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418 a.a.
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218 a.a.
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211 a.a.
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* Residue conservation analysis
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PDB id:
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Transport protein
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Title:
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X-ray crystal structure of an arginine agmatine antiporter (adic) in complex with a fab fragment
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Structure:
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Arginine/agmatine antiporter. Chain: a, b, c, d. Engineered: yes. Fab-light-chain. Chain: q, p. Engineered: yes. Fab-heavy-chain. Chain: w, s. Engineered: yes
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Source:
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Salmonella enterica subsp. Enterica serovar typhimurium. Organism_taxid: 90371. Gene: adic, anic, p60066, stm4294. Expressed in: escherichia coli. Expression_system_taxid: 562. Mus musculus. Mouse. Organism_taxid: 10090.
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Resolution:
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3.20Å
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R-factor:
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0.297
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R-free:
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0.324
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Authors:
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Y.Fang,H.Jayaram,T.Shane,L.Kolmakova-Partensky,F.Wu,C.Williams, Y.Xiong,C.Miller
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Key ref:
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Y.Fang
et al.
(2009).
Structure of a prokaryotic virtual proton pump at 3.2 A resolution.
Nature,
460,
1040-1043.
PubMed id:
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Date:
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07-Jun-09
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Release date:
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07-Jul-09
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PROCHECK
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Headers
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References
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P60066
(ADIC_SALTY) -
Arginine/agmatine antiporter from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
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Seq:
Struc:
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445 a.a.
418 a.a.
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Nature
460:1040-1043
(2009)
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PubMed id:
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Structure of a prokaryotic virtual proton pump at 3.2 A resolution.
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Y.Fang,
H.Jayaram,
T.Shane,
L.Kolmakova-Partensky,
F.Wu,
C.Williams,
Y.Xiong,
C.Miller.
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ABSTRACT
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To reach the mammalian gut, enteric bacteria must pass through the stomach. Many
such organisms survive exposure to the harsh gastric environment (pH 1.5-4) by
mounting extreme acid-resistance responses, one of which, the arginine-dependent
system of Escherichia coli, has been studied at levels of cellular physiology,
molecular genetics and protein biochemistry. This multiprotein system keeps the
cytoplasm above pH 5 during acid challenge by continually pumping protons out of
the cell using the free energy of arginine decarboxylation. At the heart of the
process is a 'virtual proton pump' in the inner membrane, called AdiC, that
imports L-arginine from the gastric juice and exports its decarboxylation
product agmatine. AdiC belongs to the APC superfamily of membrane proteins,
which transports amino acids, polyamines and organic cations in a multitude of
biological roles, including delivery of arginine for nitric oxide synthesis,
facilitation of insulin release from pancreatic beta-cells, and, when
inappropriately overexpressed, provisioning of certain fast-growing neoplastic
cells with amino acids. High-resolution structures and detailed transport
mechanisms of APC transporters are currently unknown. Here we describe a crystal
structure of AdiC at 3.2 A resolution. The protein is captured in an
outward-open, substrate-free conformation with transmembrane architecture
remarkably similar to that seen in four other families of apparently unrelated
transport 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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A.Picollo,
Y.Xu,
N.Johner,
S.Bernèche,
and
A.Accardi
(2012).
Synergistic substrate binding determines the stoichiometry of transport of a prokaryotic H(+)/Cl(-) exchanger.
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Nat Struct Mol Biol,
19,
525.
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C.Perez,
C.Koshy,
O.Yildiz,
and
C.Ziegler
(2012).
Alternating-access mechanism in conformationally asymmetric trimers of the betaine transporter BetP.
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Nature,
490,
126-130.
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PDB codes:
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D.Ma,
P.Lu,
C.Yan,
C.Fan,
P.Yin,
J.Wang,
and
Y.Shi
(2012).
Structure and mechanism of a glutamate-GABA antiporter.
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Nature,
483,
632-636.
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PDB codes:
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L.Sun,
X.Zeng,
C.Yan,
X.Sun,
X.Gong,
Y.Rao,
and
N.Yan
(2012).
Crystal structure of a bacterial homologue of glucose transporters GLUT1-4.
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Nature,
490,
361-366.
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PDB codes:
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F.Lu,
S.Li,
Y.Jiang,
J.Jiang,
H.Fan,
G.Lu,
D.Deng,
S.Dang,
X.Zhang,
J.Wang,
and
N.Yan
(2011).
Structure and mechanism of the uracil transporter UraA.
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Nature,
472,
243-246.
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PDB code:
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R.M.Bill,
P.J.Henderson,
S.Iwata,
E.R.Kunji,
H.Michel,
R.Neutze,
S.Newstead,
B.Poolman,
C.G.Tate,
and
H.Vogel
(2011).
