Filling out the structural map of the NTF2-like superfamily

BMC Bioinformatics

Ruth Y Eberhardt²  Yuanyuan Chang³  Alex Bateman²  Alexey G Murzin⁴  Herbert L Axelrod⁵  William C Hwang³  L Aravind¹ 

[1] National Center for Biotechnology Information, NLM, NIH, Bethesda, MD, 20814, USA

[2] European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridgeshire, CB10 1SD, UK

[3] Sanford Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA

[4] MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK

[5] Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA

关键词: Protein family;    3D structure;    JCSG;    Ligand-binding;    Protein structure;    Protein function prediction;    NTF2-like superfamily;   

Others  :  1087710
DOI  :  10.1186/1471-2105-14-327

 received in 2013-07-11, accepted in 2013-11-15,  发布年份 2013

【 摘 要 】

Background

The 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.

Results

Here 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.

Conclusions

Our 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).

【 授权许可】

   
2013 Eberhardt et al.; licensee BioMed Central Ltd.

【 图 表 】

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