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PDBsum entry 1fts
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Signal recognition particle receptor
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PDB id
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1fts
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Contents |
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* Residue conservation analysis
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Enzyme class:
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E.C.3.6.5.4
- signal-recognition-particle GTPase.
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Reaction:
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GTP + H2O = GDP + phosphate + H+
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GTP
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+
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H2O
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=
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GDP
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+
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phosphate
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+
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H(+)
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Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
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Nature
385:365-368
(1997)
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PubMed id:
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Crystal structure of the NG domain from the signal-recognition particle receptor FtsY.
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G.Montoya,
C.Svensson,
J.Luirink,
I.Sinning.
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ABSTRACT
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Newly synthesized proteins destined either for secretion or incorporation into
membranes are targeted to the membrane translocation machinery by a ubiquitous
system consisting of a signal-recognition particle (SRP) and its receptor. Both
the SRP receptor and the protein within the SRP that binds the signal sequence
contain GTPases. These two proteins, together with the RNA component of the SRP,
form a complex and thereby regulate each other's GTPase activity. Here we report
the structure of the GTPase-containing portion of FtsY, the functional homologue
of the SRP receptor of Escherichia coli, at 2.2 A resolution without bound
nucleotide. This so-called NG domain displays similarities to the Ras-related
GTPases, as well as features unique to the SRP-type GTPases, such as a separate
amino-terminal domain, an insertion within the p21ras (Ras) effector domain, and
a wide-open GTP-binding region. The structure explains the low affinity of FtsY
for GTP, and suggests rearrangements that may occur on nucleotide binding. It
also identifies regions potentially involved in the transmission of signals
between domains and in interactions with regulatory proteins.
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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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G.Bange,
N.Kümmerer,
P.Grudnik,
R.Lindner,
G.Petzold,
D.Kressler,
E.Hurt,
K.Wild,
and
I.Sinning
(2011).
Structural basis for the molecular evolution of SRP-GTPase activation by protein.
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Nat Struct Mol Biol,
18,
1376-1380.
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PDB code:
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L.F.Estrozi,
D.Boehringer,
S.O.Shan,
N.Ban,
and
C.Schaffitzel
(2011).
Cryo-EM structure of the E. coli translating ribosome in complex with SRP and its receptor.
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Nat Struct Mol Biol,
18,
88-90.
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PDB code:
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M.J.Yang,
and
X.Zhang
(2011).
Molecular dynamics simulations reveal structural coordination of Ffh-FtsY heterodimer toward GTPase activation.
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Proteins,
79,
1774-1785.
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N.Pawlowski,
A.Khaminets,
J.P.Hunn,
N.Papic,
A.Schmidt,
R.C.Uthaiah,
R.Lange,
G.Vopper,
S.Martens,
E.Wolf,
and
J.C.Howard
(2011).
The activation mechanism of Irga6, an interferon-inducible GTPase contributing to mouse resistance against Toxoplasma gondii.
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BMC Biol,
9,
7.
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K.W.Hung,
Y.W.Chang,
E.T.Eng,
J.H.Chen,
Y.C.Chen,
Y.J.Sun,
C.D.Hsiao,
G.Dong,
K.A.Spasov,
V.M.Unger,
and
T.H.Huang
(2010).
Structural fold, conservation and Fe(II) binding of the intracellular domain of prokaryote FeoB.
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J Struct Biol,
170,
501-512.
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PDB codes:
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M.E.Reinau,
I.B.Thøgersen,
J.J.Enghild,
K.L.Nielsen,
and
D.E.Otzen
(2010).
The diversity of FtsY-lipid interactions.
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Biopolymers,
93,
595-606.
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M.Yang,
X.Zhang,
and
K.Han
(2010).
Molecular dynamics simulation of SRP GTPases: towards an understanding of the complex formation from equilibrium fluctuations.
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Proteins,
78,
2222-2237.
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S.J.Facey,
and
A.Kuhn
(2010).
Biogenesis of bacterial inner-membrane proteins.
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Cell Mol Life Sci,
67,
2343-2362.
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V.Q.Lam,
D.Akopian,
M.Rome,
D.Henningsen,
and
S.O.Shan
(2010).
Lipid activation of the signal recognition particle receptor provides spatial coordination of protein targeting.
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J Cell Biol,
190,
623-635.
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A.Mateja,
A.Szlachcic,
M.E.Downing,
M.Dobosz,
M.Mariappan,
R.S.Hegde,
and
R.J.Keenan
(2009).
