Structural and sequencing analysis of local target DNA recognition by MLV integrase

Target-site selection by retroviral integrase (IN) proteins profoundly affects viral pathogenesis. We describe the solution nuclear magnetic resonance structure of the Moloney murine leukemia virus IN (M-MLV) C-terminal domain (CTD) and a structural homology model of the catalytic core domain (CCD)....

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Main Authors:	Aiyer, Sriram, Rossi, Paolo, Malani, Nirav, Schneider, William M., Chandar, Ashwin, Bushman, Frederic D., Montelione, Gaetano T., Roth, Monica J.
Format:	Online
Language:	English
Published:	Oxford University Press 2015
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4477651/

id	pubmed-4477651
recordtype	oai_dc
spelling	pubmed-44776512015-06-29 Structural and sequencing analysis of local target DNA recognition by MLV integrase Aiyer, Sriram Rossi, Paolo Malani, Nirav Schneider, William M. Chandar, Ashwin Bushman, Frederic D. Montelione, Gaetano T. Roth, Monica J. Structural Biology Target-site selection by retroviral integrase (IN) proteins profoundly affects viral pathogenesis. We describe the solution nuclear magnetic resonance structure of the Moloney murine leukemia virus IN (M-MLV) C-terminal domain (CTD) and a structural homology model of the catalytic core domain (CCD). In solution, the isolated MLV IN CTD adopts an SH3 domain fold flanked by a C-terminal unstructured tail. We generated a concordant MLV IN CCD structural model using SWISS-MODEL, MMM-tree and I-TASSER. Using the X-ray crystal structure of the prototype foamy virus IN target capture complex together with our MLV domain structures, residues within the CCD α2 helical region and the CTD β1-β2 loop were predicted to bind target DNA. The role of these residues was analyzed in vivo through point mutants and motif interchanges. Viable viruses with substitutions at the IN CCD α2 helical region and the CTD β1-β2 loop were tested for effects on integration target site selection. Next-generation sequencing and analysis of integration target sequences indicate that the CCD α2 helical region, in particular P187, interacts with the sequences distal to the scissile bonds whereas the CTD β1-β2 loop binds to residues proximal to it. These findings validate our structural model and disclose IN-DNA interactions relevant to target site selection. Oxford University Press 2015-06-23 2015-05-12 /pmc/articles/PMC4477651/ /pubmed/25969444 http://dx.doi.org/10.1093/nar/gkv410 Text en © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Aiyer, Sriram Rossi, Paolo Malani, Nirav Schneider, William M. Chandar, Ashwin Bushman, Frederic D. Montelione, Gaetano T. Roth, Monica J.
spellingShingle	Aiyer, Sriram Rossi, Paolo Malani, Nirav Schneider, William M. Chandar, Ashwin Bushman, Frederic D. Montelione, Gaetano T. Roth, Monica J. Structural and sequencing analysis of local target DNA recognition by MLV integrase
author_facet	Aiyer, Sriram Rossi, Paolo Malani, Nirav Schneider, William M. Chandar, Ashwin Bushman, Frederic D. Montelione, Gaetano T. Roth, Monica J.
author_sort	Aiyer, Sriram
title	Structural and sequencing analysis of local target DNA recognition by MLV integrase
title_short	Structural and sequencing analysis of local target DNA recognition by MLV integrase
title_full	Structural and sequencing analysis of local target DNA recognition by MLV integrase
title_fullStr	Structural and sequencing analysis of local target DNA recognition by MLV integrase
title_full_unstemmed	Structural and sequencing analysis of local target DNA recognition by MLV integrase
title_sort	structural and sequencing analysis of local target dna recognition by mlv integrase
description	Target-site selection by retroviral integrase (IN) proteins profoundly affects viral pathogenesis. We describe the solution nuclear magnetic resonance structure of the Moloney murine leukemia virus IN (M-MLV) C-terminal domain (CTD) and a structural homology model of the catalytic core domain (CCD). In solution, the isolated MLV IN CTD adopts an SH3 domain fold flanked by a C-terminal unstructured tail. We generated a concordant MLV IN CCD structural model using SWISS-MODEL, MMM-tree and I-TASSER. Using the X-ray crystal structure of the prototype foamy virus IN target capture complex together with our MLV domain structures, residues within the CCD α2 helical region and the CTD β1-β2 loop were predicted to bind target DNA. The role of these residues was analyzed in vivo through point mutants and motif interchanges. Viable viruses with substitutions at the IN CCD α2 helical region and the CTD β1-β2 loop were tested for effects on integration target site selection. Next-generation sequencing and analysis of integration target sequences indicate that the CCD α2 helical region, in particular P187, interacts with the sequences distal to the scissile bonds whereas the CTD β1-β2 loop binds to residues proximal to it. These findings validate our structural model and disclose IN-DNA interactions relevant to target site selection.
publisher	Oxford University Press
publishDate	2015
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4477651/
_version_	1613239199955156992

Structural and sequencing analysis of local target DNA recognition by MLV integrase

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