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Structural insights into the elevator-like mechanism of the sodium/citrate symporter CitS. Sci Rep 2017; 7:2548. [PMID: 28566738 PMCID: PMC5451387 DOI: 10.1038/s41598-017-02794-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 04/19/2017] [Indexed: 11/09/2022] Open
Abstract
The sodium-dependent citrate transporter of Klebsiella pneumoniae (KpCitS) belongs to the 2-hydroxycarboxylate transporter (2-HCT) family and allows the cell to use citrate as sole carbon and energy source in anaerobic conditions. Here we present crystal structures of KpCitS in citrate-bound outward-facing, citrate-bound asymmetric, and citrate-free inward-facing state. The structures reveal that the KpCitS dimerization domain remains stationary throughout the transport cycle due to a hydrogen bond network as well as extensive hydrophobic interactions. In contrast, its transport domain undergoes a ~35° rigid-body rotation and a ~17 Å translocation perpendicular to the membrane to expose the substrate-binding site alternately to either side of the membrane. Furthermore, homology models of two other 2-HCT proteins based on the KpCitS structure offer structural insights into their differences in substrate specificity at a molecular level. On the basis of our results and previous biochemical data, we propose that the activity of the 2-HCT CitS involves an elevator-like movement in which the transport domain itself traverses the lipid bilayer, carrying the substrate into the cell in a sodium-dependent manner.
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2
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Structure and elevator mechanism of the Na +-citrate transporter CitS. Curr Opin Struct Biol 2016; 45:1-9. [PMID: 27776291 DOI: 10.1016/j.sbi.2016.10.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 10/04/2016] [Accepted: 10/05/2016] [Indexed: 10/20/2022]
Abstract
The recently determined crystal structure of the bacterial Na+-citrate symporter CitS provides unexpected structural and mechanistic insights. The protein has a fold that has not been seen in other proteins, but the oligomeric state, domain organization and proposed transport mechanism strongly resemble those of the sodium-dicarboxylate symporter vcINDY, and the putative exporters YdaH and MtrF, thus hinting at convergence in structure and function. CitS and the related proteins are predicted to translocate their substrates by an elevator-like mechanism, in which a compact transport domain slides up and down through the membrane while the dimerization domain is stably anchored. Here we review the large body of available biochemical data on CitS in the light of the new crystal structure. We show that the biochemical data are fully consistent with the proposed elevator mechanism, but also demonstrate that the current structural data cannot explain how strict coupling of citrate and Na+ transport is achieved. We propose a testable model for the coupling mechanism.
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3
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Kolbusz MA, Slotboom DJ, Lolkema JS. Genomic distribution of the small multidrug resistance protein EmrE over 29Escherichia colistrains reveals two forms of the protein. FEBS J 2012; 280:244-55. [DOI: 10.1111/febs.12065] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Revised: 11/08/2012] [Accepted: 11/12/2012] [Indexed: 11/29/2022]
Affiliation(s)
- Magdalena A. Kolbusz
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute; University of Groningen; The Netherlands
| | - Dirk J. Slotboom
- Membrane Enzymology, Groningen Biomolecular Sciences and Biotechnology Institute; University of Groningen; The Netherlands
| | - Juke S. Lolkema
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute; University of Groningen; The Netherlands
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4
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Krupnik T, Sobczak-Elbourne I, Lolkema JS. Turnover and accessibility of a reentrant loop of the Na+-glutamate transporter GltS are modulated by the central cytoplasmic loop. Mol Membr Biol 2011; 28:462-72. [PMID: 21995702 DOI: 10.3109/09687688.2011.624989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
GltS of Escherichia coli is a secondary transporter that catalyzes Na+-glutamate symport. The structural model of GltS shows two homologous domains with inverted membrane topology that are connected by a central loop that resides in the cytoplasm. Each domain contains a reentrant loop structure. Accessibility of the Cys residues in two GltS mutants in which Pro351 and Asn356 in the reentrant loop in the C-terminal domain were replaced by Cys is demonstrated to be sensitive to the catalytic state supporting a role for the reentrant loops in catalysis. Saturating concentrations of the substrate L-glutamate protected both mutants against inactivation by thiol reagents, while the presence of the co-ion Na+ stimulated the inactivation of both mutants. Insertion of the 10 kDa biotin acceptor domain (BAD) of oxaloacetate decarboxylase of Klebsiella pneumoniae in the central cytoplasmic loop blocked the access pathway from the periplasmic side of the membrane to the cysteine residues in mutants P351C and N356C in the reentrant loop. Kinetically, insertion of BAD increased the maximal rate of uptake 2.7-fold while leaving the apparent affinity constants for L-glutamate and Na+ unaltered. The data suggests that insertion of BAD in the central loop results in conformational changes at the translocation site that lower the activation energy of the translocation step without affecting the access pathway from the periplasmic side for substrate and co-ions. It is concluded that changes in the central loop that connects the two domains may have a regulatory function on the activity of the transporter.