The structural basis of tail-anchored membrane protein recognition by Get3.
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Nature,
461,
361-366.
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PDB codes:
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C.J.Suloway,
J.W.Chartron,
M.Zaslaver,
and
W.M.Clemons
(2009).
Model for eukaryotic tail-anchored protein binding based on the structure of Get3.
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Proc Natl Acad Sci U S A,
106,
14849-14854.
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PDB codes:
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G.Bozkurt,
G.Stjepanovic,
F.Vilardi,
S.Amlacher,
K.Wild,
G.Bange,
V.Favaloro,
K.Rippe,
E.Hurt,
B.Dobberstein,
and
I.Sinning
(2009).
Structural insights into tail-anchored protein binding and membrane insertion by Get3.
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Proc Natl Acad Sci U S A,
106,
21131-21136.
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PDB codes:
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I.A.Buskiewicz,
J.Jöckel,
M.V.Rodnina,
and
W.Wintermeyer
(2009).
Conformation of the signal recognition particle in ribosomal targeting complexes.
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RNA,
15,
44-54.
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P.Grudnik,
G.Bange,
and
I.Sinning
(2009).
Protein targeting by the signal recognition particle.
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Biol Chem,
390,
775-782.
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P.Jaru-Ampornpan,
T.X.Nguyen,
and
S.O.Shan
(2009).
A distinct mechanism to achieve efficient signal recognition particle (SRP)-SRP receptor interaction by the chloroplast srp pathway.
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Mol Biol Cell,
20,
3965-3973.
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S.O.Shan,
S.L.Schmid,
and
X.Zhang
(2009).
Signal recognition particle (SRP) and SRP receptor: a new paradigm for multistate regulatory GTPases.
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Biochemistry,
48,
6696-6704.
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A.J.Driessen,
and
N.Nouwen
(2008).
Protein translocation across the bacterial cytoplasmic membrane.
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Annu Rev Biochem,
77,
643-667.
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E.T.Eng,
A.R.Jalilian,
K.A.Spasov,
and
V.M.Unger
(2008).
Characterization of a novel prokaryotic GDP dissociation inhibitor domain from the G protein coupled membrane protein FeoB.
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J Mol Biol,
375,
1086-1097.
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P.F.Egea,
H.Tsuruta,
G.P.de Leon,
J.Napetschnig,
P.Walter,
and
R.M.Stroud
(2008).
Structures of the signal recognition particle receptor from the archaeon Pyrococcus furiosus: implications for the targeting step at the membrane.
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PLoS ONE,
3,
e3619.
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PDB codes:
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S.B.Neher,
N.Bradshaw,
S.N.Floor,
J.D.Gross,
and
P.Walter
(2008).
SRP RNA controls a conformational switch regulating the SRP-SRP receptor interaction.
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Nat Struct Mol Biol,
15,
916-923.
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U.D.Ramirez,
P.J.Focia,
and
D.M.Freymann
(2008).
Nucleotide-binding flexibility in ultrahigh-resolution structures of the SRP GTPase Ffh.
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Acta Crystallogr D Biol Crystallogr,
64,
1043-1053.
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PDB codes:
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C.L.Reyes,
E.Rutenber,
P.Walter,
and
R.M.Stroud
(2007).
X-ray structures of the signal recognition particle receptor reveal targeting cycle intermediates.
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PLoS ONE,
2,
e607.
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PDB codes:
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G.Bange,
G.Petzold,
K.Wild,
and
I.Sinning
(2007).
Expression, purification and preliminary crystallographic characterization of FlhF from Bacillus subtilis.
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Acta Crystallogr Sect F Struct Biol Cryst Commun,
63,
449-451.
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G.Bange,
G.Petzold,
K.Wild,
R.O.Parlitz,
and
I.Sinning
(2007).
The crystal structure of the third signal-recognition particle GTPase FlhF reveals a homodimer with bound GTP.
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Proc Natl Acad Sci U S A,
104,
13621-13625.
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PDB codes:
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J.Gawronski-Salerno,
and
D.M.Freymann
(2007).
Structure of the GMPPNP-stabilized NG domain complex of the SRP GTPases Ffh and FtsY.
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J Struct Biol,
158,
122-128.
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PDB code:
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J.Gawronski-Salerno,
J.S.Coon,
P.J.Focia,
and
D.M.Freymann
(2007).
