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
E. coli, has been studied at levels of cellular physiology, molecular genetics, and
protein biochemistry1–7. This multi-protein 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
pump8” in the inner membrane - AdiC3,4 - that imports L-arginine (Arg) from the gastric
juice and exports its decarboxylation product agmatine (Agm). AdiC belongs to the
APC superfamily of membrane proteins6,7,9, which transport
a
mino acids,
p
olyamines, and organic
c
ations in a multitude of biological roles, including delivery of arginine for nitric
oxide synthesis10, facilitation of insulin release from pancreatic β-cells11, and,
when inappropriately overexpressed, provisioning certain fast-growing neoplastic cells
with amino acids12,13. High-resolution structures and detailed transport mechanisms
of APC transporters are currently unknown. This report describes a crystal structure
of AdiC at 3.2 Å 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.
The proton-extrusion function of AdiC, formally an Arg-Agm antiporter, arises from
linkage of transport to substrate decarboxylation (Fig 1a), a reaction carried out
by a separate enzyme, AdiA, wherein an aqueous proton replaces the α-carboxyl group
of Arg to form a C-H bond on Agm; export of this “virtual proton” counteracts cytoplasmic
acidification that would otherwise occur at low extracellular pH. Physiological imperatives
demand that AdiC specifically imports the deprotonated-carboxylate Arg+1 form, which
below pH 2 represents a minor fraction of extracellular Arg2,6; transport of the predominant
Arg+2 form would produce an futile cycle useless for acid-resistance, since a carboxyl
proton would enter for each virtual proton pumped out. Transport of the Arg+2 form
cannot be directly measured in our E. coli AdiC-reconstituted liposomes at pH 6, but
argininamide+2 (Arg-NH2), an isosteric proxy for protonated Arg+2, is readily tested.
In these experiments (Fig 1b), 14C-Arg is allowed to accumulate into liposomes pre-loaded
with Arg. Radiolabel is then expelled from the liposomes by addition of a low concentration
(0.1 mM) of unlabelled Arg to the external medium, according to competition for uptake
between labeled and unlabeled substrate. A repeat of this assay with Arg-NH2 shows
that this analogue is, as expected, a poor substrate for transport, since >30-fold
higher concentration is required to mimic competition by Arg+1. A negatively charged
carboxylate cannot be a general requirement for transport, however, since the physiological
substrate Agm is an excellent substrate6. Figure 1b also presents negative transport-controls
using mutations at certain conserved aromatic residues that inhibit activity without
affecting protein assembly7. In contrast to many broad-spectrum amino acid transporters
of the APC superfamily, AdiC and homologous virtual proton pumps exhibit substantial
substrate specificity6,7,14, the structural determinants of which are not known.
AdiC is a homodimer in detergent micelles and phospholipid membranes6,7. Is subunit
cooperation required for transport, or is each subunit a self-contained transporter?
This fundamental question must be settled before details of mechanism can be sensibly
examined. We therefore designed tandem constructs containing two AdiC subunits joined
together by a short linker. The “WT-WT” tandem containing two wildtype subunits migrates
identically to the WT homodimer on a size-exclusion column and shows similar transport
activity (Fig 1c), a result etablishing that the tandem subunits fold and assemble
normally. The transport-disruptive mutation W293L was then introduced into one of
the subunits to form a “WT-MUT” tandem for comparison of its transport activity to
WT-WT. The result is clear (Fig 1d): the WT-MUT tandem is functionally active, with
an initial rate of Arg uptake roughly half of the WT-WT rate. Since the W293L substitution
abolishes Arg binding7, this experiment eliminates any transport model that requires
substrate binding to both subunits during a single transport cycle, as in cooperative,
half-of-sites mechanisms. The result implies that each subunit is itself a transporter,
and that the mechanistic underpinnings of substrate exchange are to be found within
the subunit itself, as proposed previously on the basis of whole-cell studies for
a homologous APC-superfamily protein14.
