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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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DOI no:
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Protein Sci
10:2002-2007
(2001)
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PubMed id:
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An ancestral nuclear protein assembly: crystal structure of the Methanopyrus kandleri histone.
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R.L.Fahrner,
D.Cascio,
J.A.Lake,
A.Slesarev.
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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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Selected figure(s)
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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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Figures were
selected
by the author.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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P.B.Talbert,
and
S.Henikoff
(2010).
Histone variants--ancient wrap artists of the epigenome.
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Nat Rev Mol Cell Biol,
11,
264-275.
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S.P.Wilkinson,
M.Ouhammouch,
and
E.P.Geiduschek
(2010).
Transcriptional activation in the context of repression mediated by archaeal histones.
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Proc Natl Acad Sci U S A,
107,
6777-6781.
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S.Payankaulam,
L.M.Li,
and
D.N.Arnosti
(2010).
Transcriptional repression: conserved and evolved features.
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Curr Biol,
20,
R764-R771.
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N.Altman-Price,
and
M.Mevarech
(2009).
Genetic evidence for the importance of protein acetylation and protein deacetylation in the halophilic archaeon Haloferax volcanii.
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J Bacteriol,
191,
1610-1617.
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U.Friedrich-Jahn,
J.Aigner,
G.Längst,
J.N.Reeve,
and
H.Huber
(2009).
Nanoarchaeal origin of histone H3?
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J Bacteriol,
191,
1092-1096.
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V.Alva,
M.Ammelburg,
J.Söding,
and
A.N.Lupas
(2007).
On the origin of the histone fold.
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BMC Struct Biol,
7,
17.
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K.Sandman,
and
J.N.Reeve
(2006).
Archaeal histones and the origin of the histone fold.
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Curr Opin Microbiol,
9,
520-525.
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Y.Qiu,
V.Tereshko,
Y.Kim,
R.Zhang,
F.Collart,
M.Yousef,
A.Kossiakoff,
and
A.Joachimiak
(2006).
The crystal structure of Aq_328 from the hyperthermophilic bacteria Aquifex aeolicus shows an ancestral histone fold.
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Proteins,
62,
8.
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PDB code:
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B.D.Silverman
(2005).
Asymmetry in the burial of hydrophobic residues along the histone chains of eukarya, archaea and a transcription factor.
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BMC Struct Biol,
5,
20.
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C.Greco,
E.Sacco,
M.Vanoni,
and
L.De Gioia
(2005).
Identification and in silico analysis of a new group of double-histone fold-containing proteins.
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J Mol Model,
12,
76-84.
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C.Greco,
P.Fantucci,
and
L.De Gioia
(2005).
In silico functional characterization of a double histone fold domain from the Heliothis zea virus 1.
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BMC Bioinformatics,
6,
S15.
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H.S.Malik,
and
S.Henikoff
(2003).
Phylogenomics of the nucleosome.
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Nat Struct Biol,
10,
882-891.
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H.Sondermann,
S.M.Soisson,
D.Bar-Sagi,
and
J.Kuriyan
(2003).
Tandem histone folds in the structure of the N-terminal segment of the ras activator Son of Sevenless.
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Structure,
11,
1583-1593.
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PDB code:
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J.N.Reeve
(2003).
Archaeal chromatin and transcription.
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Mol Microbiol,
48,
587-598.
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W.Martin,
and
M.J.Russell
(2003).
On the origins of cells: a hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells.
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Philos Trans R Soc Lond B Biol Sci,
358,
59.
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D.Musgrave,
X.Zhang,
and
M.Dinger
(2002).
Archaeal genome organization and stress responses: implications for the origin and evolution of cellular life.
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Astrobiology,
2,
241-253.
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M.F.White,
and
S.D.Bell
(2002).
Holding it together: chromatin in the Archaea.
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Trends Genet,
18,
621-626.
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N.A.Pavlov,
D.I.Cherny,
I.V.Nazimov,
A.I.Slesarev,
and
V.Subramaniam
(2002).
Identification, cloning and characterization of a new DNA-binding protein from the hyperthermophilic methanogen Methanopyrus kandleri.
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Nucleic Acids Res,
30,
685-694.
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
code is
shown on the right.
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Links
