Database accession: MF2130001
Name: Archaeal histone hMfB
PDB ID: 1bfm
Experimental method: NMR
Assembly: Homodimer
Source organism: Methanothermus fervidus
Primary publication of the structure:
Starich MR, Sandman K, Reeve JN, Summers MF
NMR structure of HMfB from the hyperthermophile, Methanothermus fervidus, confirms that this archaeal protein is a histone.
(1996) J. Mol. Biol. 255: 187-203
PMID: 8568866
Abstract:
The three-dimensional structure of the recombinant histone rHMfB from Methanothermus fervidus, an archaeon that grows optimally at 83 degrees C, has been determined by nuclear magnetic resonance methods. This is only the third structure of a protein from a hyperthermophilic organism (optimal growth at temperatures above 80 degrees C). Signal assignments were made using a combination of homonuclear-correlated, 15N-double resonance and 15N, 13C triple resonance NMR experiments. Long range dipolar interactions for the symmetric homodimer were identified from two-dimensional 13C-double half-filtered and three-dimensional 13C-filtered NMR data obtained for a heterolabeled-dimer. A family of 33 structures was calculated using DSPACE with a total of 609 NOE-derived interproton distance restraints, including 22 intraresidue, 192 sequential, 300 medium-range (two to five residues), 86 long-range intramolecular (more than five residues) and 112 intermolecular distance restraints. The monomer subunits consist of three alpha-helices, extending from residues Pro4 to Ala15 (helix I), Ser21 to Ala50 (helix II) and Lys56 to Lys68 (helix III), as well as two short segments of beta-strand comprised of residues Arg19 to Ser21 and Thr54 to Ile55. Helices I, II and III contain N-terminal capping boxes, and helices I and II contain C-terminal caps. The structure of the (rHMfB)2 dimer appears very similar to the dimer subunits within the histone core octamer of the chicken nucleosome. The presence of a canonical "histone fold" motif in rHMfB is consistent with the HMf family of archaeal histones and the eukaryal nucleosome core histones having evolved from a common ancestor. The (rHMfB)2 dimer contains several structural features that may impart thermal stability (or non-lability), including two novel hydrophobic "proline Ncaps", four interhelical hydrogen bonds and short N- and C-terminal disordered tails.
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
protein homooligomerization protein homooligomerization
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-2
Source organism: Methanothermus fervidus
Length: 69 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMELPIAPIGRIIKDAGAERVSDDARITLAKILEEMGRDIASEAIKLARHAGRKTIKAEDIELAVRRFKK
UniProtKB AC: P19267 (positions: 1-69)
Coverage: 100%
Name: DNA-binding protein HMf-2
Source organism: Methanothermus fervidus
Length: 69 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMELPIAPIGRIIKDAGAERVSDDARITLAKILEEMGRDIASEAIKLARHAGRKTIKAEDIELAVRRFKK
UniProtKB AC: P19267 (positions: 1-69)
Coverage: 100%
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)
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