A Salmonella AdiC homologue, 95% identical to the E. coli sequence, produced crystals
diffracting anisotropically to 3.5 Å. Crystals of AdiC complexed with a FAB fragment
diffracted to 3.2 Å, and these, along with SeMet derivatives, were used for phasing
(Supp Table 1). Serviceable crystals formed only in the absence of substrate. Experimental
electron density maps of the FAB complex (Supp Fig 1a) were sufficient for model-building
of the AdiC polypeptide chain, save for the first 10 and last 4 residues, and for
two disordered loops (residues 174–182, 316–321). Poly-Ala was built into a 22-residue
extracellular loop linking transmembrane (TM) helices 5 and 6 and into several poorly
ordered regions of the FABs. The crystallographic arrangement of the complexes is
somewhat unusual (Supp Fig 1b), as the asymmetric unit contains two AdiC homodimers
but only two FABs, rather than four. This occurs because each FAB, by straddling the
intracellular subunit interface near the homodimer’s twofold axis, occludes the symmetry-related
epitope. Most of the crystal-contacts are mediated by FABs, and only a few by feeble
head-to-head encounters at neighboring AdiC extracellular surfaces. A lower-resolution,
molecular replacement structure without FAB closely recapitulates the TM helices in
the complex (Supp Fig 1b), and thereby rules out problematic structural distortion
by the FAB.
The roughly barrel-shaped AdiC subunit of ~45 Å diameter consists of 12 TM helices
(Fig 2), TM1 and TM6 being interrupted by short non-helical stretches in the middle
of their transmembrane spans. Biochemical analysis of homologues place the N- and
C- termini on the intracellular side of the membrane15,16. TMs 1–10 surround a large
cavity exposed to the extracellular solution. These ten helices reprise in AdiC the
remarkable inverted structural repeats in membrane protein families as functionally
disparate as water / glycerol channels, H+-coupled Cl− antiporters, and Na+-coupled
symporters for a variety of bio-organic compounds17–22. TMs 1–5 of AdiC align well
with TMs 6–10 turned “upside down” around a pseudo-twofold axis nearly parallel to
the membrane plane (α-carbon rmsd ~ 3.4 Å, Supp Fig 2); thus, TM1 pairs with TM6,
TM2 with TM7, etc, but no hint of this alignment appears in the primary sequence.
Helices TM11 and TM12, non-participants in this repeat, provide most of the 2500 Å2
homodimeric interface. Moreover, AdiC mirrors the common fold observed unexpectedly
in four phylogenetically unrelated families of Na+-coupled solute transporters19–23.
This result, illustrated (Fig 3a) by a structural alignment with the amino acid transporter
LeuT, dramatically confirms a recent prediction based on hydropathy analysis of APC-superfamily
proteins24. Beyond the impressive match of the TM helices, the alignment also shows
substrate bound in LeuT coincident with the region of AdiC where the functionally
critical residues Y93 and W293 reside. As a Na+-independent antiporter joining the
cluster of structurally similar families of Na+-coupled symporters (Fig 3b), AdiC
further highlights emerging questions of convergent evolution vs deep links among
ostensibly unrelated membrane proteins.
The central cavity stands out as a prominent feature of the structure (Fig 4). This
extracellular-facing aqueous cavern, ~25 Å wide at the rim, tapers to a floor situated
in the center of the protein about halfway through the membrane. The floor is formed
by a pair of aromatic side chains, Y93 and W293, projecting inward from TM3 and TM8,
the long, tilted helices paired by the inverted repeat-domains. An additional aromatic,
W202, hangs 10–15 Å away on the cavity wall. These conserved residues have been variously
proposed to contribute to substrate binding and transport in APC-type virtual proton
pumps7,14,25, as indicated above for AdiC (Fig 1B). The wall, otherwise festooned
with hydrophobic and polar moieties, is completely devoid of charged side chains.
The cavity is unambiguously cut off from the cytoplasmic solution by a ~15 Å thickness
of tightly packed protein.
Discussion
The operation of any membrane transporter relies on a cycle of distinct protein conformations
that expose substrate-binding sites alternately to the cytoplasmic and extracellular
solutions and may additionally employ intermediate “occluded” states with substrates
buried. Transport mechanisms are defined by rules linking substrate binding to transitions
among these conformations. Since x-ray structures from the APC superfamily have not
previously been described, the present view of AdiC in a single, substrate-free conformation
is inadequate for laying out a mechanistic framework for this family of transporters.
But the outward-facing structure here identifies a likely locale for substrate binding
at the cavity’s floor. This suggestion is bolstered by three lines of argument. First,
the narrowest part of a wide vestibule is a general expectation for the transport
site in a coupled transporter26. Second, mutation of aromatic residues at this site
inhibits transport activity in AdiC and homologues7,14,25. Finally, bound substrate
in structurally aligned LeuT is found in this region of AdiC (Fig 3a).
