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PDBsum entry 2j9d
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Membrane transport
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PDB id
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2j9d
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Contents |
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(+ 0 more)
102 a.a.
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(+ 0 more)
116 a.a.
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References listed in PDB file
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Key reference
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Title
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Structure of glnk1 with bound effectors indicates regulatory mechanism for ammonia uptake.
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Authors
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O.Yildiz,
C.Kalthoff,
S.Raunser,
W.Kühlbrandt.
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Ref.
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EMBO J, 2007,
26,
589-599.
[DOI no: ]
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PubMed id
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Note In the PDB file this reference is
annotated as "TO BE PUBLISHED".
The citation details given above were identified by an automated
search of PubMed on title and author
names, giving a
perfect match.
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Abstract
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A binary complex of the ammonia channel Amt1 from Methanococcus jannaschii and
its cognate P(II) signalling protein GlnK1 has been produced and characterized.
Complex formation is prevented specifically by the effector molecules Mg-ATP and
2-ketoglutarate. Single-particle electron microscopy of the complex shows that
GlnK1 binds on the cytoplasmic side of Amt1. Three high-resolution X-ray
structures of GlnK1 indicate that the functionally important T-loop has an
extended, flexible conformation in the absence of Mg-ATP, but assumes a compact,
tightly folded conformation upon Mg-ATP binding, which in turn creates a
2-ketoglutarate-binding site. We propose a regulatory mechanism by which
nitrogen uptake is controlled by the binding of both effector molecules to
GlnK1. At normal effector levels, a 2-ketoglutarate molecule binding at the apex
of the compact T-loop would prevent complex formation, ensuring uninhibited
ammonia uptake. At low levels of Mg-ATP, the extended loops would seal the
ammonia channels in the complex. Binding of both effector molecules to P(II)
signalling proteins may thus represent an effective feedback mechanism for
regulating ammonium uptake through the membrane.
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Figure 4.
Figure 4 X-ray structures of GlnK1 (A) in the absence of added
nucleotide at 2.1 Å; (B) with bound Mg-ATP at 1.2 Å;
(C) with Mg-ATP and 2-KG at 1.6 Å resolution. On the left
is the trimer with the Amt1 interaction surface facing up.
Individual protein monomers are drawn as blue, green and gray
ribbon diagrams. Bound cofactors are shown as ball-and-stick
models. In (A), one out of three monomers binds ADP; in (B), all
three monomers bind Mg-ATP; in (C), all three monomers bind ATP,
but only the blue monomer binds Mg^2+ as well, plus a single
molecule of 2-KG. The center of the trimer holds either an
acetate (A) or a chloride ion (yellow sphere). The corresponding
monomer side views are shown on the right. (A) Superposition of
six monomers with resolved T-loops in the extended conformation
(Supplementary Figure 4). (B) Superposition of three monomers of
one Mg-ATP-binding trimer, with T-loops in the compact
conformation. Color coding as in Supplementary Figures 3 and 4.
(C) Single monomer binding Mg-ATP and 2-KG.
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Figure 5.
Figure 5 Stereo diagrams showing details of the electron density
of T-loop residues and the nucleotide-binding pocket at the
interface between two adjacent GlnK1 monomers (blue and green).
(A) Without added Mg-ATP, occasional sites are occupied by ADP
(red) or AMP from the expressing cells. The T-loop is in an
extended conformation, with arginines 45, 47 and 49 and Tyr51at
the tip. (B) Mg-ATP (red) fixes the T-loop in the compact
conformation through main-chain interactions with the ATP  -phosphate
and hydrogen bonds with Mg-coordinated water molecules,
positioning Glu44 to form a salt bridge with Lys58. (C) By
fixing the T-loop in its compact conformation, Mg-ATP (red)
creates a binding site for 2-KG (yellow) on the far side of
Tyr51. The density above the keto oxygen of 2-KG is due to an
ordered water molecule.
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The above figures are
reprinted
from an Open Access publication published by Macmillan Publishers Ltd:
EMBO J
(2007,
26,
589-599)
copyright 2007.
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