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PDBsum entry 1bb8
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* Residue conservation analysis
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DOI no:
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Nat Struct Biol
5:546-550
(1998)
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PubMed id:
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Site-specific DNA binding using a variation of the double stranded RNA binding motif.
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K.M.Connolly,
J.M.Wojciak,
R.T.Clubb.
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ABSTRACT
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The integrase family of site-specific recombinases catalyze a diverse array of
DNA rearrangements in archaebacteria, eubacteria and yeast. The solution
structure of the DNA binding domain of the integrase protein from the
conjugative transposon Tn916 has been determined using NMR spectroscopy. The
structure provides the first insights into distal site DNA binding by a
site-specific integrase and reveals that the N-terminal domain is structurally
similar to the double stranded RNA binding domain (dsRBD). The results of
chemical shift mapping experiments suggest that the integrase protein interacts
with DNA using residues located on the face of its three stranded beta-sheet.
This surface differs from the proposed RNA binding surface in dsRBDs, suggesting
that different surfaces on the same protein fold can be used to bind DNA and RNA.
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Selected figure(s)
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Figure 1.
Figure 1. The Tn916 transposon. Binding sites for the N- and
C-terminal domains of integrase are shown as triangles and
diamonds respectively. Binding sites for the accessory factor
xis are shown as hexagons.
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Figure 4.
Figure 4. Comparison of the structures of a, Int^N domain
(residues Arg 6−Asp 70 ) and b, staufen dsRBD III protein^22.
Homologous secondary structural elements are colored purple.
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nat Struct Biol
(1998,
5,
546-550)
copyright 1998.
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Figures were
selected
by an automated process.
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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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U.Dobrindt,
M.G.Chowdary,
G.Krumbholz,
and
J.Hacker
(2010).
Genome dynamics and its impact on evolution of Escherichia coli.
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Med Microbiol Immunol,
199,
145-154.
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A.Szwagierczak,
U.Antonenka,
G.M.Popowicz,
T.Sitar,
T.A.Holak,
and
A.Rakin
(2009).
Structures of the arm-type binding domains of HPI and HAI7 integrases.
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J Biol Chem,
284,
31664-31671.
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PDB codes:
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E.A.Fadeev,
M.D.Sam,
and
R.T.Clubb
(2009).
NMR structure of the amino-terminal domain of the lambda integrase protein in complex with DNA: immobilization of a flexible tail facilitates beta-sheet recognition of the major groove.
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J Mol Biol,
388,
682-690.
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PDB code:
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A.Ebihara,
M.Manzoku,
H.Iino,
M.Kanagawa,
A.Shinkai,
S.Yokoyama,
and
S.Kuramitsu
(2008).
Crystal structure of uncharacterized protein TTHA1756 from Thermus thermophilus HB8: Structural variety in UPF0150 family proteins.
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Proteins,
71,
2097-2101.
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PDB code:
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K.Y.Chang,
and
A.Ramos
(2005).
The double-stranded RNA-binding motif, a versatile macromolecular docking platform.
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FEBS J,
272,
2109-2117.
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G.P.Scarlett,
S.J.Elgar,
P.D.Cary,
A.M.Noble,
R.L.Orford,
G.G.Kneale,
and
M.J.Guille
(2004).
Intact RNA-binding domains are necessary for structure-specific DNA binding and transcription control by CBTF122 during Xenopus development.
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J Biol Chem,
279,
52447-52455.
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A.A.Gorfe,
and
I.Jelesarov
(2003).
Energetics of sequence-specific protein-DNA association: computational analysis of integrase Tn916 binding to its target DNA.
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Biochemistry,
42,
11568-11576.
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H.Fan,
and
A.E.Mark
(2003).
Relative stability of protein structures determined by X-ray crystallography or NMR spectroscopy: a molecular dynamics simulation study.
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Proteins,
53,
111-120.
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M.L.Hung,
P.Chao,
and
K.Y.Chang
(2003).
dsRBM1 and a proline-rich domain of RNA helicase A can form a composite binder to recognize a specific dsDNA.
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Nucleic Acids Res,
31,
5741-5753.
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V.V.Rogov,
C.Lücke,
L.Muresanu,
H.Wienk,
I.Kleinhaus,
K.Werner,
F.Löhr,
P.Pristovsek,
and
H.Rüterjans
(2003).
Solution structure and stability of the full-length excisionase from bacteriophage HK022.
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Eur J Biochem,
270,
4846-4858.
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PDB code:
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J.M.Wojciak,
D.Sarkar,
A.Landy,
and
R.T.Clubb
(2002).
Arm-site binding by lambda -integrase: solution structure and functional characterization of its amino-terminal domain.
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Proc Natl Acad Sci U S A,
99,
3434-3439.
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PDB code:
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K.M.Connolly,
M.Iwahara,
and
R.T.Clubb
(2002).
Xis protein binding to the left arm stimulates excision of conjugative transposon Tn916.
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J Bacteriol,
184,
2088-2099.
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D.Hinerfeld,
and
G.Churchward
(2001).
Xis protein of the conjugative transposon Tn916 plays dual opposing roles in transposon excision.
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Mol Microbiol,
41,
1459-1467.
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D.Sarkar,
M.Radman-Livaja,
and
A.Landy
(2001).
The small DNA binding domain of lambda integrase is a context-sensitive modulator of recombinase functions.
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EMBO J,
20,
1203-1212.
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J.Iwahara,
and
R.T.Clubb
(1999).
Solution structure of the DNA binding domain from Dead ringer, a sequence-specific AT-rich interaction domain (ARID).
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EMBO J,
18,
6084-6094.
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PDB code:
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T.Komano
(1999).
Shufflons: multiple inversion systems and integrons.
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Annu Rev Genet,
33,
171-191.
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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
codes are
shown on the right.
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