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Affiliation(s)
- Tomas Krupnik
- Department of Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
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5
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Krupnik T, Dobrowolski A, Lolkema JS. Cross-linking of dimeric CitS and GltS transport proteins. Mol Membr Biol 2011; 28:243-53. [DOI: 10.3109/09687688.2011.581252] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Tomasz Krupnik
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute,
University of Groningen, The Netherlands
| | - Adam Dobrowolski
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute,
University of Groningen, The Netherlands
| | - Juke S. Lolkema
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute,
University of Groningen, The Netherlands
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6
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Trip H, Mulder NL, Rattray FP, Lolkema JS. HdcB, a novel enzyme catalysing maturation of pyruvoyl-dependent histidine decarboxylase. Mol Microbiol 2011; 79:861-71. [PMID: 21208300 DOI: 10.1111/j.1365-2958.2010.07492.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Pyruvoyl-dependent histidine decarboxylases are produced as proenzymes that mature by cleavage followed by formation of the pyruvoyl prosthetic group. The histidine decarboxylation pathway of Streptococcus thermophilus CHCC1524 that consists of the pyruvoyl-dependent histidine decarboxylase HdcA and the histidine/histamine exchanger HdcP was functionally expressed in Lactococcus lactis. The operon encoding the pathway contains in addition to the hdcA and hdcP genes a third gene hdcB. Expression of different combinations of the genes in L. lactis and Escherichia coli followed by analysis of the protein products demonstrated the involvement of HdcB in the cleavage of the HdcA proenzyme. The HdcA proenzyme and HdcB protein were purified to homogeneity and cleavage and activation of the histidine decarboxylase activity was demonstrated in vitro. Substoichiometric amounts of HdcB were required to cleave HdcA showing that HdcB functions as an enzyme. In agreement, expression levels of HdcB in the cells were low relative to those of HdcA. The turnover number of HdcB in vitro was extremely low (0.05 min⁻¹) which was due to a very slow association/dissociation of the enzyme/substrate complex. In fact, HdcB was shown to co-purify both with the HdcA S82A mutant that mimics the proenzyme and with the mature HdcA complex.
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Affiliation(s)
- Hein Trip
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
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7
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Dobrowolski A, Fusetti F, Lolkema JS. Cross-linking of trans reentrant loops in the Na(+)-citrate transporter CitS of Klebsiella pneumoniae. Biochemistry 2010; 49:4509-15. [PMID: 20420430 DOI: 10.1021/bi100336s] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The membrane topology model of the Na(+)-citrate transporter CitS of Klebsiella pneumoniae shows a core of two homologous domains with opposite orientation in the membrane and each containing a so-called reentrant loop. A split version of CitS was constructed to study domain interactions and proximity relationships of the putative reentrant loops. Split CitS retained 50% transport activity of the wild-type version in membrane vesicles. Unspecific cross-linking of the purified complex with glutaraldehyde revealed a tetrameric complex with two N and two C domains corresponding to dimeric CitS. The separately expressed domains were not detected in the membrane. Strong interaction between the two domains followed from successful purification of the whole complex by Ni(2+)-NTA chromatography when only one domain was His-tagged. The presence of citrate and/or the co-ion Na(+) during purification did not seem to affect the interaction significantly. Successful disulfide cross-linking was obtained between single cysteine residues introduced in the highly conserved GGNG sequence motif at the vertex of the reentrant loop in the N domain and either of two endogenous cysteine residues at the base of the reentrant loop in the C domain. The disulfide bond was formed within one subunit in the dimer. A model is proposed in which the reentrant loops in the N and C domains are overlapping at the domain interface in the 3D structure where they form (part of) the translocation pathway for substrate and co-ions.
