Crystal Structure of the Shrimp Proliferating Cell Nuclear Antigen: Structural Complementarity with WSSV DNA Polymerase PIP-Box

Abstract

DNA replication requires processivity factors that allow replicative DNA polymerases to extend long stretches of DNA. Some DNA viruses encode their own replicative DNA polymerase, such as the white spot syndrome virus (WSSV) that infects decapod crustaceans but still require host replication accessory factors. We have determined by X-ray diffraction the three-dimensional structure of the Pacific white leg shrimp Litopenaeus vannamei Proliferating Cell Nuclear Antigen (LvPCNA). This protein is a member of the sliding clamp family of proteins, that binds DNA replication and DNA repair proteins through a motif called PIP-box (PCNA-Interacting Protein). The crystal structure of LvPCNA was refined to a resolution of 3 Å, and allowed us to determine the trimeric protein assembly and details of the interactions between PCNA and the DNA. To address the possible interaction between LvPCNA and the viral DNA polymerase, we docked a theoretical model of a PIP-box peptide from the WSSV DNA polymerase within LvPCNA crystal structure. The theoretical model depicts a feasible model of interaction between both proteins. The crystal structure of shrimp PCNA allows us to further understand the mechanisms of DNA replication processivity factors in non-model systems.

Novel transcriptome assembly and improved annotation of the whiteleg shrimp (Litopenaeus vannamei), a dominant crustacean in global seafood mariculture

“…Figure 3 shows an example of this analysis denoting the transcripts identified by our study involved in DNA replication. The protein products of several of these transcripts are required for White Spot Syndrome Virus (WSSV) replication 21 and offer potential targets for interference with the pathogen's replication cycle 22 . An additional 337 pathways with shrimp orthologs represented in our transcriptome highlighted are available from the authors.…”

Molecular Mechanisms of White Spot Syndrome Virus Infection and Perspectives on Treatments

“…This motif is present on WSSV DNA polymerase [ 157 ]. To investigate the possibility of interaction with a host processivity factor in L. vannamei , the 3D structure of Proliferating Cell Nuclear Antigen (LvPCNA) was elucidated [ 104 , 158 ]. Likely PIP-box interaction models between LvPCNA and WSSV DNA polymerase were established but have yet to be confirmed experimentally.…”

Structure of the sliding clamp from the fungal pathogen Aspergillus fumigatus (AfumPCNA) and interactions with Human p21

“…The AfumPCNA data were processed in space group P2 1 using iMosflm and solved by molecular replacement using phaserMR with a homology model built using chainsaw . The Litopenaeus vannamei PCNA crystal structure (PDB: http://www.rcsb.org/pdb/search/structidSearch.do?structureId=4CS5) was used as a template for the homology model. The structure was refined by iterations of manual rebuilding using Coot and refinement using phenix.refine .…”