A structural basis for Mg2+ homeostasis and the CorA translocation cycle

Mg2+-sensing mechanism of Mg2+ transporter MgtE probed by molecular dynamics study

Proper regulation of the intracellular ion concentration is essential to maintain life and is achieved by ion transporters that transport their substrates across the membrane in a strictly regulated manner. MgtE is a Mg(2+) transporter that may function in the homeostasis of the intracellular Mg(2+) concentration. A recent crystallographic study revealed that its cytosolic domain undergoes a Mg(2+)-dependent structural change, which is proposed to gate the ion-conducting pore passing through the transmembrane domain. However, the dynamics of Mg(2+) sensing, i.e., how MgtE responds to the change in the intracellular Mg(2+) concentration, remained elusive. Here we performed molecular dynamics simulations of the MgtE cytosolic domain. The simulations successfully reproduced the structural changes of the cytosolic domain upon binding or releasing Mg(2+), as well as the ion selectivity. These results suggested the roles of the N and CBS domains in the cytosolic domain and their respective Mg(2+) binding sites. Combined with the current crystal structures, we propose an atomically detailed model of Mg(2+) sensing by MgtE.

There is a baby in the bath water: AcrB contamination is a major problem in membrane-protein crystallization

In the course of a crystallographic study of the Methanosarcina mazei CorA transporter, the membrane protein was obtained with at least 95% purity and was submitted to crystallization trials. Small crystals (<100 microm) were grown that diffracted to 3.42 A resolution and belonged to space group R32, with unit-cell parameters a = b = 145.74, c = 514.0 A. After molecular-replacement attempts using available CorA structures as search models failed to yield a solution, it was discovered that the crystals consisted of an Escherichia coli contaminating protein, acriflavine resistance protein B (AcrB), that was present at less than 5% in the protein preparations. AcrB contamination is a major problem when expressing membrane proteins in E. coli since it binds naturally to immobilized metal-ion affinity chromatography (IMAC) resins. Here, the structure is compared with previously deposited AcrB structures and strategies are proposed to avoid this contamination.

Probing structure-function relationships and gating mechanisms in the CorA Mg2+ transport system

Recent crystal structures of the CorA Mg(2+) transport protein from Thermotoga maritima (TmCorA) revealed an unusually long ion pore putatively gated by hydrophobic residues near the intracellular end and by universally conserved asparagine residues at the periplasmic entrance. A conformational change observed in an isolated funnel domain structure also led to a proposal for the structural basis of gating. Because understanding the molecular mechanisms underlying ion channel and transporter gating remains an important challenge, we have undertaken a structure-guided engineering approach to probe structure-function relationships in TmCorA. The intracellular funnel domain is shown to constitute an allosteric regulatory module that can be engineered to promote an activated or closed state. A periplasmic gate centered about a proline-induced kink of the pore-lining helix is described where "helix-straightening" mutations produce a dramatic gain-of-function. Mutation to the narrowest constriction along the pore demonstrates that a hydrophobic gate is operational within this Mg(2+)-selective transport protein and likely forms an energetic barrier to ion flux. We also provide evidence that highly conserved acidic residues found in the short periplasmic loop are not essential for TmCorA function or Mg(2+) selectivity but may be required for proper protein folding and stability. This work extends our gating model for the CorA-Alr1-Mrs2 superfamily and reveals features that are characteristic of an ion channel. Aspects of these results that have broader implications for a range of channel and transporter families are highlighted.

Bacterial homologs of eukaryotic membrane proteins: the 2-TM-GxN family of Mg(2+) transporters

Magnesium is essential for all forms of life. It is the cofactor for many enzymes and plays a key role in many biological processes. Thus, the acquisition of Mg(2+) is crucial for cell survival. The best characterized Mg(2+) transporters to date belong to the 2-TM-GxN type family of transporters. The name indicates the two C-terminal transmembrane (TM) domains and a conserved GxN motif present in all members of this family towards the C-terminal end of TM1. In most members of the family, this conserved motif is generally YGMNF. The prototypical member of this family is CorA. Other characterized members of this family include Mrs2p, Alr, Mnr, AtMGT and ZntB. CorA is widely distributed throughout the prokaryotic world. It is the primary Mg(2+) uptake system in most bacteria and many Archaea. A homolog, Mrs2p, is a eukaryotic mitochondrial Mg(2+) channel. The Mrs2p related AtMGT transporters are found in plants and other eukaryotes. Alr1p and Mnr are Mg(2+) transporters found in the plasma membrane of many fungi. ZntB is a bacterial member of the 2-TM-GxN family but mediates efflux of Zn(2+) instead of influx of Mg(2+). The recent crystal structure of a bacterial CorA shows that the structure of this family is unlike that of any other class of transporter or channel currently known.

