Archaeal Histones

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Histones HMfA and HMfB from Methanothermus fervidus

"The hyperthermophilic archaeon Methanothermus fervidus contains two small basic proteins, HMfA (68 amino acid residues) and HMfB (69 residues)that share a common ancestry with the eukaryal nucleosome core histones H2A, H2B, H3, and H4. HMfA and HMfB have sequences that differ at 11 locations, they have different structural stabilities, and the complexes that they form with DNA have different electrophoretic mobilities." - From abstract of [1]

Comparison of Structures


Comparing the above sequences one can see that an important difference is that A has a glycine at position 2 which is lacking in B. In addition to that deletion, there are a number of substitutions which creates differences in the sequence of the two peptides. As a consequence of this similarity of primary structure, as shown in the two applets below, the tertiary structures of both peptides are quite similar (, ). All archaeal and also eukaryal histones[1] have this tertiary structure of helix-loop-helix-loop-helix which is called the histone fold. View the tertiary structure of eukaryal histones as well as the structure of an eukaryal Nucleosome. Since the primary structure of the two histones are similar, the nonpolar residues within their tertiary structure are similarly located as well: , .

HMfA, PDB ID:1hta

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HMfB, PDB ID: 1a7w

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Dimer of HMfA, PDB ID:1b67

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Dimer Structure

The significance of exposed areas of hydrophobic side chains are that they are potential sites of monomeric interaction to form dimers. In the applet to the right the orthorombic form of HMfA (PDB:1B67) is shown as a dimer structure (). The HMfB dimer can be viewed by right clicking on the Jmol frank or icon and selecting from the menu '1A7W | Biomolecule | load biomolecule 1'. In order to compare the structure to that of the A dimer, change the display by selecting from the menu 'Style | Structure | Cartoon'. Heterodimers of HNfA and HMfB can form as well. [2] Displaying the reveals that many of the hydrophobic residues that were exposed in the monomeric structure are involved in the associative binding of the dimer.

Some areas of nonpolar residues that remain exposed in the dimer would be involved in the tetrameric structure, and there is evidence for this higher level of structure. [3] [4] [5] The area of hydrophobic residues containing a would not be included in tetramer formation. The prolines which form the tetrad are present in the N terminus of each chain, and this tetrad structure is found in most archaeal homo- and heterodimeric histones but are not present in eukaryal histone dimers. [6] [7] shows that the rings are close enough to form attractive London forces, and these forces keep properly aligned so that with their positive charges they can bind with DNA. There are also that are involved in DNA binding.

Two separate in HMfA[8] have been made, M36C and A64C. In the dimer both of these mutations are on the side opposite of the DNA binding site, and the cysteines provide sites for covalent modification.

Notes and References

  1. 1.0 1.1 K. Decanniere, A. M. Babu, K. Sandman, J. N. Reeve, U. Heinemann Crystal Structure of Recombinant Histones HMfA and HMfB from the Hyperthermophilic Methanothermus fervidus. J. Mol. Biol., 303, 35-47, 2000
  2. Sandman, K., Grayling, R. A., Dobrinski, B., Lurz, R. & Reeve, J. N., Growth phase dependent synthesis of histones in the archaeon Methanothermus fervidus. Proc. Natl Acad. Sci. USA, 91, 12624-12628, 1994.
  3. Luger, K., MaÈ der, A. W., Richmond, R. K., Sargent, D. F. & Richmond, T. J., Crystal structure of the nucleosome core particle at 2.8 AÊ resolution, Nature, 389, 251-260, 1997.
  4. Xie, X., Kokubo, T., Cohen, S. L., Mirza, U. A., Hoffmann, A., Chait, B. T., Roeder, R. G., Nakatani, Y. & Burley, S. K., Structural similarity between TAFs and the heterotetrameric core of the histone octamer. Nature, 380, 316-322, 1996.
  5. Birck, C., Poch, O., Romier, C., Ruff, M., Mengus, G., Lavigne, A.-C., Davidson, I. & Moras, D. Human TAFII28 and TAFII18 interact through a histone fold encoded by atypical evolutionary conserved motifs also found in the SPT3 family, Cell, 94, 239-249, 1998.
  6. Sandman, K., Pereira, S. L. & Reeve, J. N. Diversity of prokaryotic chromosomal proteins and the origin of the nucleosome. Cell. Mol. Life Sci. 54, 1350-1364, 1998.
  7. Higashibata, H., Fujiwara, S., Takagi, M. & Imanaka, T., Analysis of DNA compaction pro®le and intracellular contents of archaeal histones from Pyrococcus kodakaraensis KOD1. Biochem. Biophys. Res. Commun. 258, 416-424, 1999
  8. Sandman, K. and Reeve, J. N., Chromosome Packaging by Archaeal Histones, Advances in Applied Microbiology, 50, 75-99, 2001

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