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PDBsum entry 2ffh
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Protein transport
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PDB id
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2ffh
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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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Crystal structure of the signal sequence binding subunit of the signal recognition particle.
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Authors
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R.J.Keenan,
D.M.Freymann,
P.Walter,
R.M.Stroud.
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Ref.
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Cell, 1998,
94,
181-191.
[DOI no: ]
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PubMed id
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Abstract
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The crystal structure of the signal sequence binding subunit of the signal
recognition particle (SRP) from Thermus aquaticus reveals a deep groove bounded
by a flexible loop and lined with side chains of conserved hydrophobic residues.
The groove defines a flexible, hydrophobic environment that is likely to
contribute to the structural plasticity necessary for SRP to bind signal
sequences of different lengths and amino acid sequence. The structure also
reveals a helix-turn-helix motif containing an arginine-rich alpha helix that is
required for binding to SRP RNA and is implicated in forming the core of an
extended RNA binding surface.
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Figure 6.
Figure 6. The Hydrophobic Groove of the M Domain Is Not
Empty in the CrystalThe flexible finger loop of one M domain
(magenta; residues 337–355 shown) inserts into the proposed
signal sequence binding groove of another M domain (white,
molecular surface representation), forming a hydrophobic cavity
in the center of the groove that may contain detergent from the
crystallization solution. This protein–protein interaction may
represent an example of the extent to which the M domain has
evolved to accommodate a wide variety of hydrophobic sequences.
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Figure 7.
Figure 7. The Arginine-Rich, Helix-Turn-Helix Motif of the
M Domain(A) Stereo view of the HTH motif (αM3 to αM4) and a
third helix (αM2) of the M domain (green) superimposed onto the
corresponding region from the lac repressor (blue) ([9]). The
least-squares overlap of α carbons was performed using LSQMAN (
[24]). Conserved residues contributing to the compact
hydrophobic core of the lac repressor are indicated, along with
their counterparts in the M domain. Helix αM4 extends beyond
helix α2 of the lac repressor by  vert,
similar 3 additional turns and contains basic residues at an
extended C terminus; these characteristics are similar to the
recognition helix of homeodomain DNA-binding proteins ([14]).(B)
Stereo view of the conserved SRP RNA-binding motif of Ffh. This
view is rotated vert,
similar 90° about the vertical axis with respect to the
orientation in Figure 7A. Positively charged side chains located
in helix αM3 are likely to mediate the specific interaction of
the M domain with SRP RNA. Arg-387 and Arg-361 form well-ordered
salt bridges with the conserved residues Glu-373 and Glu-398,
respectively.
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The above figures are
reprinted
by permission from Cell Press:
Cell
(1998,
94,
181-191)
copyright 1998.
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Secondary reference #1
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Title
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Structure of the conserved gtpase domain of the signal recognition particle.
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Authors
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D.M.Freymann,
R.J.Keenan,
R.M.Stroud,
P.Walter.
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Ref.
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Nature, 1997,
385,
361-364.
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PubMed id
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