Identification and characterization of a new HNH restriction endonuclease with unusual properties

Santoshi, M and Engleng, B and Eligar, SM and Ratnakar, IS and Nagamalleshwari, E and Nagaraja, V (2023) Identification and characterization of a new HNH restriction endonuclease with unusual properties. In: Applied Microbiology and Biotechnology, 107 (20). 6263 -6275.

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Abstract

Restriction–modification (R-M) systems form a large superfamily constituting bacterial innate immunity mechanism. The restriction endonucleases (REases) are very diverse in subunit structure, DNA recognition, co-factor requirement, and mechanism of action. Among the different catalytic motifs, HNH active sites containing REases are the second largest group distinguished by the presence of the ββα-metal finger fold. KpnI is the first member of the HNH-family REases whose homologs are present in many bacteria of Enterobacteriaceae having varied degrees of sequence similarity between them. Considering that the homologs with a high similarity may have retained KpnI-like properties, while those with a low similarity could be different, we have characterized a distant KpnI homolog present in a pathogenic Klebsiella pneumoniae NTUH K2044. A comparison of the properties of KpnI and KpnK revealed that despite their similarity and the HNH motif, these two enzymes have different properties viz oligomerization, cleavage pattern, metal ion requirement, recognition sequence, and sequence specificity. Unlike KpnI, KpnK is a monomer in solution, nicks double-stranded DNA, recognizes degenerate sequence, and catalyses the degradation of DNA into smaller products after the initial cleavage at preferred sites. Due to several distinctive properties, it can be classified as a variant of the Type IIS enzyme having nicking endonuclease activity. Key points: • KpnK is a distant homolog of KpnI and belongs to the ββα-metal finger superfamily. • Both KpnI and KpnK have widespread occurrence in K. pneumoniae strains. • KpnK is a Type IIS restriction endonuclease with a single-strand nicking property. © 2023, The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.

Item Type:	Journal Article
Publication:	Applied Microbiology and Biotechnology
Publisher:	Springer Science and Business Media Deutschland GmbH
Additional Information:	The copyright for this article belongs to the Springer Science and Business Media Deutschland GmbH.
Keywords:	Bacteria; Enzymes; Metal ions, Active site; HNH active site; Immunity mechanism; Innate immunity; Klebsiella pneumoniae; Nicking endonuclease; Property; Restriction endonucleases; Restriction-modification systems; Type IIS restriction endonuclease, DNA
Department/Centre:	Division of Biological Sciences > Microbiology & Cell Biology
Date Deposited:	05 Nov 2023 05:34
Last Modified:	05 Nov 2023 05:34
URI:	https://eprints.iisc.ac.in/id/eprint/83089

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