The crystal structure of DynF from the dynemicin-biosynthesis pathway of Micromonospora chersina

Kosgei, A.J.; Miller, M.D.; Bhardwaj, M.; Xu, W.; Thorson, J.S.; Van Lanen, S.G.; Phillips, G.N.

doi:10.1107/S2053230X21012322

Figure 3
Structure of DynF. (a) A ribbon diagram of the crystal structure of DynF (PDB entry 6ubl) viewed down its noncrystallogaphic twofold axis. The ligand is represented as spheres embedded in the DynF β-barrels. Each protomer of DynF comprises an eight-stranded antiparallel β-barrel connected by loops and two helical segments. Strands 4, 5, 6 and 7 are interrupted by dimerization interactions. This figure was generated in PyMOL (version 2.4.1; Schrödinger). (b) A topology diagram of DynF generated using TopDraw (Bond, 2003

) shows that each strand is connected to its next neighbor, as is typical of most eight-stranded antiparallel β-barrel structures. (c) The final 2mF_o − mF_c map (contoured at 1 r.m.s.d) in blue with ±3 r.m.s.d. contours of the polder omit map in green/red represented in Coot. The green positive difference density clearly shows the location of the bound ligand (palmitic acid) that was omitted from the model phases for the polder map calculation. (d) The ligand in the DynF structure is surrounded by hydrophobic amino-acid groups, except for residues that interact with the carboxylic group at one end of the palmitic acid. This figure was generated with the FLEV (Flatland Ligand Environment View) tool in Coot.

STRUCTURAL BIOLOGY
COMMUNICATIONS

ISSN: 2053-230X

Volume 78| Part 1| January 2022| Pages 1-7

https://doi.org/10.1107/S2053230X21012322

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