title: Crystal structure of a [NiFe] hydrogenase maturation protease HybD from Thermococcus kodakarensis KOD1.
abstract: A [NiFe] hydrogenase maturation protease HybD from Thermococcus kodakarensis KOD1 (TkHybD) is involved in the cleavage of the C-terminal residues of [NiFe] hydrogenase large subunits by Ni recognition. Here, we report the crystal structure of TkHybD at 1.82 Å resolution to better understand this process. TkHybD exhibits an α/β/α sandwich fold with conserved residues responsible for the Ni recognition. Comparisons of TkHybD with homologous proteins also reveal that they share a common overall architecture, suggesting that they have similar catalytic functions. Our results including metal binding site prediction provide insight into the substrate recognition and catalysis mechanism of TkHybD. Proteins 2016; 84:1321-1327. © 2016 Wiley Periodicals, Inc.
authors.affiliation: Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-Ku, Kyoto, 606-8502, Japan.
authors.forename: Sunghark
authors.initials: S
authors.lastname: Kwon
authors.affiliation: Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-Ku, Kyoto, 606-8502, Japan.
authors.forename: Yuichi
authors.initials: Y
authors.lastname: Nishitani
authors.affiliation: Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-Ku, Sendai, 980-8577, Japan.
authors.forename: Satoshi
authors.initials: S
authors.lastname: Watanabe
authors.affiliation: Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-Ku, Kyoto, 615-8510, Japan.
authors.forename: Yoshinori
authors.initials: Y
authors.lastname: Hirao
authors.affiliation: Research Organization of Science and Technology, Ritsumeikan University, Kusatsu, 525-8577, Japan.
authors.forename: Tadayuki
authors.initials: T
authors.lastname: Imanaka
authors.affiliation: Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-Ku, Kyoto, 615-8510, Japan.|Japan Science and Technology Agency, CREST, 7, Gobancho, Chiyoda-Ku, Tokyo, 102-0076, Japan.
authors.forename: Tamotsu
authors.initials: T
authors.lastname: Kanai
authors.affiliation: Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-Ku, Kyoto, 615-8510, Japan.|Japan Science and Technology Agency, CREST, 7, Gobancho, Chiyoda-Ku, Tokyo, 102-0076, Japan.
authors.forename: Haruyuki
authors.initials: H
authors.lastname: Atomi
authors.affiliation: Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-Ku, Kyoto, 606-8502, Japan.|Japan Science and Technology Agency, CREST, 7, Gobancho, Chiyoda-Ku, Tokyo, 102-0076, Japan.
authors.forename: Kunio
authors.initials: K
authors.lastname: Miki
mesh_terms: D000595:Amino Acid Sequence; D019843:Archaeal Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D001665:Binding Sites; D020134:Catalytic Domain; D003001:Cloning, Molecular; D017124:Conserved Sequence; D018360:Crystallography, X-Ray; D010450:Endopeptidases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D015870:Gene Expression; D006864:Hydrogenase / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D008958:Models, Molecular; D009532:Nickel / Q000737:chemistry / Q000378:metabolism; D011485:Protein Binding; D054730:Protein Interaction Domains and Motifs; D017433:Protein Structure, Secondary; D021122:Protein Subunits / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D011994:Recombinant Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D016415:Sequence Alignment; D040681:Structural Homology, Protein; D019712:Thermococcus / Q000737:chemistry* / Q000201:enzymology
chemical_list: D019843:Archaeal Proteins; D021122:Protein Subunits; D011994:Recombinant Proteins; D009532:Nickel; C043296:nickel-iron hydrogenase; D006864:Hydrogenase; D010450:Endopeptidases; C119558:hydrogenase maturating endopeptidase HYBD
keywords: C-terminal cleavage; Ni binding; hyperthermophilic archaea; protease; substrate recognition