X-ray structure of the T. aquaticus FtsY:GDP complex suggests functional roles for the C-terminal helix of the SRP GTPases.
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Proteins,
66,
984-995.
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PDB code:
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L.Bahari,
R.Parlitz,
A.Eitan,
G.Stjepanovic,
E.S.Bochkareva,
I.Sinning,
and
E.Bibi
(2007).
Membrane targeting of ribosomes and their release require distinct and separable functions of FtsY.
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J Biol Chem,
282,
32168-32175.
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P.Jaru-Ampornpan,
S.Chandrasekar,
and
S.O.Shan
(2007).
Efficient interaction between two GTPases allows the chloroplast SRP pathway to bypass the requirement for an SRP RNA.
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Mol Biol Cell,
18,
2636-2645.
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R.Parlitz,
A.Eitan,
G.Stjepanovic,
L.Bahari,
G.Bange,
E.Bibi,
and
I.Sinning
(2007).
Escherichia coli signal recognition particle receptor FtsY contains an essential and autonomous membrane-binding amphipathic helix.
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J Biol Chem,
282,
32176-32184.
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S.O.Shan,
S.Chandrasekar,
and
P.Walter
(2007).
Conformational changes in the GTPase modules of the signal reception particle and its receptor drive initiation of protein translocation.
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J Cell Biol,
178,
611-620.
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S.Wu,
A.Ke,
and
J.A.Doudna
(2007).
A fast and efficient procedure to produce scFvs specific for large macromolecular complexes.
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J Immunol Methods,
318,
95.
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K.Römisch,
F.W.Miller,
B.Dobberstein,
and
S.High
(2006).
Human autoantibodies against the 54 kDa protein of the signal recognition particle block function at multiple stages.
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Arthritis Res Ther,
8,
R39.
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U.D.Ramirez,
and
D.M.Freymann
(2006).
Analysis of protein hydration in ultrahigh-resolution structures of the SRP GTPase Ffh.
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Acta Crystallogr D Biol Crystallogr,
62,
1520-1534.
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PDB codes:
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I.Buskiewicz,
A.Kubarenko,
F.Peske,
M.V.Rodnina,
and
W.Wintermeyer
(2005).
Domain rearrangement of SRP protein Ffh upon binding 4.5S RNA and the SRP receptor FtsY.
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RNA,
11,
947-957.
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E.C.Mandon,
and
R.Gilmore
(2004).
GTPase twins in the SRP family.
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Nat Struct Mol Biol,
11,
115-116.
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F.Chu,
S.O.Shan,
D.T.Moustakas,
F.Alber,
P.F.Egea,
R.M.Stroud,
P.Walter,
and
A.L.Burlingame
(2004).
Unraveling the interface of signal recognition particle and its receptor by using chemical cross-linking and tandem mass spectrometry.
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Proc Natl Acad Sci U S A,
101,
16454-16459.
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J.A.Doudna,
and
R.T.Batey
(2004).
Structural insights into the signal recognition particle.
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Annu Rev Biochem,
73,
539-557.
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K.Wild,
K.R.Rosendal,
and
I.Sinning
(2004).
A structural step into the SRP cycle.
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Mol Microbiol,
53,
357-363.
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K.Wild,
M.Halic,
I.Sinning,
and
R.Beckmann
(2004).
SRP meets the ribosome.
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Nat Struct Mol Biol,
11,
1049-1053.
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P.F.Egea,
S.O.Shan,
J.Napetschnig,
D.F.Savage,
P.Walter,
and
R.M.Stroud
(2004).
Substrate twinning activates the signal recognition particle and its receptor.
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Nature,
427,
215-221.
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PDB code:
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P.J.Focia,
H.Alam,
T.Lu,
U.D.Ramirez,
and
D.M.Freymann
(2004).
Novel protein and Mg2+ configurations in the Mg2+GDP complex of the SRP GTPase ffh.
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Proteins,
54,
222-230.
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PDB code:
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P.J.Focia,
I.V.Shepotinovskaya,
J.A.Seidler,
and
D.M.Freymann
(2004).
Heterodimeric GTPase core of the SRP targeting complex.
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Science,
303,
373-377.
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PDB code:
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S.O.Shan,
R.M.Stroud,
and
P.Walter
(2004).
Mechanism of association and reciprocal activation of two GTPases.
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PLoS Biol,
2,
e320.
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T.Lichi,
G.Ring,
and
J.Eichler
(2004).
