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PDBsum entry 1u7c
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Transport protein
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PDB id
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1u7c
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Contents |
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* Residue conservation analysis
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DOI no:
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Science
305:1587-1594
(2004)
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PubMed id:
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Mechanism of ammonia transport by Amt/MEP/Rh: structure of AmtB at 1.35 A.
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S.Khademi,
J.O'Connell,
J.Remis,
Y.Robles-Colmenares,
L.J.Miercke,
R.M.Stroud.
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ABSTRACT
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The first structure of an ammonia channel from the Amt/MEP/Rh protein
superfamily, determined to 1.35 angstrom resolution, shows it to be a channel
that spans the membrane 11 times. Two structurally similar halves span the
membrane with opposite polarity. Structures with and without ammonia or methyl
ammonia show a vestibule that recruits NH4+/NH3, a binding site for NH4+, and a
20 angstrom-long hydrophobic channel that lowers the NH4+ pKa to below 6 and
conducts NH3. Favorable interactions for NH3 are seen within the channel and use
conserved histidines. Reconstitution of AmtB into vesicles shows that AmtB
conducts uncharged NH3.
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Selected figure(s)
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Figure 4.
Fig. 4. (A) Electron density (2Fo-Fc) contoured at 1.5  (blue) for the
two-histidine region and surrounding structure, including
conserved Asp160 that accepts four short hydrogen bonds (dashed
yellow). Additional peaks Am2, Am3, and Am4 seen when
crystallized with 25 mM ammonium sulfate are defined in the
Fo-Fc omit map at 1.5 (in red),
indicating putative NH[3] molecule positions (blue spheres). The
hydrogen-bonding network shows interactions between His168 and
His318 and NH[3] peaks in yellow (distances in red). (B) Stereo
view of the two-histidine center of the channel. Surrounding
hydrophobic residues are shown in ball and stick representation.
The surface representation covers other surrounding amino acids.
Three ammonia-dependent sites are shown (blue spheres) with
associated distances (dashed yellow line and yellow labels).
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Figure 6.
Fig. 6. The deduced mechanism of conductance is summarized. The
low electron density for NH[3] may represent substitutional
interchange or relative freedom of NH[3] within the hydrophobic
channel. NH[3] normally undergoes rapid inversion. This may be
impeded against the weak hydrogen bond C-H donors of imidazole.
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The above figures are
reprinted
by permission from the AAAs:
Science
(2004,
305,
1587-1594)
copyright 2004.
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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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C.A.Wagner,
O.Devuyst,
H.Belge,
S.Bourgeois,
and
P.Houillier
(2011).
The rhesus protein RhCG: a new perspective in ammonium transport and distal urinary acidification.
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Kidney Int,
79,
154-161.
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L.Graff,
P.Obrdlik,
L.Yuan,
D.Loqué,
W.B.Frommer,
and
N.von Wirén
(2011).
N-terminal cysteines affect oligomer stability of the allosterically regulated ammonium transporter LeAMT1;1.
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J Exp Bot,
62,
1361-1373.
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N.M.Burton,
and
G.Daniels
(2011).
Structural modelling of red cell surface proteins.
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Vox Sang,
100,
129-139.
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S.Y.Lu,
Y.J.Jiang,
J.W.Zou,
H.B.Luo,
and
T.X.Wu
(2011).
Insight into analysis of interactions of GW9508 to wild-type and H86F and H137F GPR40: a combined QM/MM study and pharmacophore modeling.
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J Mol Graph Model,
29,
818-825.
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U.Akgun,
and
S.Khademi
(2011).
Periplasmic vestibule plays an important role for solute recruitment, selectivity, and gating in the Rh/Amt/MEP superfamily.
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Proc Natl Acad Sci U S A,
108,
3970-3975.
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A.B.Waight,
J.Love,
and
D.N.Wang
(2010).
Structure and mechanism of a pentameric formate channel.
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Nat Struct Mol Biol,
17,
31-37.
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PDB codes:
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A.M.Zimmer,
C.M.Nawata,
and
C.M.Wood
(2010).
Physiological and molecular analysis of the interactive effects of feeding and high environmental ammonia on branchial ammonia excretion and Na+ uptake in freshwater rainbow trout.
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J Comp Physiol B,
180,
1191-1204.
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C.H.Huang,
and
M.Ye
(2010).
The Rh protein family: gene evolution, membrane biology, and disease association.
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Cell Mol Life Sci,
67,
1203-1218.
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F.Gruswitz,
S.Chaudhary,
J.D.Ho,
A.Schlessinger,
B.Pezeshki,
C.M.Ho,
A.Sali,
C.M.Westhoff,
and
R.M.Stroud
(2010).