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Affiliation(s)
- Adam Dobrowolski
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
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Ter Horst R, Lolkema JS. Rapid screening of membrane topology of secondary transport proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2009; 1798:672-80. [PMID: 19932679 DOI: 10.1016/j.bbamem.2009.11.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2009] [Revised: 11/06/2009] [Accepted: 11/13/2009] [Indexed: 11/25/2022]
Abstract
Limited experimental data may be very useful to discriminate between membrane topology models of membrane proteins derived from different methods. A membrane topology screening method is proposed by which the cellular disposition of three positions in a membrane protein are determined, the N- and the C-termini and a position in the middle of the protein. The method involves amplification of the encoding genes or gene fragments by PCR, rapid cloning in dedicated vectors by ligation independent cloning, and determination of the cellular disposition of the three sites using conventional techniques. The N-terminus was determined by labeling with a fluorescent probe, the central position and the C-terminus by the reporter fusion technique using alkaline phosphatase (PhoA) and green fluorescence protein (GFP) as reporters. The method was evaluated using 16 transporter proteins of known function from four different structural classes. For 13 proteins a complete set of three localizations was obtained. The experimental data was used to discriminate between membrane topology models predicted by TMHMM, a widely used predictor using the amino acid sequence as input and by MemGen that uses hydropathy profile alignment and known 3D structures or existing models. It follows that in those cases where the models from the two methods were similar, the models were consistent with the experimental data. In those cases where the models differed, the MemGen model agreed with the experimental data. Three more recent predictors, MEMSAT3, OCTOPUS and TOPCONS showed a significantly higher consistency with the experimental data than observed with TMHMM.
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Affiliation(s)
- Ramon Ter Horst
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
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Dobrowolski A, Lolkema JS. Functional Importance of GGXG Sequence Motifs in Putative Reentrant Loops of 2HCT and ESS Transport Proteins. Biochemistry 2009; 48:7448-56. [DOI: 10.1021/bi9004914] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Adam Dobrowolski
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Haren, The Netherlands
| | - Juke S. Lolkema
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Haren, The Netherlands
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Mościcka KB, Krupnik T, Boekema EJ, Lolkema JS. Projection structure by single-particle electron microscopy of secondary transport proteins GltT, CitS, and GltS. Biochemistry 2009; 48:6618-23. [PMID: 19518127 DOI: 10.1021/bi900838d] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The structure of three secondary transporter proteins, GltT of Bacillus stearothermophilus, CitS of Klebsiella pneumoniae, and GltS of Escherichia coli, was studied. The proteins were purified to homogeneity in detergent solution by Ni(2+)-NTA affinity chromatography, and the complexes were determined by BN-PAGE to be trimeric, dimeric, and dimeric for GltT, CitS, and GltS, respectively. The subunit stoichiometry correlated with the binding affinity of the Ni(2+)-NTA resin for the protein complexes. Projection maps of negatively stained transporter particles were obtained by single-particle electron microscopy. Processing of the GltT particles revealed a projection map possessing 3-fold rotational symmetry, in good agreement with the trimer observed in the crystal structure of a homologous protein, Glt(Ph) of Pyrococcus horikoshii. The CitS protein showed up in two main views: as a kidney-shaped particle and a biscuit-shaped particle, both with a long axis of 160 A. The latter has a width of 84 A, the former of 92 A. Symmetry considerations identify the biscuit shape as a top view and the kidney shape as a side view from within the membrane. Combining the two images shows that the CitS dimer is a protein with a strong curvature at one side of the membrane and, at the opposite side, an indentation in the middle at the subunit interface. The GltS protein was shaped like CitS with dimensions of 145 A x 84 A. The shapes and dimensions of the CitS and GltS particles are consistent with a similar structure of these two unrelated proteins.
