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PDBsum entry 1sso
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DNA binding protein
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PDB id
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1sso
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Nat Struct Biol
1:808-819
(1994)
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PubMed id:
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Solution structure and DNA-binding properties of a thermostable protein from the archaeon Sulfolobus solfataricus.
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H.Baumann,
S.Knapp,
T.Lundbäck,
R.Ladenstein,
T.Härd.
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ABSTRACT
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The archaeon Sulfolobus solfataricus expresses large amounts of a small basic
protein, Sso7d, which was previously identified as a DNA-binding protein
possibly involved in compaction of DNA. We have determined the solution
structure of Sso7d. The protein consists of a triple-stranded anti-parallel
beta-sheet onto which an orthogonal double-stranded beta-sheet is packed. This
topology is very similar to that found in eukaryotic Src homology-3 (SH3)
domains. Sso7d binds strongly (Kd < 10 microM) to double-stranded DNA and
protects it from thermal denaturation. In addition, we note that
epsilon-mono-methylation of lysine side chains of Sso7d is governed by cell
growth temperatures, suggesting that methylation is related to the heat-shock
response.
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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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C.D.Hardy,
and
P.K.Martin
(2008).
Biochemical characterization of DNA-binding proteins from Pyrobaculum aerophilum and Aeropyrum pernix.
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Extremophiles,
12,
235-246.
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L.Guo,
Y.Feng,
Z.Zhang,
H.Yao,
Y.Luo,
J.Wang,
and
L.Huang
(2008).
Biochemical and structural characterization of Cren7, a novel chromatin protein conserved among Crenarchaea.
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Nucleic Acids Res,
36,
1129-1137.
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PDB code:
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G.Renzone,
R.M.Vitale,
A.Scaloni,
M.Rossi,
P.Amodeo,
and
A.Guagliardi
(2007).
Structural characterization of the functional regions in the archaeal protein Sso7d.
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Proteins,
67,
189-197.
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R.Consonni,
I.Arosio,
T.Recca,
P.Fusi,
and
L.Zetta
(2007).
Structural determinants responsible for the thermostability of Sso7d and its single point mutants.
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Proteins,
67,
766-775.
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PDB code:
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A.Napoli,
A.Valenti,
V.Salerno,
M.Nadal,
F.Garnier,
M.Rossi,
and
M.Ciaramella
(2005).
Functional interaction of reverse gyrase with single-strand binding protein of the archaeon Sulfolobus.
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Nucleic Acids Res,
33,
564-576.
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J.Eichler,
and
M.W.Adams
(2005).
Posttranslational protein modification in Archaea.
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Microbiol Mol Biol Rev,
69,
393-425.
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A.Brehm,
K.R.Tufteland,
R.Aasland,
and
P.B.Becker
(2004).
The many colours of chromodomains.
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Bioessays,
26,
133-140.
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A.Merlino,
G.Graziano,
and
L.Mazzarella
(2004).
Structural and dynamic effects of alpha-helix deletion in Sso7d: implications for protein thermal stability.
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Proteins,
57,
692-701.
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H.Lou,
Z.Duan,
X.Huo,
and
L.Huang
(2004).
Modulation of hyperthermophilic DNA polymerase activity by archaeal chromatin proteins.
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J Biol Chem,
279,
127-132.
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Y.Wang,
D.E.Prosen,
L.Mei,
J.C.Sullivan,
M.Finney,
and
P.B.Vander Horn
(2004).
A novel strategy to engineer DNA polymerases for enhanced processivity and improved performance in vitro.
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Nucleic Acids Res,
32,
1197-1207.
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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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R.Guo,
H.Xue,
and
L.Huang
(2003).
Ssh10b, a conserved thermophilic archaeal protein, binds RNA in vivo.
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Mol Microbiol,
50,
1605-1615.
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A.Guagliardi,
L.Cerchia,
and
M.Rossi
(2002).
The Sso7d protein of Sulfolobus solfataricus: in vitro relationship among different activities.
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Archaea,
1,
87-93.
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A.Napoli,
Y.Zivanovic,
C.Bocs,
C.Buhler,
M.Rossi,
P.Forterre,
and
M.Ciaramella
(2002).
DNA bending, compaction and negative supercoiling by the architectural protein Sso7d of Sulfolobus solfataricus.
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Nucleic Acids Res,
30,
2656-2662.
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H.Delbrück,
G.Ziegelin,
E.Lanka,
and
U.Heinemann
(2002).
An Src homology 3-like domain is responsible for dimerization of the repressor protein KorB encoded by the promiscuous IncP plasmid RP4.
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J Biol Chem,
277,
4191-4198.
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PDB codes:
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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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X.Chen,
R.Guo,
L.Huang,
and
R.Hong
(2002).
Evolutionary conservation and DNA binding properties of the Ssh7 proteins fromSulfolobus shibatae.
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Sci China C Life Sci,
45,
583-592.
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K.Gunasekaran,
S.J.Eyles,
A.T.Hagler,
and
L.M.Gierasch
(2001).
Keeping it in the family: folding studies of related proteins.