Function of human Rh based on structure of RhCG at 2.1 A.
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Proc Natl Acad Sci U S A,
107,
9638-9643.
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PDB code:
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J.L.Robertson,
L.Kolmakova-Partensky,
and
C.Miller
(2010).
Design, function and structure of a monomeric ClC transporter.
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Nature,
468,
844-847.
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PDB code:
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J.Love,
F.Mancia,
L.Shapiro,
M.Punta,
B.Rost,
M.Girvin,
D.N.Wang,
M.Zhou,
J.F.Hunt,
T.Szyperski,
E.Gouaux,
R.MacKinnon,
A.McDermott,
B.Honig,
M.Inouye,
G.Montelione,
and
W.A.Hendrickson
(2010).
The New York Consortium on Membrane Protein Structure (NYCOMPS): a high-throughput platform for structural genomics of integral membrane proteins.
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J Struct Funct Genomics,
11,
191-199.
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K.McLuskey,
A.W.Roszak,
Y.Zhu,
and
N.W.Isaacs
(2010).
Crystal structures of all-alpha type membrane proteins.
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Eur Biophys J,
39,
723-755.
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K.R.Vinothkumar,
and
R.Henderson
(2010).
Structures of membrane proteins.
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Q Rev Biophys,
43,
65.
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L.Li,
and
R.F.Ismagilov
(2010).
Protein crystallization using microfluidic technologies based on valves, droplets, and SlipChip.
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Annu Rev Biophys,
39,
139-158.
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N.D.Shetty,
M.C.Reddy,
S.K.Palaninathan,
J.L.Owen,
and
J.C.Sacchettini
(2010).
Crystal structures of the apo and ATP bound Mycobacterium tuberculosis nitrogen regulatory PII protein.
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Protein Sci,
19,
1513-1524.
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PDB codes:
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A.Missner,
and
P.Pohl
(2009).
110 years of the Meyer-Overton rule: predicting membrane permeability of gases and other small compounds.
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Chemphyschem,
10,
1405-1414.
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D.G.Tamang,
R.Rabus,
R.D.Barabote,
and
M.H.Saier
(2009).
Comprehensive analyses of transport proteins encoded within the genome of "Aromatoleum aromaticum" strain EbN1.
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J Membr Biol,
229,
53-90.
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D.Loqué,
S.I.Mora,
S.L.Andrade,
O.Pantoja,
and
W.B.Frommer
(2009).
Pore mutations in ammonium transporter AMT1 with increased electrogenic ammonium transport activity.
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J Biol Chem,
284,
24988-24995.
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E.J.Levin,
M.Quick,
and
M.Zhou
(2009).
Crystal structure of a bacterial homologue of the kidney urea transporter.
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Nature,
462,
757-761.
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PDB codes:
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J.M.Thevelein,
and
K.Voordeckers
(2009).
Functioning and evolutionary significance of nutrient transceptors.
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Mol Biol Evol,
26,
2407-2414.
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L.J.Bruce,
H.Guizouarn,
N.M.Burton,
N.Gabillat,
J.Poole,
J.F.Flatt,
R.L.Brady,
F.Borgese,
J.Delaunay,
and
G.W.Stewart
(2009).
The monovalent cation leak in overhydrated stomatocytic red blood cells results from amino acid substitutions in the Rh-associated glycoprotein.
|
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Blood,
113,
1350-1357.
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L.R.Forrest,
and
G.Rudnick
(2009).
The rocking bundle: a mechanism for ion-coupled solute flux by symmetrical transporters.
|
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Physiology (Bethesda),
24,
377-386.
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L.Yuan,
L.Graff,
D.Loqué,
S.Kojima,
Y.N.Tsuchiya,
H.Takahashi,
and
N.von Wirén
(2009).
AtAMT1;4, a Pollen-Specific High-Affinity Ammonium Transporter of the Plasma Membrane in Arabidopsis.
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Plant Cell Physiol,
50,
13-25.
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M.A.Knepper,
and
J.A.Mindell
(2009).
Structural biology: Molecular coin slots for urea.
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Nature,
462,
733-734.
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N.Dabas,
S.Schneider,
and
J.Morschhäuser
(2009).
Mutational analysis of the Candida albicans ammonium permease Mep2p reveals residues required for ammonium transport and signaling.
|
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Eukaryot Cell,
8,
147-160.
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P.L.Tremblay,
and
P.C.Hallenbeck
(2009).
Of blood, brains and bacteria, the Amt/Rh transporter family: emerging role of Amt as a unique microbial sensor.
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Mol Microbiol,
71,
12-22.
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R.Musa-Aziz,
L.Jiang,
L.M.Chen,
K.L.Behar,
and
W.F.Boron
(2009).
