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An ancestral nuclear protein assembly: Crystal structure of the Methanopyrus kandleri histone

¹ Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1570, USA
² UCLA–DOE Laboratory of Structural Biology and Molecular Medicine, University of California, Los Angeles, California 90095-1570, USA
³ Molecular Biology Institute, University of California, Los Angeles, California 90095-1570, USA
⁴ Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California 90095-1570, USA
⁵ M.M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, RAS, Moscow, Russia
⁶ Fidelity Systems, Inc., Gaithersburg, Maryland 20876, USA

Reprint requests to: Dr. James A Lake, Molecular Biology Institute, University of California, Los Angeles, Box 951570, CA 90095-1570, USA; e-mail: lake{at}mbi.ucla.edu; fax: (310) 206-7286.

Eukaryotic histone proteins condense DNA into compact structures called nucleosomes. Nucleosomes were viewed as a distinguishing feature of eukaryotes prior to ideication of histone orthologs in methanogens. Although evolutionarily distinct from methanogens, the methane-producing hyperthermophile Methanopyrus kandleri produces a novel, 154-residue histone (HMk). Amino acid sequence comparisons show that HMk differs from both methanogenic and eukaryotic histones, in that it contains two histone-fold ms within a single chain. The two HMk histone-fold ms, N and C terminal, are 28% identical in amino acid sequence to each other and 21% identical in amino acid sequence to other histone proteins. Here we present the 1.37-Å-resolution crystal structure of HMk and report that the HMk monomer structure is homologous to the eukaryotic histone heterodimers. In the crystal, HMk forms a dimer homologous to [H3–H4]₂ in the eukaryotic nucleosome. Based on the spatial similarities to structural ms found in the eukaryotic nucleosome that are important for DNA-binding, we infer that the Methanopyrus histone binds DNA in a manner similar to the eukaryotic histone tetramer [H3–H4]₂.

Keywords: Hyperthermophiles; DNA-binding proteins; high resolution; histone; MAD phasing; methanogen; molecular models; nucleosome; recombinant proteins; selenomethionine

Abbreviations: H2A, eukaryotic histone 2A • H2B, eukaryotic histone 2B • H3, eukaryotic histone 3 • H4, eukaryotic histone 4 • HMk, histone from Methanopyrus kandleri • HMfB, histone from Methanothermus fervidus type B • MAD, multiwavelength anomalous dispersion • RMSD, root mean square deviation • Se-Met, selenomethionine • SeHMk, selenomethionyl histone from Methanopyrus kandleri • NSLS, National Synchrotron Light Source • SSRL, Stanford Synchrotron Radiation Laboratory

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