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Sobczak I, Lolkema JS. The 2-hydroxycarboxylate transporter family: physiology, structure, and mechanism. Microbiol Mol Biol Rev 2006; 69:665-95. [PMID: 16339740 PMCID: PMC1306803 DOI: 10.1128/mmbr.69.4.665-695.2005] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The 2-hydroxycarboxylate transporter family is a family of secondary transporters found exclusively in the bacterial kingdom. They function in the metabolism of the di- and tricarboxylates malate and citrate, mostly in fermentative pathways involving decarboxylation of malate or oxaloacetate. These pathways are found in the class Bacillales of the low-CG gram-positive bacteria and in the gamma subdivision of the Proteobacteria. The pathways have evolved into a remarkable diversity in terms of the combinations of enzymes and transporters that built the pathways and of energy conservation mechanisms. The transporter family includes H+ and Na+ symporters and precursor/product exchangers. The proteins consist of a bundle of 11 transmembrane helices formed from two homologous domains containing five transmembrane segments each, plus one additional segment at the N terminus. The two domains have opposite orientations in the membrane and contain a pore-loop or reentrant loop structure between the fourth and fifth transmembrane segments. The two pore-loops enter the membrane from opposite sides and are believed to be part of the translocation site. The binding site is located asymmetrically in the membrane, close to the interface of membrane and cytoplasm. The binding site in the translocation pore is believed to be alternatively exposed to the internal and external media. The proposed structure of the 2HCT transporters is different from any known structure of a membrane protein and represents a new structural class of secondary transporters.
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Affiliation(s)
- Iwona Sobczak
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands
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Lolkema JS, Sobczak I, Slotboom DJ. Secondary transporters of the 2HCT family contain two homologous domains with inverted membrane topology and trans re-entrant loops. FEBS J 2005; 272:2334-44. [PMID: 15853816 DOI: 10.1111/j.1742-4658.2005.04665.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The 2-hydroxycarboxylate transporter (2HCT) family of secondary transporters belongs to a much larger structural class of secondary transporters termed ST3 which contains about 2000 transporters in 32 families. The transporters of the 2HCT family are among the best studied in the class. Here we detect weak sequence similarity between the N- and C-terminal halves of the proteins using a sensitive method which uses a database containing the N- and C-terminal halves of all the sequences in ST3 and involves blast searches of each sequence in the database against the whole database. Unrelated families of secondary transporters of the same length and composition were used as controls. The sequence similarity involved major parts of the N- and C-terminal halves and not just a small stretch. The membrane topology of the homologous N- and C-terminal domains was deduced from the experimentally determined topology of the members of the 2HCT family. The domains consist of five transmembrane segments each and have opposite orientations in the membrane. The N terminus of the N-terminal domain is extracellular, while the N terminus of the C-terminal domain is cytoplasmic. The loops between the fourth and fifth transmembrane segment in each domain are well conserved throughout the class and contain a high fraction of residues with small side chains, Gly, Ala and Ser. Experimental work on the citrate transporter CitS in the 2HCT family indicates that the loops are re-entrant or pore loops. The re-entrant loops in the N- and C-terminal domains enter the membrane from opposite sides (trans-re-entrant loops). The combination of inverted membrane topology and trans-re-entrant loops represents a new fold for secondary transporters and resembles the structure of aquaporins and models proposed for Na+/Ca2+ exchangers.
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Affiliation(s)
- Juke S Lolkema
- Molecular Microbiology, Biomolecular Sciences and Biotechnology Institute, University of Groningen, the Netherlands.
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13
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Abstract
Recent reports on the three-dimensional structure of secondary transporters have dramatically increased our knowledge of the translocation mechanism of ions and solutes. The structures of five transporters at atomic resolution have yielded four different folds and as many different translocation mechanisms. The structure of the glutamate transporter homologue GltPh confirmed the role of pore-loop structures as essential parts of the translocation mechanism in one family of secondary transporters. Biochemical evidence for pore-loop structures in several other families suggest that they might be common in secondary transporters, adding to the structural and mechanistic diversity of secondary transporters.
