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. 2009 Apr;75(1):264-71.
doi: 10.1002/prot.22338.

Crystal structure of the Fic (Filamentation induced by cAMP) family protein SO4266 (gi|24375750) from Shewanella oneidensis MR-1 at 1.6 A resolution

Debanu Das  1 , S Sri Krishna, Daniel McMullan, Mitchell D Miller, Qingping Xu, Polat Abdubek, Claire Acosta, Tamara Astakhova, Herbert L Axelrod, Prasad Burra, Dennis Carlton, Hsiu-Ju Chiu, Thomas Clayton, Marc C Deller, Lian Duan, Ylva Elias, Marc-André Elsliger, Dustin Ernst, Julie Feuerhelm, Anna Grzechnik, Slawomir K Grzechnik, Joanna Hale, Gye Won Han, Lukasz Jaroszewski, Kevin K Jin, Heath E Klock, Mark W Knuth, Piotr Kozbial, Abhinav Kumar, David Marciano, Andrew T Morse, Kevin D Murphy, Edward Nigoghossian, Linda Okach, Silvya Oommachen, Jessica Paulsen, Ron Reyes, Christopher L Rife, Natasha Sefcovic, Henry Tien, Christine B Trame, Christina V Trout, Henry van den Bedem, Dana Weekes, Aprilfawn White, Keith O Hodgson, John Wooley, Ashley M Deacon, Adam Godzik, Scott A Lesley, Ian A Wilson
Affiliations

Crystal structure of the Fic (Filamentation induced by cAMP) family protein SO4266 (gi|24375750) from Shewanella oneidensis MR-1 at 1.6 A resolution

Debanu Das et al. Proteins. 2009 Apr.
No abstract available

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Figures

Figure 1
Figure 1
A) Stereo representation of the crystal structure of the chain A monomer of the SO4266 protein. The peptide modeled as `MEWQ' corresponds to residues 1-4 of the crystallographic symmetry-related B chain and is shown in ball-and-stick. B) Diagram showing the secondary structure elements of SO4266 superimposed on the primary amino acid sequence. The helices, β-strands, γ-turns, and β-turns are indicated. The β-hairpins are indicated as red loops. Residues absent from the monomer A (G0, M1, Q344, S345, A371 and L372) are indicated by lack of a secondary structure trace.
Figure 2
Figure 2
The monomers of SO4266 assume a closed fist-like shape, with a back-to-back association of the monomers forming a “transcription factor-like” dimer. The core of the Fic domain is made up of residues 100-290 (magenta), with a long, mostly α-helical insert region at the N-terminus (residues 1-100; blue) that is involved in dimerization. Residues 290-370 of the C-terminus form a winged helix-turn-helix (wHTH) DNA-binding domain (green) similar to that seen in several transcriptional regulators (e.g. PDB id 2d1h). The peptide `MEWQ' bound to chain A that corresponds to residues 1-4 of the crystallographic symmetry-related B chain is shown (yellow).
Figure 3
Figure 3
A) Superimposition of the SO4266 monomers (magenta and green) with the Fic family proteins from Neisseria meningitidis (194 residues, 2g03, yellow), Helicobacter pylori (201 residues, 2f6s, grey) and Bacteroides thetaiotaomicron vpi-5482 (262 residues, 3cuc, blue), reveal the similarity in their structures despite the absence of the C-terminal domain of SO4266 (green) in the other Fic proteins. They align on SO4266 with RMSDs of 3.1 Å, 3.2 Å and 2.8 Å, Z-scores of 10.5, 10.4 and 18.5 (DaliLite), and sequence identities of 12%, 14% and 16%, respectively. The peptide is shown (yellow ball-and-stick). B) The structure of the H. pylori Fic protein (grey) contains a zinc ion (grey) interacting with His 96 of the conserved HPFXXGNG motif. In the structure of SO4266 (magenta), the tryptophan residue of the peptide (yellow ball-and-stick) partially overlaps with the location of the Zn2+ ion and it is unlikely that the protein can bind metal and the peptide at the same time (grey).
Figure 4
Figure 4
A) Density modified electron density map from experimental phases at 1.0 σ with the N-terminal B1-B4 peptide sequence `MEWQ' (yellow) modeled near the HPFXXGNG motif (cyan) in SO4266, with the tryptophan facing and within interaction distance to His198. B) A surface rendering of the most prominent cleft in SO4266, with the B1-B4 peptide shown (`MEWQ', yellow). The rest of the peptide is close to residues 143-148 of chain A, which forms part of a β-hairpin between helices H6 and H7. This region of the protein forms a lid over the binding cleft. In addition to this lid, the binding cleft is situated between helices H8, H9, and H11. The green region corresponds to Thr248, Leu244, Tyr241, Leu145, Tyr155, and Leu245 that are proximal to the other extra electron density that was modeled as a PGE molecule from the crystallization condition.
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