1IK7

Crystal Structure of the Uncomplexed Pelle Death Domain

Summary for 1IK7

• Entry DOI: 10.2210/pdb1ik7/pdb
• Related: 1D2Z
• Descriptor: PROBABLE SERINE/THREONINE-PROTEIN KINASE Pelle, 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, (4S)-2-METHYL-2,4-PENTANEDIOL, ... (4 entities in total)
• Functional Keywords: single helix, mpd crystallization, structural transition, transferase
• Biological source: Drosophila melanogaster (fruit fly)
• Cellular location: Cell membrane: Q05652
• Total number of polymer chains: 2
• Total formula weight: 25499.43

Authors

Xiao, T.,Gardner, K.H.,Sprang, S.R. (deposition date: 2001-05-02, release date: 2002-07-31, Last modification date: 2024-02-07)

Primary citation

Xiao, T.,Gardner, K.H.,Sprang, S.R.
Cosolvent-induced transformation of a death domain tertiary structure
Proc.Natl.Acad.Sci.USA, 99:11151-11156, 2002

PubMed Abstract: The death domain (DD) of the protein kinase Pelle adopts a six-helix bundle fold in the crystal structure of the complex with its dimerization partner, Tube-DD. However, in crystals obtained from a solution of 45% 2-methyl-2,4-pentanediol (MPD), the C-terminal half of Pelle-DD folds into a single helix, and the N-terminal half of the molecule is disordered. The helical segment forms an antiparallel dimer with the corresponding helix of a symmetry-related molecule, and together they form extensive lattice interactions similar in number, composition, and buried surface to those in the six-helix bundle of the native fold. Secondary structure analysis by heteronuclear nuclear magnetic resonance spectroscopy (NMR) demonstrates that Pelle-DD adopts a six-helix bundle fold in aqueous solution. The fold is perturbed by MPD, with the largest chemical shift changes in one helix and two loop regions that encompass the Tube-DD binding site. Pelle-DD is stable to urea denaturation with a folding free energy of 7.9 kcal/mol at 25 degrees C but is destabilized, with loss of urea binding sites, in the presence of MPD. The data are consistent with a cosolvent denaturation model in which MPD denatures the N terminus of Pelle-DD but induces the C terminus to form a more compact structure and aggregate. A similar perturbation in vivo might occur at the plasma membrane and could have consequences for Pelle-mediated regulation. Generally, crystallographers should be aware that high concentrations of MPD or related cosolvents can alter the tertiary structure of susceptible proteins.

PubMed: 12177432
DOI: 10.1073/pnas.172188399

Experimental method

X-RAY DIFFRACTION (2.3 Å)