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  • 1
    Publication Date: 2010-09-25
    Description: Gram-negative bacteria, such as Escherichia coli, frequently use tripartite efflux complexes in the resistance-nodulation-cell division (RND) family to expel various toxic compounds from the cell. The efflux system CusCBA is responsible for extruding biocidal Cu(I) and Ag(I) ions. No previous structural information was available for the heavy-metal efflux (HME) subfamily of the RND efflux pumps. Here we describe the crystal structures of the inner-membrane transporter CusA in the absence and presence of bound Cu(I) or Ag(I). These CusA structures provide new structural information about the HME subfamily of RND efflux pumps. The structures suggest that the metal-binding sites, formed by a three-methionine cluster, are located within the cleft region of the periplasmic domain. This cleft is closed in the apo-CusA form but open in the CusA-Cu(I) and CusA-Ag(I) structures, which directly suggests a plausible pathway for ion export. Binding of Cu(I) and Ag(I) triggers significant conformational changes in both the periplasmic and transmembrane domains. The crystal structure indicates that CusA has, in addition to the three-methionine metal-binding site, four methionine pairs-three located in the transmembrane region and one in the periplasmic domain. Genetic analysis and transport assays suggest that CusA is capable of actively picking up metal ions from the cytosol, using these methionine pairs or clusters to bind and export metal ions. These structures suggest a stepwise shuttle mechanism for transport between these sites.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2946090/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2946090/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Long, Feng -- Su, Chih-Chia -- Zimmermann, Michael T -- Boyken, Scott E -- Rajashankar, Kanagalaghatta R -- Jernigan, Robert L -- Yu, Edward W -- GM 072014/GM/NIGMS NIH HHS/ -- GM 074027/GM/NIGMS NIH HHS/ -- GM 081680/GM/NIGMS NIH HHS/ -- GM 086431/GM/NIGMS NIH HHS/ -- R01 GM072014/GM/NIGMS NIH HHS/ -- R01 GM074027/GM/NIGMS NIH HHS/ -- R01 GM074027-05/GM/NIGMS NIH HHS/ -- R01 GM086431/GM/NIGMS NIH HHS/ -- R01 GM086431-01A2/GM/NIGMS NIH HHS/ -- RR-15301/RR/NCRR NIH HHS/ -- England -- Nature. 2010 Sep 23;467(7314):484-8. doi: 10.1038/nature09395.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Molecular, Cellular and Developmental Biology Interdepartmental Graduate Program, Iowa State University, Iowa 50011, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20865003" target="_blank"〉PubMed〈/a〉
    Keywords: Apoproteins/chemistry/metabolism ; Binding Sites ; Cell Membrane/metabolism ; Copper/chemistry/*metabolism ; Crystallography, X-Ray ; Cytosol/metabolism ; Escherichia coli/*chemistry ; Escherichia coli Proteins/*chemistry/*metabolism ; Ion Transport ; Membrane Transport Proteins/*chemistry/*metabolism ; Methionine/*metabolism ; Models, Biological ; Models, Molecular ; Periplasm/metabolism ; Protein Structure, Quaternary ; Protein Structure, Tertiary ; Silver/chemistry/*metabolism ; Structure-Activity Relationship
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  • 2
    Publication Date: 2008-11-01
    Description: Nuclear pore complexes (NPCs) facilitate nucleocytoplasmic transport. These massive assemblies comprise an eightfold symmetric scaffold of architectural proteins and central-channel phenylalanine-glycine-repeat proteins forming the transport barrier. We determined the nucleoporin 85 (Nup85)*Seh1 structure, a module in the heptameric Nup84 complex, at 3.5 angstroms resolution. Structural, biochemical, and genetic analyses position the Nup84 complex in two peripheral NPC rings. We establish a conserved tripartite element, the ancestral coatomer element ACE1, that reoccurs in several nucleoporins and vesicle coat proteins, providing structural evidence of coevolution from a common ancestor. We identified interactions that define the organization of the Nup84 complex on the basis of comparison with vesicle coats and confirmed the sites by mutagenesis. We propose that the NPC scaffold, like vesicle coats, is composed of polygons with vertices and edges forming a membrane-proximal lattice that provides docking sites for additional nucleoporins.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2680690/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2680690/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Brohawn, Stephen G -- Leksa, Nina C -- Spear, Eric D -- Rajashankar, Kanagalaghatta R -- Schwartz, Thomas U -- GM68762/GM/NIGMS NIH HHS/ -- GM77537/GM/NIGMS NIH HHS/ -- R01 GM077537/GM/NIGMS NIH HHS/ -- R01 GM077537-02/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2008 Nov 28;322(5906):1369-73. doi: 10.1126/science.1165886. Epub 2008 Oct 30.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18974315" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Coated Vesicles/*chemistry ; Crystallography, X-Ray ; Dimerization ; Evolution, Molecular ; Membrane Proteins/chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Mutagenesis ; Nuclear Pore/*chemistry ; Nuclear Pore Complex Proteins/*chemistry/genetics/metabolism ; Nuclear Proteins/chemistry/metabolism ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Saccharomyces cerevisiae Proteins/*chemistry/genetics/metabolism ; Vesicular Transport Proteins/*chemistry
