PDBsum entry 2k9c

Hydrolase

PDB id: 2k9c

Contents

Protein chain

152 a.a.

Metals

_CO

References listed in PDB file

Key reference

Title

Paramagnetic shifts in solid-State nmr of proteins to elicit structural information.

Authors

S.Balayssac, I.Bertini, A.Bhaumik, M.Lelli, C.Luchinat.

Ref.

Proc Natl Acad Sci U S A, 2008, 105, 17284-17289. [DOI no: 10.1073/pnas.0708460105]

PubMed id

18988744

Abstract

The recent observation of pseudocontact shifts (pcs) in (13)C high-resolution solid-state NMR of paramagnetic proteins opens the way to their application as structural restraints. Here, by investigating a microcrystalline sample of cobalt(II)-substituted matrix metalloproteinase 12 [CoMMP-12 (159 AA, 17.5 kDa)], it is shown that a combined strategy of protein labeling and dilution of the paramagnetic species (i.e., (13)C-,(15)N-labeled CoMMP-12 diluted in unlabeled ZnMMP-12, and (13)C-,(15)N-labeled ZnMMP-12 diluted in unlabeled CoMMP-12) allows one to easily separate the pcs contributions originated from the protein internal metal (intramolecular pcs) from those due to the metals in neighboring proteins in the crystal lattice (intermolecular pcs) and that both can be used for structural purposes. It is demonstrated that intramolecular pcs are significant structural restraints helpful in increasing both precision and accuracy of the structure, which is a need in solid-state structural biology nowadays. Furthermore, intermolecular pcs provide unique information on positions and orientations of neighboring protein molecules in the solid phase.

Figure 1.
Representative parts of the PDSD spectra of fully labeled ZnMMP-12 (orange), fully labeled CoMMP-12 (purple), diluted CoMMP-12 (green), and diluted ZnMMP-12 (cyan). (A and C) The peaks of Val-217, which is affected only by intramolecular pcs, and thus the shifts observed in full-labeled samples are analogous to those observed in diluted samples. (B and D) The peaks of Thr-154, which is strongly affected only by intermolecular pcs, and the shifts observed in fully-labeled samples differ from those observed in diluted samples by the intermolecular contributions.

Figure 2.
^13C pcs observed (blue lines) for fully labeled CoMMP-12 (A), diluted CoMMP-12 (B), and diluted ZnMMP-12 (C). The green lines are calculated as the sum of contributions from the internal and external cobalt(II) ions (A), from the internal cobalt(II) ion only (B), and from the external cobalt(II) ions only (C).