Multiple crystal forms of N,N′-diacetylchitobiose deacetylase from Pyrococcus furiosus

• Published in: Acta crystallographica. Section F, Structural biology communications Vol. 71; no. 6; pp. 657 - 662
• Main Authors: Nakamura, Tsutomu, Niiyama, Mayumi, Hashimoto, Wakana, Ida, Kurumi, Abe, Manabu, Morita, Junji, Uegaki, Koichi
• Format: Journal Article
• Language: English
• Published: 5 Abbey Square, Chester, Cheshire CH1 2HU, England International Union of Crystallography 01.06.2015; Wiley Subscription Services, Inc
• Subjects: Amidohydrolases - chemistry; Amidohydrolases - genetics; Archaeal Proteins - chemistry; Archaeal Proteins - genetics; Cadmium; Cadmium - chemistry; cadmium complex; Cations, Divalent; Crystal structure; crystal-packing interaction; Crystallization; Crystallography, X-Ray; Diffraction; Disaccharides - chemistry; Escherichia coli - genetics; Escherichia coli - metabolism; Gene Expression; Hydrogen Bonding; Models, Molecular; N,N′‐diacetylchitobiose deacetylase; N′-diacetylchitobiose deacetylase; Pyrococcus furiosus - chemistry; Pyrococcus furiosus - enzymology; Recombinant Proteins - chemistry; Recombinant Proteins - genetics; Research Communications; Selenium - chemistry; selenomethionine; Selenomethionine - chemistry; Static Electricity; Sulfur - chemistry; cadmium complex; selenomethionine; N,N′-diacetylchitobiose deacetylase; crystal-packing interaction
• ISSN: 2053-230X; 2053-230X
• DOI: 10.1107/S2053230X15005695

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.