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 3
    Publication Date: 2014-05-31
    Description: Netrins are secreted proteins that regulate axon guidance and neuronal migration. Deleted in colorectal cancer (DCC) is a well-established netrin-1 receptor mediating attractive responses. We provide evidence that its close relative neogenin is also a functional netrin-1 receptor that acts with DCC to mediate guidance in vivo. We determined the structures of a functional netrin-1 region, alone and in complexes with neogenin or DCC. Netrin-1 has a rigid elongated structure containing two receptor-binding sites at opposite ends through which it brings together receptor molecules. The ligand/receptor complexes reveal two distinct architectures: a 2:2 heterotetramer and a continuous ligand/receptor assembly. The differences result from different lengths of the linker connecting receptor domains fibronectin type III domain 4 (FN4) and FN5, which differs among DCC and neogenin splice variants, providing a basis for diverse signaling outcomes.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4369087/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4369087/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Xu, Kai -- Wu, Zhuhao -- Renier, Nicolas -- Antipenko, Alexander -- Tzvetkova-Robev, Dorothea -- Xu, Yan -- Minchenko, Maria -- Nardi-Dei, Vincenzo -- Rajashankar, Kanagalaghatta R -- Himanen, Juha -- Tessier-Lavigne, Marc -- Nikolov, Dimitar B -- P41 GM103403/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2014 Jun 13;344(6189):1275-9. doi: 10.1126/science.1255149. Epub 2014 May 29.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA. ; Laboratory of Brain Development and Repair, Rockefeller University, New York, NY 10065, USA. ; Department of Chemistry and Chemical Biology, Cornell University and Northeastern Collaborative Access Team, Advanced Photon Source, Argonne, IL 60439, USA. ; Laboratory of Brain Development and Repair, Rockefeller University, New York, NY 10065, USA. nikolovd@mskcc.org marctl@mail.rockefeller.edu. ; Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA. nikolovd@mskcc.org marctl@mail.rockefeller.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24876346" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Axons/*physiology ; Cell Movement ; Fibronectins/chemistry ; Ligands ; Membrane Proteins/*chemistry/genetics/ultrastructure ; Mice ; Mice, Inbred C57BL ; Mice, Mutant Strains ; Nerve Growth Factors/*chemistry/genetics/ultrastructure ; Neurons/physiology ; Protein Multimerization ; Protein Structure, Tertiary ; Receptors, Cell Surface/*chemistry/genetics/ultrastructure ; Tumor Suppressor Proteins/*chemistry/genetics/ultrastructure
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  • 4
    Publication Date: 2011-04-08
    Description: Saccharides have a central role in the nutrition of all living organisms. Whereas several saccharide uptake systems are shared between the different phylogenetic kingdoms, the phosphoenolpyruvate-dependent phosphotransferase system exists almost exclusively in bacteria. This multi-component system includes an integral membrane protein EIIC that transports saccharides and assists in their phosphorylation. Here we present the crystal structure of an EIIC from Bacillus cereus that transports diacetylchitobiose. The EIIC is a homodimer, with an expansive interface formed between the amino-terminal halves of the two protomers. The carboxy-terminal half of each protomer has a large binding pocket that contains a diacetylchitobiose, which is occluded from both sides of the membrane with its site of phosphorylation near the conserved His250 and Glu334 residues. The structure shows the architecture of this important class of transporters, identifies the determinants of substrate binding and phosphorylation, and provides a framework for understanding the mechanism of sugar translocation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3201810/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3201810/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cao, Yu -- Jin, Xiangshu -- Levin, Elena J -- Huang, Hua -- Zong, Yinong -- Quick, Matthias -- Weng, Jun -- Pan, Yaping -- Love, James -- Punta, Marco -- Rost, Burkhard -- Hendrickson, Wayne A -- Javitch, Jonathan A -- Rajashankar, Kanagalaghatta R -- Zhou, Ming -- DK088057/DK/NIDDK NIH HHS/ -- GM05026/GM/NIGMS NIH HHS/ -- GM05026-SUB0007/GM/NIGMS NIH HHS/ -- GM098878/GM/NIGMS NIH HHS/ -- K05 DA022413/DA/NIDA NIH HHS/ -- P30 EB009998/EB/NIBIB NIH HHS/ -- R01 DK088057/DK/NIDDK NIH HHS/ -- R01 GM098878/GM/NIGMS NIH HHS/ -- T32HL087745/HL/NHLBI NIH HHS/ -- England -- Nature. 2011 May 5;473(7345):50-4. doi: 10.1038/nature09939. Epub 2011 Apr 6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physiology & Cellular Biophysics, College of Physicians and Surgeons, Columbia University, 630 West 168th Street, New York, New York 10032, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21471968" target="_blank"〉PubMed〈/a〉
