PDBsum entry 1b67

DNA binding protein

PDB id: 1b67

Contents

Protein chains

68 a.a. *

Ligands

SO4

Waters ×77

* Residue conservation analysis

PDB id:

1b67

Name:

DNA binding protein

Title:

Crystal structure of the histone hmfa from methanothermus fervidus

Structure:

Protein (histone hmfa). Chain: a, b. Engineered: yes

Source:

Methanothermus fervidus. Organism_taxid: 2180. Gene: hmfa. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

1.48Å R-factor: 0.193 R-free: 0.266

Authors:

K.Decanniere,K.Sandman,J.N.Reeve,U.Heinemann

Key ref:

K.Decanniere et al. (2000). Crystal structures of recombinant histones HMfA and HMfB from the hyperthermophilic archaeon Methanothermus fervidus. J Mol Biol, 303, 35-47. PubMed id: 11021968 DOI: 10.1006/jmbi.2000.4104

Date:

19-Jan-99 Release date: 17-Jan-00

Protein chains

P48781  (HMFA_METFE) -  DNA-binding protein HMf-1 from Methanothermus fervidus

Seq: 69 a.a.

Struc: 68 a.a.

DOI no: 10.1006/jmbi.2000.4104

J Mol Biol 303:35-47 (2000)

PubMed id: 11021968

Crystal structures of recombinant histones HMfA and HMfB from the hyperthermophilic archaeon Methanothermus fervidus.

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

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.

Selected figure(s)

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.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2000, 303, 35-47) copyright 2000.

Figures were selected by the author.