Database accession: MF7000004
Name: Archaeal histone hMfA
PDB ID: 1b67
Experimental method: X-ray (1.48 Å)
Assembly: Homodimer
Source organism: Methanothermus fervidus
Primary publication of the structure:
Decanniere K, Babu AM, Sandman K, Reeve JN, Heinemann U
Crystal structures of recombinant histones HMfA and HMfB from the hyperthermophilic archaeon Methanothermus fervidus.
(2000) J. Mol. Biol. 303: 35-47
PMID: 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.
Annotations from the GeneOntology database. Only terms that fit at least two of the interacting proteins are shown. Molecular function:
double-stranded DNA binding double-stranded DNA binding
protein heterodimerization activity protein heterodimerization activity
protein homodimerization activity protein homodimerization activity
Biological process:
DNA topological change DNA topological change
Cellular component:
chromosome chromosome
cytoplasm cytoplasm
Structural annotations of the participating protein chains.Entry contents: 2 distinct polypeptide molecules
Chains: A, B
Notes: All chains according to the most probable oligomerization state stored in PDBe were considered.
Number of unique protein segments: 1
Name: DNA-binding protein HMf-1
Source organism: Methanothermus fervidus
Length: 69 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMGELPIAPIGRIIKNAGAERVSDDARIALAKVLEEMGEEIASEAVKLAKHAGRKTIKAEDIELARKMFK
UniProtKB AC: P48781 (positions: 2-69)
Coverage: 98%
Name: DNA-binding protein HMf-1
Source organism: Methanothermus fervidus
Length: 69 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMGELPIAPIGRIIKNAGAERVSDDARIALAKVLEEMGEEIASEAVKLAKHAGRKTIKAEDIELARKMFK
UniProtKB AC: P48781 (positions: 3-67)
Coverage: 94%
Evidence demonstrating that the participating proteins are unstructured prior to the interaction and their folding is coupled to binding. Representative domain in related structures: Histone-like transcription factor (CBF/NF-Y) and archaeal histone
Evidence level: Direct evidence
Evidence coverage: The full structure participates in mutual synergistic folding.
Complex Evidence:
Data on the GdmCl-induced unfolding and refolding transitions of the dimer (monitored by stopped-flow far UV CD) fitted to a two-state model (PMID:15313621).
Chain A:
N/A
Chain B:
N/A
Surface and contacts features:
Structures from the PDB that contain the same number of proteins, and the proteins from the two structures show a sufficient degree of pairwise similarity, i.e. they belong to the same UniRef90 cluster (the full proteins exhibit at least 90% sequence identity) and convey roughly the same region to their respective interactions (the two regions from the two proteins share a minimum of 70% overlap). Download the CIF file (.cif)
Download this entry's XML file (.xml)
Download this entry's JSON file (.json)