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Affiliation(s)
- Iwona Sobczak
- Department of Microbiology, Groningen Biomolecular and Biotechnology Institute, University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands
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Sobczak I, Lolkema JS. Alternating Access and a Pore-Loop Structure in the Na+-Citrate Transporter CitS of Klebsiella pneumoniae. J Biol Chem 2004; 279:31113-20. [PMID: 15148311 DOI: 10.1074/jbc.m404283200] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
CitS of Klebsiella pneumoniae is a secondary transporter that transports citrate in symport with 2 Na(+) ions. Reaction of Cys-398 and Cys-414, which are located in a cytoplasmic loop of the protein that is believed to be involved in catalysis, with thiol reagents resulted in significant inhibition of uptake activity. The reactivity of the two residues was determined in single Cys mutants in different catalytic states of the transporter and from both sides of the membrane. The single Cys mutants were shown to have the same transport stoichiometry as wild type CitS, but the C398S mutation was responsible for a 10-fold loss of affinity for Na(+). Both cysteine residues were accessible from the periplasmic as well as from the cytoplasmic side of the membrane by the membrane-impermeable thiol reagent [2-(trimethylammonium)ethyl] methanethiosulfonate bromide (MTSET) suggesting that the residues are part of the translocation site. Binding of citrate to the outward facing binding site of the transporter resulted in partial protection against inactivation by N-ethylmaleimide, whereas binding to the inward facing binding site resulted in essentially complete protection. A 10-fold higher concentration of citrate was required at the cytoplasmic rather than at the periplasmic side of the membrane to promote protection. Only marginal effects of citrate binding were seen on reactivity with MTSET. Binding of Na(+) at the periplasmic side of the transporter protected both Cys-398 and Cys-414 against reaction with the thiol reagents, whereas binding at the cytoplasmic side was less effective and discriminated between Cys-398 and Cys-414. A model is presented in which part of the cytoplasmic loop containing Cys-398 and Cys-414 folds back into the translocation pore as a pore-loop structure. The loop protrudes into the pore beyond the citrate-binding site that is situated at the membrane-cytoplasm interface.
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Affiliation(s)
- Iwona Sobczak
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9751 NN Haren, The Netherlands
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Röthlisberger D, Pos KM, Plückthun A. An antibody library for stabilizing and crystallizing membrane proteins - selecting binders to the citrate carrier CitS. FEBS Lett 2004; 564:340-8. [PMID: 15111119 DOI: 10.1016/s0014-5793(04)00359-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2003] [Accepted: 02/23/2004] [Indexed: 11/24/2022]
Abstract
Co-crystallization of membrane proteins with antibody fragments may emerge as a general tool to facilitate crystal growth and improve crystal quality. The bound antibody fragment enlarges the hydrophilic part of the mostly hydrophobic membrane protein, thereby increasing the interaction area for possible protein-protein contacts in the crystal. Additionally, it may restrain flexible parts or lock the membrane protein in a defined conformational state. For successful co-crystallization trials, the antibody fragments must be stable in detergents during the extended period of crystal growth and must be easily produced in amounts necessary for crystallography. Therefore, we constructed a library of antibody Fab fragments from a framework subset of the HuCAL GOLD library (Morphosys, Munich, Germany). By combining the most stable and well expressed frameworks, V(H)3 and V(kappa)3, with the further stabilizing constant domains, a Fab library with the desired properties was obtained in a standard phage display format. As a proof of principle, we selected binders with phage display against the detergent-solubilized citrate transporter CitS of Klebsiella pneumoniae. We describe efficient methods for the immobilization of the membrane protein during selection, for ELISA screening, and for BIAcore evaluation. We demonstrate that the selected Fab fragments form stable complexes with native CitS and recognize conformational epitopes with affinities in the low nanomolar range.
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Affiliation(s)
- Daniela Röthlisberger
- Biochemisches Institut, Universität Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
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