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. 2010 Oct 1;66(Pt 10):1148-52.
doi: 10.1107/S1744309110001685. Epub 2010 Mar 5.

DUFs: families in search of function

Alex Bateman  1 , Penny Coggill, Robert D Finn
Affiliations

DUFs: families in search of function

Alex Bateman et al. Acta Crystallogr Sect F Struct Biol Cryst Commun. .

Abstract

Domains of unknown function (DUFs) are a large set of uncharacterized protein families that are found in the Pfam database. Here, the scale and growth of functionally uncharacterized families in biological databases are surveyed and the prospects for discovering their function are examined. In particular, the important role that structural genomics can play in identifying potential function is evaluated.

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Figures

Figure 1
Figure 1
(a) The EAL domain (PF00563, magenta) from PDB entry 2bas (Minasov et al., 2009 ▶), formerly known as DUF2, is now known to function as a cyclic diguanylate-specific phosphodiesterase enzyme. The structure of the associated C-terminal domain YkuI_C (PF10388) is coloured gold. (b) The GGDEF domain (in green) from PDB entry 1w25 (Chan et al., 2004 ▶), formerly known as DUF1, is now known to function as a diguanylate cyclase enzyme. There are two copies of the response regulator receiver domain (PF00072, red) found at the N-terminus of each monomer within the dimeric structure. Figs. 1 and 4 were produced using OpenAstexViewer 3.0 (Hartshorn, 2002 ▶).
Figure 2
Figure 2
A graph showing the growth of DUFs as a percentage of all families added to Pfam at the time of release 23.0.
Figure 3
Figure 3
Venn diagrams showing (a) the distribution of DUF families (including Pfam UPFs) in different kingdoms and (b) the distribution of all other Pfam families in different kingdoms.
Figure 4
Figure 4
TM841 protein binding to palmitate (represented as sticks) from PDB entry 1mgp. The protein–ligand interaction interface is represented as a semi-transparent grey surface.
See this image and copyright information in PMC

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