Viewed as a binding site for extracellular Arg, the cavity raises questions of molecular
recognition underlying the protein’s essential proton-extrusion function. Since Arg,
Agm, and analogues with similarly disposed charged groups are transported by AdiC6,7,
the protein might be expected to offer oppositely charged residues for salt-bridge
stabilization of substrates. But AdiC’s physiological role in acid resistance quashes
this expectation, since in a hydrated region exposed to pH 2, Glu/Asp side chains
would be fully protonated and incapable of forming coulombic contacts. Indeed, charged
residues are conspicuously absent from the cavity. The structure thus suggests - and
we propose - that the outward-facing binding site neatly solves its electrostatic
problem with aromatic sidechains, which stabilize substrates with cation-π interactions27,28.
A similar “aromatic box” was recently observed at the binding site of a Na+/betaine
symporter22. It is clear, though, that W202 is too far above the cavity’s floor for
Arg α-amino and γ-guanidino groups to contact all of these aromatics simultaneously,
and that the aromatics cannot by themselves mediate the nuanced substrate specificities
of APC-type virtual proton pumps. We also note several backbone carbonyl oxygens on
the repeat-related, non-helical stretches of TM1 and TM6, which might help stabilize
substrates via any of the five H-bond donors of substrate guanidino groups. Resolution
of the crucial biological issue - selectivity for the rare, negatively charged carboxylate
of extracellular Arg+1 - will require crystals with bound substrate, which we have
so far failed to obtain by co-crystallization or soaking.
An alternative possibility exists, however, which if true would nullify all the above
ruminations on substrate selectivity. The structure here, while certainly outward-open,
might not represent an Arg-binding form of the transport cycle at all, but rather
an Agm-expelling form whose biological purpose is to efficiently rid the protein of
substrate before beginning a new transport cycle. In other words, two different outward-open
conformations, of high and low substrate affinities, might operate in transport; a
similar situation might also apply to inward-facing forms. “Dual-open” mechanisms
like this have not been seriously considered for antiporters, but they are not a priori
implausible. Indeed, such a mechanism would be well-suited to the logic of virtual
proton pumping, whereby Arg and Agm both move thermodynamiccaly downhill, binding
at high concentration and dissociating at low, with gradients maintained by Arg decarboxylation.
This structure provides no information about inward-open forms of AdiC, but a recent
projection structure of AdiC in 2-dimensional membrane crystals7 could represent such
a conformation, since it differs dramatically from the same projection of our x-ray
structure (Supp Fig 3). Resolution of issues like this must await structures of AdiC
under different conditions with substrates, and of other members of the APC superfamily.
Methods Summary
AdiC was expressed in E. coli, purified, and reconstituted in liposomes6. AdiC function
was assessed using the E. coli homologue by 14C-Arg-Arg exchange (5 mM Arg inside,
50 µM 14C-Arg outside), at protein density 0.2–2 µg AdiC/mg lipid6. Two tandem constructs
used a 6-residue linker (GSAGGT) connecting the C-terminus of the first AdiC subunit
to the N-terminus of the second. Monoclonal antibodies were raised by inoculating
mice with E. coli AdiC and screening ELISA-positive hybridomas for stable complexes
by size-exclusion chromatography, crystallization, and diffraction quality. Approximately
25 monoclonals were tested for crystallization to obtain FAB fragment #21 used here,
which was derived from a type-2a IgG.
Salmonella serovar typhimurium
AdiC complexed with FAB21 was purified on Superdex 200 in 100 mM NaCl, 5 mM decylmaltoside,
20 mM tris-HCl pH 8, concentrated to 8 mg/mL, mixed with an equal volume of 30–35%(w/v)
PEG 400, 100–200 mM CaCl2, 100 mM glycine pH 9–9.5, and crystallized in hanging drops
at 20°C. Crystals were frozen after 2–4 weeks, and datasets were collected at NSLS,
APS, and ALS. SeMet derivatives were similarly treated. To increase redundancy of
the anomalous signal in the P1 spacegroup, datasets were collected with 4–6 360° passes.
Experimental phases determined to 3.5 Å resolution by anomalous dispersion from two
SeMet crystals - one at one wavelength and the other at two wavelengths - were combined
using Sigmaa29 and extended to 3.2 Å by noncrystallographic symmetry averaging (8-fold
for AdiC in the two crystal forms and 2-fold for FAB21) and solvent flattening. Multi-domain,
multi-crystal averaging using Dmmulti30 greatly improved the phases. Sharpening of
the data by a temperature factor of −80 Å2 significantly enhanced the details of the
electron density maps. Anomalous difference density maps identified 14 of the 15 Se
atoms expected per subunit. Attempts to observe substrate density by soaking crystals
in 5 mM substrates were unsuccessful.
Supplementary Material
1