1XYD

NMR Solution Structure of Rat Zinc-Calcium-S100B, 20 Structures

Summary for 1XYD

• Entry DOI: 10.2210/pdb1xyd/pdb
• Related: 1B4C 1DT7 1MWN 1ODB 1QLK 3PSR
• Descriptor: S-100 protein, beta chain, CALCIUM ION, ZINC ION (3 entities in total)
• Functional Keywords: metal binding protein
• Biological source: Rattus norvegicus (Norway rat)
• Cellular location: Cytoplasm (By similarity): P04631
• Total number of polymer chains: 2
• Total formula weight: 21807.23

Authors

Wilder, P.T.,Varney, K.M.,Weber, D.J. (deposition date: 2004-11-09, release date: 2005-06-07, Last modification date: 2024-05-22)

Primary citation

Wilder, P.T.,Varney, K.M.,Weiss, M.B.,Gitti, R.K.,Weber, D.J.
Solution Structure of Zinc- and Calcium-Bound Rat S100B as Determined by Nuclear Magnetic Resonance Spectroscopy
Biochemistry, 44:5690-5702, 2005

PubMed Abstract: The EF-hand calcium-binding protein S100B also binds one zinc ion per subunit with a relatively high affinity (K(d) approximately 90 nM) [Wilder et al., (2003) Biochemistry 42, 13410-13421]. In this study, the structural characterization of zinc binding to calcium-loaded S100B was examined using high-resolution NMR techniques, including structural characterization of this complex in solution at atomic resolution. As with other S100 protein structures, the quaternary structure of Zn(2+)-Ca(2+)-bound S100B was found to be dimeric with helices H1, H1', H4, and H4' forming an X-type four-helix bundle at the dimer interface. NMR data together with mutational analyses are consistent with Zn(2+) coordination arising from His-15 and His-25 of one S100B subunit and from His-85 and Glu-89 of the other subunit. The addition of Zn(2+) was also found to extend helices H4 and H4' three to four residues similar to what was previously observed with the binding of target proteins to S100B. Furthermore, a kink in helix 4 was observed in Zn(2+)-Ca(2+)-bound S100B that is not in Ca(2+)-bound S100B. These structural changes upon Zn(2+)-binding could explain the 5-fold increase in affinity that Zn(2+)-Ca(2+)-bound S100B has for peptide targets such as the TRTK peptide versus Ca(2+)-bound S100B. There are also changes in the relative positioning of the two EF-hand calcium-binding domains and the respective helices comprising these EF-hands. Changes in conformation such as these could contribute to the order of magnitude higher affinity that S100B has for calcium in the presence of Zn(2+).

PubMed: 15823027
DOI: 10.1021/bi0475830

Experimental method

SOLUTION NMR