Concentration-dependent effects on intracellular and surface pH of exposing Xenopus oocytes to solutions containing NH3/NH4(+).
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J Membr Biol,
228,
15-31.
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R.Musa-Aziz,
L.M.Chen,
M.F.Pelletier,
and
W.F.Boron
(2009).
Relative CO2/NH3 selectivities of AQP1, AQP4, AQP5, AmtB, and RhAG.
|
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Proc Natl Acad Sci U S A,
106,
5406-5411.
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R.Søgaard,
M.Alsterfjord,
N.Macaulay,
and
T.Zeuthen
(2009).
Ammonium ion transport by the AMT/Rh homolog TaAMT1;1 is stimulated by acidic pH.
|
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Pflugers Arch,
458,
733-743.
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U.Ludewig,
and
M.Dynowski
(2009).
Plant aquaporin selectivity: where transport assays, computer simulations and physiology meet.
|
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Cell Mol Life Sci,
66,
3161-3175.
|
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W.B.Inwood,
J.A.Hall,
K.S.Kim,
L.Demirkhanyan,
D.Wemmer,
H.Zgurskaya,
and
S.Kustu
(2009).
Epistatic effects of the protease/chaperone HflB on some damaged forms of the Escherichia coli ammonium channel AmtB.
|
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Genetics,
183,
1327-1340.
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W.B.Inwood,
J.A.Hall,
K.S.Kim,
R.Fong,
and
S.Kustu
(2009).
Genetic evidence for an essential oscillation of transmembrane-spanning segment 5 in the Escherichia coli ammonium channel AmtB.
|
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Genetics,
183,
1341-1355.
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W.Im,
J.Lee,
T.Kim,
and
H.Rui
(2009).
Novel free energy calculations to explore mechanisms and energetics of membrane protein structure and function.
|
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J Comput Chem,
30,
1622-1633.
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Y.Lin,
Z.Cao,
and
Y.Mo
(2009).
Functional role of Asp160 and the deprotonation mechanism of ammonium in the Escherichia coli ammonia channel protein AmtB.
|
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J Phys Chem B,
113,
4922-4929.
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Y.Wang,
Y.Huang,
J.Wang,
C.Cheng,
W.Huang,
P.Lu,
Y.N.Xu,
P.Wang,
N.Yan,
and
Y.Shi
(2009).
Structure of the formate transporter FocA reveals a pentameric aquaporin-like channel.
|
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Nature,
462,
467-472.
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PDB codes:
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Z.E.Newby,
J.D.O'Connell,
F.Gruswitz,
F.A.Hays,
W.E.Harries,
I.M.Harwood,
J.D.Ho,
J.K.Lee,
D.F.Savage,
L.J.Miercke,
and
R.M.Stroud
(2009).
A general protocol for the crystallization of membrane proteins for X-ray structural investigation.
|
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Nat Protoc,
4,
619-637.
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A.Javelle,
D.Lupo,
P.Ripoche,
T.Fulford,
M.Merrick,
and
F.K.Winkler
(2008).
Substrate binding, deprotonation, and selectivity at the periplasmic entrance of the Escherichia coli ammonia channel AmtB.
|
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Proc Natl Acad Sci U S A,
105,
5040-5045.
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PDB codes:
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A.Missner,
P.Kügler,
S.M.Saparov,
K.Sommer,
J.C.Mathai,
M.L.Zeidel,
and
P.Pohl
(2008).
Carbon dioxide transport through membranes.
|
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J Biol Chem,
283,
25340-25347.
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B.Martinac,
Y.Saimi,
and
C.Kung
(2008).
Ion channels in microbes.
|
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Physiol Rev,
88,
1449-1490.
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B.Walter,
M.Küspert,
D.Ansorge,
R.Krämer,
and
A.Burkovski
(2008).
Dissection of ammonium uptake systems in Corynebacterium glutamicum: mechanism of action and energetics of AmtA and AmtB.
|
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J Bacteriol,
190,
2611-2614.
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C.C.Hung,
C.M.Nawata,
C.M.Wood,
and
P.A.Wright
(2008).
Rhesus glycoprotein and urea transporter genes are expressed in early stages of development of rainbow trout (Oncorhynchus mykiss).
|
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J Exp Zool Part A Ecol Genet Physiol,
309,
262-268.
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C.Yoshihara,
K.Inoue,
D.Schichnes,
S.Ruzin,
W.Inwood,
and
S.Kustu
(2008).
An Rh1-GFP fusion protein is in the cytoplasmic membrane of a white mutant strain of Chlamydomonas reinhardtii.
|
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Mol Plant,
1,
1007-1020.
|
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J.C.Rutherford,
G.Chua,
T.Hughes,
M.E.Cardenas,
and
J.Heitman
(2008).