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Curr Opin Struct Biol,
11,
83-93.
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V.Agrawal,
and
R.K.Kishan
(2001).
Functional evolution of two subtly different (similar) folds.
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BMC Struct Biol,
1,
5.
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V.Grantcharova,
E.J.Alm,
D.Baker,
and
A.L.Horwich
(2001).
Mechanisms of protein folding.
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Curr Opin Struct Biol,
11,
70-82.
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F.V.Murphy,
and
M.E.Churchill
(2000).
Nonsequence-specific DNA recognition: a structural perspective.
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Structure,
8,
R83-R89.
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S.D'Auria,
P.Herman,
J.R.Lakowicz,
F.Tanfani,
E.Bertoli,
G.Manco,
and
M.Rossi
(2000).
The esterase from the thermophilic eubacterium Bacillus acidocaldarius: structural-functional relationship and comparison with the esterase from the hyperthermophilic archaeon Archaeoglobus fulgidus.
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Proteins,
40,
473-481.
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A.Napoli,
J.van der Oost,
C.W.Sensen,
R.L.Charlebois,
M.Rossi,
and
M.Ciaramella
(1999).
An Lrp-like protein of the hyperthermophilic archaeon Sulfolobus solfataricus which binds to its own promoter.
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J Bacteriol,
181,
1474-1480.
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J.A.Kornblatt,
M.J.Kornblatt,
R.Lange,
E.Mombelli,
and
J.G.Guillemette
(1999).
The individual tyrosines of proteins: their spectra may or may not differ from those in water or other solvents.
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Biochim Biophys Acta,
1431,
238-248.
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P.Hindmarsh,
and
J.Leis
(1999).
Retroviral DNA integration.
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Microbiol Mol Biol Rev,
63,
836.
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F.Catanzano,
G.Graziano,
P.Fusi,
P.Tortora,
and
G.Barone
(1998).
Differential scanning calorimetry study of the thermodynamic stability of some mutants of Sso7d from Sulfolobus solfataricus.
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Biochemistry,
37,
10493-10498.
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P.Agback,
H.Baumann,
S.Knapp,
R.Ladenstein,
and
T.Härd
(1998).
Architecture of nonspecific protein-DNA interactions in the Sso7d-DNA complex.
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Nat Struct Biol,
5,
579-584.
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PDB code:
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P.López-García,
S.Knapp,
R.Ladenstein,
and
P.Forterre
(1998).
In vitro DNA binding of the archaeal protein Sso7d induces negative supercoiling at temperatures typical for thermophilic growth.
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Nucleic Acids Res,
26,
2322-2328.
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R.A.Lutzke,
and
R.H.Plasterk
(1998).
Structure-based mutational analysis of the C-terminal DNA-binding domain of human immunodeficiency virus type 1 integrase: critical residues for protein oligomerization and DNA binding.
|
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J Virol,
72,
4841-4848.
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S.D'Auria,
M.Moracci,
F.Febbraio,
F.Tanfani,
R.Nucci,
and
M.Rossi
(1998).
Structure-function studies on beta-glycosidase from Sulfolobus solfataricus. Molecular bases of thermostability.
|
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Biochimie,
80,
949-957.
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S.Knapp,
P.T.Mattson,
P.Christova,
K.D.Berndt,
A.Karshikoff,
M.Vihinen,
C.I.Smith,
and
R.Ladenstein
(1998).
Thermal unfolding of small proteins with SH3 domain folding pattern.
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Proteins,
31,
309-319.
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E.Mombelli,
M.Afshar,
P.Fusi,
M.Mariani,
P.Tortora,
J.P.Connelly,
and
R.Lange
(1997).
The role of phenylalanine 31 in maintaining the conformational stability of ribonuclease P2 from Sulfolobus solfataricus under extreme conditions of temperature and pressure.
|
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Biochemistry,
36,
8733-8742.
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L.J.Ball,
N.V.Murzina,
R.W.Broadhurst,
A.R.Raine,
S.J.Archer,
F.J.Stott,
A.G.Murzin,
P.B.Singh,
P.J.Domaille,
and
E.D.Laue
(1997).
Structure of the chromatin binding (chromo) domain from mouse modifier protein 1.
|
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EMBO J,
16,
2473-2481.
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PDB code:
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T.Lazaridis,
I.Lee,
and
M.Karplus
(1997).
Dynamics and unfolding pathways of a hyperthermophilic and a mesophilic rubredoxin.
|
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Protein Sci,
6,
2589-2605.
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W.Huang,
J.Jia,
J.Cummings,
M.Nelson,
G.Schneider,
and
Y.Lindqvist
(1997).
Crystal structure of nitrile hydratase reveals a novel iron centre in a novel fold.
|
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Structure,
5,
691-699.
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PDB code:
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C.J.Morton,
D.J.Pugh,
E.L.Brown,
J.D.Kahmann,
D.A.Renzoni,
and
I.D.Campbell
(1996).
Solution structure and peptide binding of the SH3 domain from human Fyn.
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Structure,
4,
705-714.
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PDB codes:
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
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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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