Overcoming barriers to membrane protein structure determination.
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Nat Biotechnol,
29,
335-340.
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S.Weyand,
T.Shimamura,
O.Beckstein,
M.S.Sansom,
S.Iwata,
P.J.Henderson,
and
A.D.Cameron
(2011).
The alternating access mechanism of transport as observed in the sodium-hydantoin transporter Mhp1.
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J Synchrotron Radiat,
18,
20-23.
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A.Schlessinger,
P.Matsson,
J.E.Shima,
U.Pieper,
S.W.Yee,
L.Kelly,
L.Apeltsin,
R.M.Stroud,
T.E.Ferrin,
K.M.Giacomini,
and
A.Sali
(2010).
Comparison of human solute carriers.
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Protein Sci,
19,
412-428.
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A.Watanabe,
S.Choe,
V.Chaptal,
J.M.Rosenberg,
E.M.Wright,
M.Grabe,
and
J.Abramson
(2010).
The mechanism of sodium and substrate release from the binding pocket of vSGLT.
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Nature,
468,
988-991.
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PDB code:
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C.L.Piscitelli,
H.Krishnamurthy,
and
E.Gouaux
(2010).
Neurotransmitter/sodium symporter orthologue LeuT has a single high-affinity substrate site.
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Nature,
468,
1129-1132.
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D.L.Theobald,
and
C.Miller
(2010).
Membrane transport proteins: surprises in structural sameness.
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Nat Struct Mol Biol,
17,
2-3.
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D.P.Claxton,
M.Quick,
L.Shi,
F.D.de Carvalho,
H.Weinstein,
J.A.Javitch,
and
H.S.McHaourab
(2010).
Ion/substrate-dependent conformational dynamics of a bacterial homolog of neurotransmitter:sodium symporters.
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Nat Struct Mol Biol,
17,
822-829.
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G.Christie,
H.Götzke,
and
C.R.Lowe
(2010).
Identification of a receptor subunit and putative ligand-binding residues involved in the Bacillus megaterium QM B1551 spore germination response to glucose.
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J Bacteriol,
192,
4317-4326.
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J.Chillarón,
M.Font-Llitjós,
J.Fort,
A.Zorzano,
D.S.Goldfarb,
V.Nunes,
and
M.Palacín
(2010).
Pathophysiology and treatment of cystinuria.
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Nat Rev Nephrol,
6,
424-434.
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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.Tang,
L.Bai,
W.H.Wang,
and
T.Jiang
(2010).
Crystal structure of the carnitine transporter and insights into the antiport mechanism.
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Nat Struct Mol Biol,
17,
492-496.
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PDB code:
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S.A.Shaikh,
and
E.Tajkhorshid
(2010).
Modeling and dynamics of the inward-facing state of a Na+/Cl- dependent neurotransmitter transporter homologue.
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PLoS Comput Biol,
6,
0.
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S.Chang,
J.P.Hu,
P.Y.Lin,
X.Jiao,
and
X.H.Tian
(2010).
Substrate recognition and transport behavior analyses of amino acid antiporter with coarse-grained models.
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Mol Biosyst,
6,
2430-2438.
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S.Schulze,
S.Köster,
U.Geldmacher,
A.C.Terwisscha van Scheltinga,
and
W.Kühlbrandt
(2010).
Structural basis of Na(+)-independent and cooperative substrate/product antiport in CaiT.
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Nature,
467,
233-236.
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PDB codes:
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T.Shimamura,
S.Weyand,
O.Beckstein,
N.G.Rutherford,
J.M.Hadden,
D.Sharples,
M.S.Sansom,
S.Iwata,
P.J.Henderson,
and
A.D.Cameron
(2010).
Molecular basis of alternating access membrane transport by the sodium-hydantoin transporter Mhp1.
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Science,
328,
470-473.
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PDB code:
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T.Yoshino,
A.Shimojo,
Y.Maeda,
and
T.Matsunaga
(2010).
Inducible expression of transmembrane proteins on bacterial magnetic particles in Magnetospirillum magneticum AMB-1.
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Appl Environ Microbiol,
76,
1152-1157.
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X.Gao,
L.Zhou,
X.Jiao,
F.Lu,
C.Yan,
X.Zeng,
J.Wang,
and
Y.Shi
(2010).
Mechanism of substrate recognition and transport by an amino acid antiporter.
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Nature,
463,
828-832.
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PDB code:
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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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Z.Tao,
Y.W.Zhang,
A.Agyiri,
and
G.Rudnick
(2009).
Ligand effects on cross-linking support a conformational mechanism for serotonin transport.
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J Biol Chem,
284,
33807-33814.
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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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Links
