4XM0

N,N'-diacetylchitobiose deacetylase (SeMet derivative) from Pyrococcus furiosus in the absence of cadmium

Summary for 4XM0

• Entry DOI: 10.2210/pdb4xm0/pdb
• Related: 4XLX 4XM1 4XM2
• Descriptor: Uncharacterized protein, ZINC ION (3 entities in total)
• Functional Keywords: ce-14 deacetylase, metal binding protein
• Biological source: Pyrococcus furiosus
• Total number of polymer chains: 6
• Total formula weight: 188749.49

Authors

Nakamura, T.,Niiyama, M.,Hashimoto, W.,Ida, K.,Uegaki, K. (deposition date: 2015-01-14, release date: 2015-06-10, Last modification date: 2024-11-06)

Primary citation

Nakamura, T.,Niiyama, M.,Hashimoto, W.,Ida, K.,Abe, M.,Morita, J.,Uegaki, K.
Multiple crystal forms of N,N'-diacetylchitobiose deacetylase from Pyrococcus furiosus.
Acta Crystallogr.,Sect.F, 71:657-662, 2015

PubMed Abstract: Native N,N'-diacetylchitobiose deacetylase from Pyrococcus furiosus (Pf-Dac) and its selenomethionine derivative (Se-Pf-Dac) were crystallized and analyzed in the presence and absence of cadmium ion. The four crystal structures fell into three different crystal-packing groups, with the cadmium-free Pf-Dac and Se-Pf-Dac belonging to the same space group, with homologous unit-cell parameters. The crystal structures in the presence of cadmium contained distorted octahedral cadmium complexes coordinated by three chlorides, two O atoms and an S or Se atom from the N-terminal methionine or selenomethionine, respectively. The N-terminal cadmium complex was involved in crystal contacts between symmetry-related molecules through hydrogen bonding to the N-termini. While all six N-termini of Se-Pf-Dac were involved in cadmium-complex formation, only two of the Pf-Dac N-termini participated in complex formation in the Cd-containing crystal, resulting in different crystal forms. These differences are discussed in light of the higher stability of the Cd-Se bond than the Cd-S bond. This work provides an example of the contribution of cadmium towards determining protein crystal quality and packing depending on the use of the native protein or the selenomethionine derivative.

PubMed: 26057790
DOI: 10.1107/S2053230X15005695

Experimental method

X-RAY DIFFRACTION (2.8 Å)