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Structure and computational analysis of a novel protein with metallopeptidase-like and circularly permuted winged-helix-turn-helix domains reveals a possible role in modified polysaccharide biosynthesis

Debanu Das, Alexey G Murzin, Neil D Rawlings, Robert D Finn, Penelope Coggill, Alex Bateman, Adam Godzik, L Aravind
2014 BMC Bioinformatics  
Recent Work Title Structure and computational analysis of a novel protein with metallopeptidase-like and circularly permuted winged-helix-turn-helix domains reveals a possible role in modified polysaccharide  ...  The structure revealed two extra domains: an α+β domain inserted in the metallopeptidase-like domain and a C-terminal circularly permuted winged-helix-turn-helix domain.  ...  Acknowledgements We are grateful to the Sanford Burnham Medical Research Institute and University of California, San Diego, for hosting the DUF Annotation Jamboree in June 2013, which allowed the authors  ... 
doi:10.1186/1471-2105-15-75 pmid:24646163 pmcid:PMC4000134 fatcat:jfh5gbwpefgr3d6axtopuhexj4

Jumbo Phages: A Comparative Genomic Overview of Core Functions and Adaptions for Biological Conflicts

Lakshminarayan M. Iyer, Vivek Anantharaman, Arunkumar Krishnan, A. Maxwell Burroughs, L. Aravind
2021 Viruses  
Leveraging sensitive sequence analysis methods, we identify novel protein-modifying enzymes that might help hijack the host-machinery.  ...  These findings also suggest that several jumbo phage proteins provide a snapshot of the systems found in ancient replicons preceding the last universal ancestor of cellular life.  ...  Data Availability Statement: The data presented in this study are available in Supplementary Materials. Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/v13010063 pmid:33466489 pmcid:PMC7824862 fatcat:vkmtfadkpzem7g2bgnntb7hxxa

Apprehending the NAD+–ADPr-Dependent Systems in the Virus World

Lakshminarayan M. Iyer, A. Maxwell Burroughs, Vivek Anantharaman, L. Aravind
2022 Viruses  
Contextual analysis indicates that the bacteriophage versions of ADPr-targeting domains are more likely to counter soluble ADPr derivatives, while the eukaryotic RNA viral versions might prefer macromolecular  ...  and deployed during infection to modify host macromolecules and counter NAD+-derived signals involved in viral restriction.  ...  These gene neighborhoods sometimes also code for a helix-turnhelix (HTH) domain transcription factor or a zincin-like metallopeptidase.  ... 
doi:10.3390/v14091977 pmid:36146784 pmcid:PMC9503650 fatcat:yiymzg6nsbfujfjqmrhtlttcy4