Membrane binding of SRP pathway components in the halophilic archaea Haloferax volcanii.
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Eur J Biochem,
271,
1382-1390.
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I.V.Shepotinovskaya,
P.J.Focia,
and
D.M.Freymann
(2003).
Crystallization of the GMPPCP complex of the NG domains of Thermus aquaticus Ffh and FtsY.
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Acta Crystallogr D Biol Crystallogr,
59,
1834-1837.
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K.McLuskey,
J.A.Harrison,
A.W.Schuttelkopf,
D.H.Boxer,
and
W.N.Hunter
(2003).
Insight into the role of Escherichia coli MobB in molybdenum cofactor biosynthesis based on the high resolution crystal structure.
|
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J Biol Chem,
278,
23706-23713.
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PDB code:
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K.Nagai,
C.Oubridge,
A.Kuglstatter,
E.Menichelli,
C.Isel,
and
L.Jovine
(2003).
Structure, function and evolution of the signal recognition particle.
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EMBO J,
22,
3479-3485.
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K.R.Rosendal,
K.Wild,
G.Montoya,
and
I.Sinning
(2003).
Crystal structure of the complete core of archaeal signal recognition particle and implications for interdomain communication.
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Proc Natl Acad Sci U S A,
100,
14701-14706.
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PDB codes:
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S.O.Shan,
and
P.Walter
(2003).
Induced nucleotide specificity in a GTPase.
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Proc Natl Acad Sci U S A,
100,
4480-4485.
|
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S.Q.Gu,
F.Peske,
H.J.Wieden,
M.V.Rodnina,
and
W.Wintermeyer
(2003).
The signal recognition particle binds to protein L23 at the peptide exit of the Escherichia coli ribosome.
|
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RNA,
9,
566-573.
|
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T.Schwartz,
and
G.Blobel
(2003).
Structural basis for the function of the beta subunit of the eukaryotic signal recognition particle receptor.
|
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Cell,
112,
793-803.
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PDB code:
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C.Zwieb,
and
J.Eichler
(2002).
Getting on target: the archaeal signal recognition particle.
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Archaea,
1,
27-34.
|
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J.Buglino,
V.Shen,
P.Hakimian,
and
C.D.Lima
(2002).
Structural and biochemical analysis of the Obg GTP binding protein.
|
| |
Structure,
10,
1581-1592.
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PDB code:
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L.Liu,
X.H.Liang,
S.Uliel,
R.Unger,
E.Ullu,
and
S.Michaeli
(2002).
RNA interference of signal peptide-binding protein SRP54 elicits deleterious effects and protein sorting defects in trypanosomes.
|
| |
J Biol Chem,
277,
47348-47357.
|
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A.A.Herskovits,
A.Seluanov,
R.Rajsbaum,
C.M.ten Hagen-Jongman,
T.Henrichs,
E.S.Bochkareva,
G.J.Phillips,
F.J.Probst,
T.Nakae,
M.Ehrmann,
J.Luirink,
and
E.Bibi
(2001).
Evidence for coupling of membrane targeting and function of the signal recognition particle (SRP) receptor FtsY.
|
| |
EMBO Rep,
2,
1040-1046.
|
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H.H.Niemann,
M.L.Knetsch,
A.Scherer,
D.J.Manstein,
and
F.J.Kull
(2001).
Crystal structure of a dynamin GTPase domain in both nucleotide-free and GDP-bound forms.
|
| |
EMBO J,
20,
5813-5821.
|
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PDB codes:
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J.R.Jagath,
N.B.Matassova,
E.de Leeuw,
J.M.Warnecke,
G.Lentzen,
M.V.Rodnina,
J.Luirink,
and
W.Wintermeyer
(2001).
Important role of the tetraloop region of 4.5S RNA in SRP binding to its receptor FtsY.
|
| |
RNA,
7,
293-301.
|
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O.Weichenrieder,
C.Stehlin,
U.Kapp,
D.E.Birse,
P.A.Timmins,
K.Strub,
and
S.Cusack
(2001).
Hierarchical assembly of the Alu domain of the mammalian signal recognition particle.
|
| |
RNA,
7,
731-740.
|
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P.Peluso,
S.O.Shan,
S.Nock,
D.Herschlag,
and
P.Walter
(2001).
Role of SRP RNA in the GTPase cycles of Ffh and FtsY.
|
| |
Biochemistry,
40,
15224-15233.
|
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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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