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PDBsum entry 1f1e
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DNA binding protein
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PDB id
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1f1e
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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An ancestral nuclear protein assembly: crystal structure of the methanopyrus kandleri histone.
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Authors
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R.L.Fahrner,
D.Cascio,
J.A.Lake,
A.Slesarev.
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Ref.
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Protein Sci, 2001,
10,
2002-2007.
[DOI no: ]
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PubMed id
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Abstract
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Eukaryotic histone proteins condense DNA into compact structures called
nucleosomes. Nucleosomes were viewed as a distinguishing feature of eukaryotes
prior to identification of histone orthologs in methanogens. Although
evolutionarily distinct from methanogens, the methane-producing hyperthermophile
Methanopyrus kandleri produces a novel, 154-residue histone (HMk). Amino acid
sequence comparisons show that HMk differs from both methanogenic and eukaryotic
histones, in that it contains two histone-fold ms within a single chain. The two
HMk histone-fold ms, N and C terminal, are 28% identical in amino acid sequence
to each other and approximately 21% identical in amino acid sequence to other
histone proteins. Here we present the 1.37-A-resolution crystal structure of HMk
and report that the HMk monomer structure is homologous to the eukaryotic
histone heterodimers. In the crystal, HMk forms a dimer homologous to [H3-H4](2)
in the eukaryotic nucleosome. Based on the spatial similarities to structural ms
found in the eukaryotic nucleosome that are important for DNA-binding, we infer
that the Methanopyrus histone binds DNA in a manner similar to the eukaryotic
histone tetramer [H3-H4](2).
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Figure 2.
Fig. 2. Nomenclature and schematic representation of
assemblies observed for several histones. The histone fold is
stylized here as a pointed N terminus representing the short
helix 1, a long central region representing the longer helix 2,
and a rounded C terminus representing the short helix 3. A
eukaryotic nucleosome is comprised of 145-147 bp of DNA and two
copies each of four histone proteins (H2A, H2B, H3, and H4)
(Thomas and Kornberg 1975; Arents and Moudrianakis 1995; Luger
et al. 1997). A complete nucleosome histone octomer may be
viewed as a left-handed spiral protein assembly constructed from
three subassemblies. (A) (Left) An HMk monomer contains two
histone-fold ms, the N- and C-terminal domains, tethered by a
13-residue loop. (Right) An HMk dimer formed through
crystallographic contacts associates through C-terminal helices
of the N-terminal domain. (B) (Left) The eight histone proteins
assemble as two copies each of two different heterodimers
(H2A-H2B and H3-H4) (Thomas and Kornberg 1975; Luger et al.
1997). (Center) [H3-H4] assembles as [H3-H4][2]. This complex
initiates DNA-binding, positions the nucleosome, and forms
stable nucleosomelike structures in complex with DNA (Dong and
van Holde 1991; Hayes et al. 1991). (Right) The nucleosome is
completed by adding [H2A-H2B] to each end of the [H3-H4][2]
tetramer.
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Figure 4.
Fig. 4. Ribbon diagrams of HMk (cyan) aligned to various
histone proteins. (A) HMk aligned to H2A-H2B (Luger et al.
1997). (B) HMk aligned to H3-H4 (Luger et al. 1997). (C)
C-Terminal domain of HMk aligned to HMfB (Starich et al. 1996).
(D) Superposition of HMk dimer created from the crystallographic
2-fold axis (cyan) and (H3-H4)[2] tetramer. Note the structural
similarity between HMk and the other histones. Also note the
similar arrangement of domains and interfaces between HMk and
[H3-H4]. However, in the HMk structure, the C termini contact
one another, whereas in the nucleosome structure the [H3-H4][2]
has a gap. Structure alignments were performed using ALIGN
(Satow et al. 1986).
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The above figures are
reprinted
by permission from the Protein Society:
Protein Sci
(2001,
10,
2002-2007)
copyright 2001.
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