PROSITE documentation PDOC50965

NERD domain profile

The nuclease-related domain (NERD) is an about 117-amino acid module found in a broad range of bacterial, as well as single archaeal and plant proteins. The majority of NERD-containing proteins are single-domain, in several cases with additional (predicted) transmembrane helices. In only a few instances, proteins containing NERD domains have additional domains (mostly involved in DNA processing), such as the HRDC, the UvrD/REP helicase, the DNA-binding C4 zinc finger or the serine/threonine and tyrosine protein kinase (see <PDOC00100>). In all cases in which a NERD domain is present in multidomain proteins, it is found at the N terminus. The NERD domain is predicted to be connected to DNA processing and genomic context and distant homology analysis suggest a nuclease function [1].

The NERD sequence is characterized by three conserved regions among weakly conserved or very diverse regions. Conserved hydrophobic, mainly aliphatic motifs (consisting of Leu, Ile and Val) and polar, mainly charged positions (e.g. Asp, His, Glu and Lys) alternate. An interesting feature of NERD domains is the existence of subgroups that have no conservation in motifs that are conserved in all other members of the family or with a charge difference. It has been hypothesized that these differences account for functional diversity within the NERD family. The NERD domain is predicted to have an α-β-β-β-(weak β/long loop)-α-β-β secondary structure [1].

Some proteins known to contain a NERD domain are listed below:

• Bacillus anthracis pXO1-01 protein. It is encoded by the virulence-related pXO1 plasmid.
• Bacteroides spp. orf8 protein.

The profile we developed covers the entire NERD domain.