Structural biology of transmembrane domains: efficient production and characterization of transmembrane peptides by NMR

Structural characterization of transmembrane peptides (TMPs) is justified because transmembrane domains of membrane proteins appear to often function independently of the rest of the protein. However, the challenge in obtaining milligrams of isotopically labeled TMPs to study these highly hydrophobic peptides by nuclear magnetic resonance (NMR) is significant. In the present work, a protocol is developed to produce, isotopically label, and purify TMPs in high yield as well as to initially characterize the TMPs with CD and both solution and solid-state NMR. Six TMPs from three integral membrane proteins, CorA, M2, and KdpF, were studied. CorA and KdpF are from Mycobacterium tuberculosis, while M2 is from influenza A virus. Several milligrams of each of these TMPs ranging from 25 to 89 residues were obtained per liter of M9 culture. The initial structural characterization results showed that these peptides were well folded in both detergent micelles and lipid bilayer preparations. The high yield, the simplicity of purification, and the convenient protocol represents a suitable approach for NMR studies and a starting point for characterizing the transmembrane domains of membrane proteins.

Mrs2p forms a high conductance Mg2+ selective channel in mitochondria

Members of the CorA-Mrs2-Alr1 superfamily of Mg²⁺ transporters are ubiquitous among pro- and eukaryotes. The crystal structure of a bacterial CorA protein has recently been solved, but the mode of ion transport of this protein family remained obscure. Using single channel patch clamping we unequivocally show here that the mitochondrial Mrs2 protein forms a Mg²⁺-selective channel of high conductance (155 pS). It has an open probability of ∼60% in the absence of Mg²⁺ at the matrix site, which decreases to ∼20% in its presence. With a lower conductance (∼45 pS) the Mrs2 channel is also permeable for Ni²⁺, whereas no permeability has been observed for either Ca²⁺, Mn²⁺, or Co²⁺. Mutational changes in key domains of Mrs2p are shown either to abolish its Mg²⁺ transport or to change its characteristics toward more open and partly deregulated states. We conclude that Mrs2p forms a high conductance Mg²⁺ selective channel that controls Mg²⁺ influx into mitochondria by an intrinsic negative feedback mechanism.

Crystal structure of the MgtE Mg2+ transporter

The magnesium ion Mg2+ is a vital element involved in numerous physiological processes. Mg2+ has the largest hydrated radius among all cations, whereas its ionic radius is the smallest. It remains obscure how Mg2+ transporters selectively recognize and dehydrate the large, fully hydrated Mg2+ cation for transport. Recently the crystal structures of the CorA Mg2+ transporter were reported. The MgtE family of Mg2+ transporters is ubiquitously distributed in all phylogenetic domains, and human homologues have been functionally characterized and suggested to be involved in magnesium homeostasis. However, the MgtE transporters have not been thoroughly characterized. Here we determine the crystal structures of the full-length Thermus thermophilus MgtE at 3.5 A resolution, and of the cytosolic domain in the presence and absence of Mg2+ at 2.3 A and 3.9 A resolutions, respectively. The transporter adopts a homodimeric architecture, consisting of the carboxy-terminal five transmembrane domains and the amino-terminal cytosolic domains, which are composed of the superhelical N domain and tandemly repeated cystathionine-beta-synthase domains. A solvent-accessible pore nearly traverses the transmembrane domains, with one potential Mg2+ bound to the conserved Asp 432 within the pore. The transmembrane (TM)5 helices from both subunits close the pore through interactions with the 'connecting helices', which connect the cystathionine-beta-synthase and transmembrane domains. Four putative Mg2+ ions are bound at the interface between the connecting helices and the other domains, and this may lock the closed conformation of the pore. A structural comparison of the two states of the cytosolic domains showed the Mg2+-dependent movement of the connecting helices, which might reorganize the transmembrane helices to open the pore. These findings suggest a homeostasis mechanism, in which Mg2+ bound between cytosolic domains regulates Mg2+ flux by sensing the intracellular Mg2+ concentration. Whether this presumed regulation controls gating of an ion channel or opening of a secondary active transporter remains to be determined.

Crystallization and preliminary X-ray diffraction analysis of the full-length Mg2+ transporter MgtE

The MgtE family of Mg(2+) transporters are ubiquitously conserved in all three domains. The genes encoding full-length MgtE from seven different species were cloned. Three of the seven MgtE transporters were overexpressed and purified for use in crystallization trials. Only Thermus thermophilus MgtE was successfully crystallized using the sitting-drop vapour-diffusion method. Selenomethionine-substituted (SeMet) crystals were obtained by cross-microseeding using the native microcrystals. The SeMet crystals diffracted X-rays to 3.5 A resolution using synchrotron radiation and belong to space group C222(1), with unit-cell parameters a = 118.3, b = 134.9, c = 366.2 A. Structure determination is in progress.