Sequence, structure and functional diversity of PD-(D/E) XK phosphodiesterase superfamily

K Steczkiewicz, A Muszewska, L Knizewski… - Nucleic acids …, 2012 - academic.oup.com
Proteins belonging to PD-(D/E) XK phosphodiesterases constitute a functionally diverse
superfamily with representatives involved in replication, restriction, DNA repair and tRNA …

[PDF][PDF] Grouping together highly diverged PD-(D/E) XK nucleases and identification of novel superfamily members using structure-guided alignment of sequence …

JM Bujnicki, L Rychlewski - Journal of molecular microbiology and …, 2001 - caister.com
Abstract The PD-(D/E) XK nuclease domains, initially identified in type II restriction enzymes,
serve as models for studying aspects of protein-DNA interactions, mechanisms of …

Realm of PD-(D/E) XK nuclease superfamily revisited: detection of novel families with modified transitive meta profile searches

L Knizewski, LN Kinch, NV Grishin, L Rychlewski… - BMC structural …, 2007 - Springer
Abstract Background PD-(D/E) XK nucleases constitute a large and highly diverse
superfamily of enzymes that display little sequence similarity despite retaining a common …

Identification of new homologs of PD-(D/E) XK nucleases by support vector machines trained on data derived from profile–profile alignments

M Laganeckas, M Margelevičius… - Nucleic acids …, 2011 - academic.oup.com
Abstract PD-(D/E) XK nucleases, initially represented by only Type II restriction enzymes,
now comprise a large and extremely diverse superfamily of proteins. They participate in …

The PD-(D/E) XK superfamily revisited: identification of new members among proteins involved in DNA metabolism and functional predictions for domains of (hitherto) …

J Kosinski, M Feder, JM Bujnicki - BMC bioinformatics, 2005 - Springer
Abstract Background The PD-(D/E) XK nuclease superfamily, initially identified in type II
restriction endonucleases and later in many enzymes involved in DNA recombination and …

The human phosphodiesterase PDE10A gene: Genomic organization and evolutionary relatedness with other PDEs containing GAF domains

K Fujishige, J Kotera, K Yuasa… - European Journal of …, 2000 - Wiley Online Library
PDE10A is a cyclic nucleotide phosphodiesterase (PDE) exhibiting properties of a cAMP
PDE and a cAMP‐inhibited cGMP PDE. The transcripts are specifically expressed in the …

Genomic organization of the human phosphodiesterase PDE11A gene: Evolutionary relatedness with other PDEs containing GAF domains

K Yuasa, Y Kanoh, K Okumura… - European Journal of …, 2001 - Wiley Online Library
PDE11A is a dual‐substrate, cAMP and cGMP, cyclic nucleotide phosphodiesterase (PDE).
Presently four unique variants carrying distinct GAF sequences in the N‐terminal region …

Identification of a new family of putative PD-(D/E) XK nucleases with unusual phylogenomic distribution and a new type of the active site

M Feder, JM Bujnicki - BMC genomics, 2005 - Springer
Background Prediction of structure and function for uncharacterized protein families by
identification of evolutionary links to characterized families and known structures is one of …

The molecular biology of cyclic nucleotide phosphodiesterases

M Conti, SLC Jin - Progress in nucleic acid research and molecular …, 1999 - Elsevier
Recent progress in the field of cyclic nucleotidos has shown that a large array of closely
related proteins is involved in each step of the signal transduction cascade. Nine families of …

Molecular cloning and chromosomal localization of PD-Iβ (PDNP3), a new member of the human phosphodiesterase I genes

P Jin-Hua, JW Goding, H Nakamura, K Sano - Genomics, 1997 - Elsevier
Phosphodiesterase I (EC 3.1. 4.1)/nucleotide pyrophosphatase (EC 3.6. 1.9) enzymes are a
family of type II transmembrane proteins that catalyze the cleavage of phosphodiester and …