Filling out the structural map of the NTF2-like superfamily.
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).
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK. re3@sanger.ac.uk.
Ruth Y
RY
Eberhardt
Yuanyuan
Y
Chang
Alex
A
Bateman
Alexey G
AG
Murzin
Herbert L
HL
Axelrod
William C
WC
Hwang
L
L
Aravind
D001426:Bacterial Proteins / Q000737:chemistry*; D001439:Bacteroides / Q000737:chemistry; D016123:Campylobacter jejuni / Q000737:chemistry; D020134:Catalytic Domain; D018360:Crystallography, X-Ray; D008024:Ligands; D029543:Nucleocytoplasmic Transport Proteins / Q000737:chemistry*; D010449:Peptide Mapping / Q000379:methods*; D017510:Protein Folding; D055503:Protein Multimerization; D017434:Protein Structure, Tertiary; D045857:Ruminococcus / Q000737:chemistry
D001426:Bacterial Proteins; D008024:Ligands; D029543:Nucleocytoplasmic Transport Proteins