Structure of the first representative of Pfam family PF09410 (DUF2006) reveals a structural signature of the calycin superfamily that suggests a role in lipid metabolism

Chiu, H.-J.; Bakolitsa, C.; Skerra, A.; Lomize, A.; Carlton, D.; Miller, M.D.; Krishna, S.S.; Abdubek, P.; Astakhova, T.; Axelrod, H.L.; Clayton, T.; Deller, M.C.; Duan, L.; Feuerhelm, J.; Grant, J.C.; Grzechnik, S.K.; Han, G.W.; Jaroszewski, L.; Jin, K.K.; Klock, H.E.; Knuth, M.W.; Kozbial, P.; Kumar, A.; Marciano, D.; McMullan, D.; Morse, A.T.; Nigoghossian, E.; Okach, L.; Paulsen, J.; Reyes, R.; Rife, C.L.; van den Bedem, H.; Weekes, D.; Xu, Q.; Hodgson, K.O.; Wooley, J.; Elsliger, M.-A.; Deacon, A.M.; Godzik, A.; Lesley, S.A.; Wilson, I.A.

doi:10.1107/S1744309109037749

Figure 3
Similarities and differences between NE1406 and the calycin superfamily. (a) Stereo ribbon diagram of the binding sites for the two buffer molecules 2-(N-cyclohexylamino)ethanesulfonic acid (CHES) and glycerol (GOL). Conserved residues are indicated. (b) NE1406 exhibits the calycin-superfamily structural signature. Stereo ribbon diagram of the N-terminal domain of NE1406 showing the stacked arginine and tryptophan residues characteristic of the calycin fold (Flower et al., 2000

). Hydrogen bonds are indicated by dashed lines. A glycerol molecule (cyan) mediates bonding of Trp50 to the 3₁₀-helix. (c) Ribbon diagrams depicting the front and back view of NE1406 (PDB code 2ich , residues 24–220; gray) superposed with nitrophorin 4 from Rhodnius prolixus (PDB code 1d2u , residues 22–205; red. The heme ligand for nitrophorin 4 is colored cyan. (d) Ribbon diagrams depicting the front and back view of NE1406 (PDB code 2ich , residues 24–220; grey) superposed with avidin from Gallus gallus (PDB code 1avd , residues 3–125; pink). The Trp-Arg signatures are represented as sticks. The biotin ligand for avidin is shown in cyan.

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ISSN: 2053-230X

Volume 66| Part 10| December 2010| Pages 1153-1159

doi:10.1107/S1744309109037749

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