate independently with respect to single-stranded nucleic acid (ssNA). Previously, its structure has only been solved in the context of the VP39 processivity factor. Here, a crystal structure of unliganded monomeric VP55 has been solved to 2.86 Å resolution, showing the first backbone structural isoforms among either VP55 or its processivity factor (VP39). Backbone differences between the two molecules of VP55 in the asymmetric unit indicated that unliganded monomeric VP55 can undergo a `rocking' motion of the N-terminal domain with respect to the other two domains, which may be `rigidified' upon VP39 docking. This observation is consistent with previously demonstrated experimental molecular dynamics of the monomer during translocation with respect to nucleic acid and with different mechanisms of translocation in the presence and absence of processivity factor VP39. Side-chain conformational changes in the absence of ligand were observed at a key primer contact site and at the catalytic center of VP55. The current structure completes the trio of possible structural forms for VP55 and VP39, namely the VP39 monomer, the VP39-VP55 heterodimer and the VP55 monomer.
- Subjects :
- Crystallography, X-Ray
DNA, Single-Stranded genetics
DNA, Single-Stranded metabolism
Ligands
Molecular Dynamics Simulation
Polynucleotide Adenylyltransferase metabolism
Protein Multimerization genetics
Vaccinia virus genetics
Vaccinia virus metabolism
Viral Proteins genetics
Viral Proteins metabolism
Catalytic Domain genetics
DNA, Single-Stranded chemistry
Motion
Polynucleotide Adenylyltransferase chemistry
Polynucleotide Adenylyltransferase genetics
Translocation, Genetic
Vaccinia virus enzymology
Viral Proteins chemistry
Subjects
Details
- Language :
- English
- ISSN :
- 1399-0047
- Volume :
- 69
- Issue :
- Pt 4
- Database :
- MEDLINE
- Journal :
- Acta crystallographica. Section D, Biological crystallography
- Publication Type :
- Academic Journal
- Accession number :
- 23519670
- Full Text :
- https://doi.org/10.1107/S0907444913000346