PDBsum entry 1b67

DNA binding protein

PDB id

1b67

Contents

			Protein chains

					68 a.a. *

			Ligands

					SO4

			Waters ×77

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Crystal structures of recombinant histones hmfa and hmfb from the hyperthermophilic archaeon methanothermus fervidus.

Authors

K.Decanniere, A.M.Babu, K.Sandman, J.N.Reeve, U.Heinemann.

Ref.

J Mol Biol, 2000, 303, 35-47. [DOI no: 10.1006/jmbi.2000.4104]

PubMed id

11021968

Abstract

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. Here, crystal structures are documented for recombinant (r) HMfA at a resolution of 1.55 A refined to a crystallographic R-value of 19.8 % (tetragonal form) and at 1.48 A refined to a R-value of 18.8 % (orthorhombic form), and for rHMfB at 1.9 A refined to a R-value of 18.0 %. The rHMfA and rHMfB monomers have structures that are just histone folds in which a long central alpha-helix (alpha2; 29 residues) is separated from shorter N-terminal (alpha1; 11 residues) and C-terminal (alpha3; 10 residues) alpha-helices by two loops (L1 and L2; both 6 residues). Within L1 and L2, three adjacent residues are in extended (beta) conformation. rHMfA and rHMfB assemble into homodimers, with the alpha2 helices anti-parallel aligned and crossing at an angle of close to 35 degrees, and with hydrogen bonds formed between the extended, parallel regions of L1 and L2 resulting in short beta-ladders. Dimerization creates a novel N-terminal structure that contains four proline residues, two from each monomer. As prolines are present at these positions in all archaeal histone sequences, this proline-tetrad structure is likely to be a common feature of all archaeal histone dimers. Almost all residues that participate in monomer-monomer interactions are conserved in HMfA and HMfB, consistent with the ability of these monomers to form both homodimers and (HMfA+HMfB) heterodimers. Differences in side-chain interactions that result from non-conservative residue differences in HMfA and HMfB are identified, and the structure of a (rHMfA)(2)-DNA complex is presented based on the structures documented here and modeled by homology to histone-DNA interactions in the eukaryal nucleosome.



	Figure 2. Figure 2. Crystal structure of (rHMfA)[2] and comparison with (rHMfB)[2]. (a) Schematic drawing of (rHMfA)[2] identifying the α-helical and loop regions of the histone fold. The molecule is color-coded to show structural similarity with (rHMfB)[2]. Based on the least-squares superposition of the dimers, the α-carbon positions deviate at most by ≤1.4 Å, in the areas indicated by red. (b) Stereographic drawing of the (HMfA)[2] crystal structure with the protein backbone drawn using heavier lines than used for the side-chains.		Figure 6. Figure 6. Model for DNA binding by (rHMfA)[2]. The model was generated by (rHMfA)[2] replacement of a (H3+H4) dimer in the eukaryal nucleosome crystal structure [Luger et al 1997] as described in the text. The L1-L2a and paired N-terminal regions predicted to contact the DNA are boxed (A and B, respectively), and shown in expanded format in Figure 7.