A Mep2-dependent transcriptional profile links permease function to gene expression during pseudohyphal growth in Saccharomyces cerevisiae.
|
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Mol Biol Cell,
19,
3028-3039.
|
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J.C.Rutherford,
X.Lin,
K.Nielsen,
and
J.Heitman
(2008).
Amt2 Permease Is Required To Induce Ammonium-Responsive Invasive Growth and Mating in Cryptococcus neoformans.
|
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Eukaryot Cell,
7,
237-246.
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J.H.Kirsten,
Y.Xiong,
C.T.Davis,
and
C.K.Singleton
(2008).
Subcellular localization of ammonium transporters in Dictyostelium discoideum.
|
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BMC Cell Biol,
9,
71.
|
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L.J.Bruce
(2008).
Red cell membrane transport abnormalities.
|
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Curr Opin Hematol,
15,
184-190.
|
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|
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L.R.Forrest,
Y.W.Zhang,
M.T.Jacobs,
J.Gesmonde,
L.Xie,
B.H.Honig,
and
G.Rudnick
(2008).
Mechanism for alternating access in neurotransmitter transporters.
|
| |
Proc Natl Acad Sci U S A,
105,
10338-10343.
|
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|
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N.H.Joh,
A.Min,
S.Faham,
J.P.Whitelegge,
D.Yang,
V.L.Woods,
and
J.U.Bowie
(2008).
Modest stabilization by most hydrogen-bonded side-chain interactions in membrane proteins.
|
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Nature,
453,
1266-1270.
|
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PDB codes:
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|
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N.M.Burton,
and
D.J.Anstee
(2008).
Structure, function and significance of Rh proteins in red cells.
|
| |
Curr Opin Hematol,
15,
625-630.
|
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|
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P.F.Teixeira,
A.Jonsson,
M.Frank,
H.Wang,
and
S.Nordlund
(2008).
Interaction of the signal transduction protein GlnJ with the cellular targets AmtB1, GlnE and GlnD in Rhodospirillum rubrum: dependence on manganese, 2-oxoglutarate and the ADP/ATP ratio.
|
| |
Microbiology,
154,
2336-2347.
|
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P.L.Tremblay,
and
P.C.Hallenbeck
(2008).
Ammonia-induced formation of an AmtB-GlnK complex is not sufficient for nitrogenase regulation in the photosynthetic bacterium Rhodobacter capsulatus.
|
| |
J Bacteriol,
190,
1588-1594.
|
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|
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R.Roth,
D.Gillespie,
W.Nonner,
and
R.E.Eisenberg
(2008).
Bubbles, gating, and anesthetics in ion channels.
|
| |
Biophys J,
94,
4282-4298.
|
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|
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S.Lammers,
S.Lutz,
and
M.Meuwly
(2008).
Reactive force fields for proton transfer dynamics.
|
| |
J Comput Chem,
29,
1048-1063.
|
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|
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T.Nagata,
S.Iizumi,
K.Satoh,
and
S.Kikuchi
(2008).
Comparative molecular biological analysis of membrane transport genes in organisms.
|
| |
Plant Mol Biol,
66,
565-585.
|
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|
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V.Nanda,
and
A.Schmiedekamp
(2008).
Are aromatic carbon donor hydrogen bonds linear in proteins?
|
| |
Proteins,
70,
489-497.
|
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|
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A.Korepanova,
J.D.Moore,
H.B.Nguyen,
Y.Hua,
T.A.Cross,
and
F.Gao
(2007).
Expression of membrane proteins from Mycobacterium tuberculosis in Escherichia coli as fusions with maltose binding protein.
|
| |
Protein Expr Purif,
53,
24-30.
|
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B.Cherif-Zahar,
A.Durand,
I.Schmidt,
N.Hamdaoui,
I.Matic,
M.Merrick,
and
G.Matassi
(2007).
Evolution and functional characterization of the RH50 gene from the ammonia-oxidizing bacterium Nitrosomonas europaea.
|
| |
J Bacteriol,
189,
9090-9100.
|
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B.J.Gaffney
(2007).
Anesthesia, analgesia, and euphoria.
|
| |
Biophys J,
92,
1-2.
|
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|
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C.J.De Feo,
S.G.Aller,
and
V.M.Unger
(2007).
A structural perspective on copper uptake in eukaryotes.
|
| |
Biometals,
20,
705-716.
|
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|
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C.M.Westhoff
(2007).
The structure and function of the Rh antigen complex.
|
| |
Semin Hematol,
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PDB codes:
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PDB codes:
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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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