The RNase H-like superfamily: new members, comparative structural analysis and evolutionary classification.

Karolina A Majorek,Marcin Nowotny,Krzysztof Ginalski,Kamil Steczkiewicz,Janusz M Bujnicki,Stanislaw Dunin-Horkawicz,Anna Muszewska

doi:10.1093/nar/gkt1414

Karolina A Majorek, Marcin Nowotny + Show 5 more

Open Access

https://doi.org/10.1093/nar/gkt1414

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Abstract

Ribonuclease H-like (RNHL) superfamily, also called the retroviral integrase superfamily, groups together numerous enzymes involved in nucleic acid metabolism and implicated in many biological processes, including replication, homologous recombination, DNA repair, transposition and RNA interference. The RNHL superfamily proteins show extensive divergence of sequences and structures. We conducted database searches to identify members of the RNHL superfamily (including those previously unknown), yielding >60 000 unique domain sequences. Our analysis led to the identification of new RNHL superfamily members, such as RRXRR (PF14239), DUF460 (PF04312, COG2433), DUF3010 (PF11215), DUF429 (PF04250 and COG2410, COG4328, COG4923), DUF1092 (PF06485), COG5558, OrfB_IS605 (PF01385, COG0675) and Peptidase_A17 (PF05380). Based on the clustering analysis we grouped all identified RNHL domain sequences into 152 families. Phylogenetic studies revealed relationships between these families, and suggested a possible history of the evolution of RNHL fold and its active site. Our results revealed clear division of the RNHL superfamily into exonucleases and endonucleases. Structural analyses of features characteristic for particular groups revealed a correlation between the orientation of the C-terminal helix with the exonuclease/endonuclease function and the architecture of the active site. Our analysis provides a comprehensive picture of sequence-structure-function relationships in the RNHL superfamily that may guide functional studies of the previously uncharacterized protein families.

Highlights

The ribonuclease H-like (RNHL) superfamily is a large group of evolutionarily related, but strongly diverged, proteins with different functions
If a region of sequence that initially seemed to be similar to known RNase H-like members displayed significant similarity to another family, known to be unrelated to RNase H, a given family was regarded as a false positive and removed from the list of RNHL superfamily candidates
This step allowed us to determine if potential active site residues were present in positions corresponding to positions of known catalytic residues in the RNHL superfamily

Summary

Introduction

The ribonuclease H-like (RNHL) superfamily is a large group of evolutionarily related, but strongly diverged, proteins with different functions. Similar spatial architecture of the catalytic domain was later identified in other enzymes involved in nucleic acid metabolism, including retroviral integrases and DNA transposases [3], Holliday junction resolvases (HJRs) [4], Piwi/Argonaute nucleases [5,6], numerous exonucleases [7] and Prp: the largest and most highly conserved spliceosomal protein considered to be a master regulator of the spliceosome [8].

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