title: Domain-level rocking motion within a polymerase that translocates on single-stranded nucleic acid.
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.
authors.affiliation: Department of Molecular Biology and Biochemistry, Xinxiang Medical University, Xinxiang, Henan 453003, People's Republic of China.
authors.forename: Huiyung
authors.initials: H
authors.lastname: Li
authors.forename: Changzheng
authors.initials: C
authors.lastname: Li
authors.forename: Sufeng
authors.initials: S
authors.lastname: Zhou
authors.forename: Thomas L
authors.initials: TL
authors.lastname: Poulos
authors.forename: Paul David
authors.initials: PD
authors.lastname: Gershon
mesh_terms: D020134:Catalytic Domain / Q000235:genetics; D018360:Crystallography, X-Ray; D004277:DNA, Single-Stranded / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D008024:Ligands; D056004:Molecular Dynamics Simulation; D009038:Motion; D011062:Polynucleotide Adenylyltransferase / Q000737:chemistry* / Q000235:genetics* / Q000378:metabolism; D055503:Protein Multimerization / Q000235:genetics; D014178:Translocation, Genetic; D014616:Vaccinia virus / Q000201:enzymology* / Q000235:genetics / Q000378:metabolism; D014764:Viral Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism
chemical_list: D004277:DNA, Single-Stranded; D008024:Ligands; C088682:VP39 protein, Vaccinia virus; D014764:Viral Proteins; D011062:Polynucleotide Adenylyltransferase
keywords: VP55; Vaccinia virus poly(A) polymerase; polymerases