Filling out the structural map of the NTF2-like superfamilyReport as inadecuate

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BMC Bioinformatics

, 14:327

Structural analysis


BackgroundThe NTF2-like superfamily is a versatile group of protein domains sharing a common fold. The sequences of these domains are very diverse and they share no common sequence motif. These domains serve a range of different functions within the proteins in which they are found, including both catalytic and non-catalytic versions. Clues to the function of protein domains belonging to such a diverse superfamily can be gleaned from analysis of the proteins and organisms in which they are found.

ResultsHere we describe three protein domains of unknown function found mainly in bacteria: DUF3828, DUF3887 and DUF4878. Structures of representatives of each of these domains: BT 3511 from Bacteroides thetaiotaomicron strain VPI-5482 PDB:3KZT, Cj0202c from Campylobacter jejuni subsp. jejuni serotype O:2 strain NCTC 11168 PDB:3K7C, rumgna 01855 and RUMGNA 01855 from Ruminococcus gnavus strain ATCC 29149 PDB:4HYZ have been solved by X-ray crystallography. All three domains are similar in structure and all belong to the NTF2-like superfamily. Although the function of these domains remains unknown at present, our analysis enables us to present a hypothesis concerning their role.

ConclusionsOur analysis of these three protein domains suggests a potential non-catalytic ligand-binding role. This may regulate the activities of domains with which they are combined in the same polypeptide or via operonic linkages, such as signaling domains e.g. serine-threonine protein kinase, peptidoglycan-processing hydrolases e.g. NlpC-P60 peptidases or nucleic acid binding domains e.g. Zn-ribbons.

KeywordsNTF2-like superfamily Protein function prediction Protein structure Ligand-binding JCSG 3D structure Protein family Electronic supplementary materialThe online version of this article doi:10.1186-1471-2105-14-327 contains supplementary material, which is available to authorized users.

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Author: Ruth Y Eberhardt - Yuanyuan Chang - Alex Bateman - Alexey G Murzin - Herbert L Axelrod - William C Hwang - L Aravind


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