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PDBsum entry 2b2h
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Transport protein
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PDB id
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2b2h
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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 archaeal ammonium transporter amt-1 from archaeoglobus fulgidus.
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Authors
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S.L.Andrade,
A.Dickmanns,
R.Ficner,
O.Einsle.
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Ref.
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Proc Natl Acad Sci U S A, 2005,
102,
14994-14999.
[DOI no: ]
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PubMed id
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Abstract
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Ammonium transporters (Amts) are integral membrane proteins found in all
kingdoms of life that fulfill an essential function in the uptake of reduced
nitrogen for biosynthetic purposes. Amt-1 is one of three Amts encoded in the
genome of the hyperthermophilic archaeon Archaeoglobus fulgidus. The crystal
structure of Amt-1 shows a compact trimer with 11 transmembrane helices per
monomer and a central channel for substrate conduction in each monomer, similar
to the known crystal structure of AmtB from Escherichia coli. Xenon
derivatization has been used to identify apolar regions of Amt-1, emphasizing
not only the hydrophobicity of the substrate channel but also the unexpected
presence of extensive internal cavities that should be detrimental for protein
stability. The substrates ammonium and methylammonium have been used for
cocrystallization experiments with Amt-1, but the identification of binding
sites that are distinct from water positions is not unambiguous. The well
ordered cytoplasmic C terminus of the protein in the Amt-1 structure has allowed
for the construction of a docking model between Amt-1 and a homology model for
its physiological interaction partner, the P(II) protein GlnB-1. In this model,
GlnB-1 binds tightly to the cytoplasmic face of the transporter, effectively
blocking conduction through the three individual substrate channels.
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Figure 2.
Fig. 2. Structure of A. fulgidus Amt-1. (A) Stereo
representation of the Amt-1 monomer. The membrane is indicated
in gray, with the extracellular side above and the cytoplasmic
side below. The protein chain is colored from blue at the N
terminus to red at the C terminus, the 11 transmembrane helices
numbered in accordance with Fig. 1. (B) The Amt-1 trimer seen
from the extracellular side. (C) B factor representation of
Amt-1. The region with the highest B factors is in the loop
between helices V and VI, connecting the pseudosymmetry-related
halves of the protein.
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Figure 4.
Fig. 4. Ammonium recruitment site and substrate channel.
 presumably
forms a hydrogen bond to the side chain of S208 on the
extracellular side of Amt-1 (at the top), stabilized by a  interaction
with the side chain of W137. The hydrophobic channel leading to
the cytoplasmic side is blocked by F96 and F204, with the latter
having significantly elevated B factors, an indication of
structural flexibility. The N[  ]atoms of two conserved
histidine residues, H157 and H305, are in hydrogen-bonding
distance and their imidazole rings are almost perfectly coplanar.
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