    Keywords: Bacillus cereus/*enzymology ; Binding Sites ; Carbohydrate Metabolism ; Crystallization ; Membrane Transport Proteins/*chemistry ; *Models, Molecular ; Phosphorylation ; Protein Structure, Quaternary ; Protein Structure, Tertiary
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  • 5
    Publication Date: 2014-09-26
    Description: The formation of branched lariat RNA is an evolutionarily conserved feature of splicing reactions for both group II and spliceosomal introns. The lariat is important for the fidelity of 5' splice-site selection and consists of a 2'-5' phosphodiester bond between a bulged adenosine and the 5' end of the intron. To gain insight into this ubiquitous intramolecular linkage, we determined the crystal structure of a eukaryotic group IIB intron in the lariat form at 3.7 A. This revealed that two tandem tetraloop-receptor interactions, eta-eta' and pi-pi', place domain VI in the core to position the lariat bond in the post-catalytic state. On the basis of structural and biochemical data, we propose that pi-pi' is a dynamic interaction that mediates the transition between the two steps of splicing, with eta-eta' serving an ancillary role. The structure also reveals a four-magnesium-ion cluster involved in both catalysis and positioning of the 5' end. Given the evolutionary relationship between group II and nuclear introns, it is likely that this active site configuration exists in the spliceosome as well.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4197185/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4197185/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Robart, Aaron R -- Chan, Russell T -- Peters, Jessica K -- Rajashankar, Kanagalaghatta R -- Toor, Navtej -- 5R01GM102216/GM/NIGMS NIH HHS/ -- 5T32GM007240/GM/NIGMS NIH HHS/ -- 5T32GM008326/GM/NIGMS NIH HHS/ -- 8P41GM103403-10/GM/NIGMS NIH HHS/ -- P41 GM103403/GM/NIGMS NIH HHS/ -- R01 GM102216/GM/NIGMS NIH HHS/ -- T32 GM007240/GM/NIGMS NIH HHS/ -- T32 GM008326/GM/NIGMS NIH HHS/ -- England -- Nature. 2014 Oct 9;514(7521):193-7. doi: 10.1038/nature13790. Epub 2014 Sep 24.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA. ; NE-CAT and Department of Chemistry and Chemical Biology, Cornell University, Argonne National Laboratory, Argonne, Illinois 60439, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25252982" target="_blank"〉PubMed〈/a〉
    Keywords: Biocatalysis ; Catalytic Domain ; Crystallography, X-Ray ; Evolution, Molecular ; *Introns/genetics ; Magnesium/metabolism/pharmacology ; Models, Molecular ; *Nucleic Acid Conformation/drug effects ; *Phaeophyta/chemistry/genetics ; RNA Splicing/genetics ; Ribosome Subunits, Large/genetics ; Spliceosomes/chemistry
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  • 6
    Publication Date: 2015-06-23
    Description: Stearoyl-CoA desaturase (SCD) is conserved in all eukaryotes and introduces the first double bond into saturated fatty acyl-CoAs. Because the monounsaturated products of SCD are key precursors of membrane phospholipids, cholesterol esters and triglycerides, SCD is pivotal in fatty acid metabolism. Humans have two SCD homologues (SCD1 and SCD5), while mice have four (SCD1-SCD4). SCD1-deficient mice do not become obese or diabetic when fed a high-fat diet because of improved lipid metabolic profiles and insulin sensitivity. Thus, SCD1 is a pharmacological target in the treatment of obesity, diabetes and other metabolic diseases. SCD1 is an integral membrane protein located in the endoplasmic reticulum, and catalyses the formation of a cis-double bond between the ninth and tenth carbons of stearoyl- or palmitoyl-CoA. The reaction requires molecular oxygen, which is activated by a di-iron centre, and cytochrome b5, which regenerates the di-iron centre. To understand better the structural basis of these characteristics of SCD function, here we crystallize and solve the structure of mouse SCD1 bound to stearoyl-CoA at 2.6 A resolution. The structure shows a novel fold comprising four transmembrane helices capped by a cytosolic domain, and a plausible pathway for lateral substrate access and product egress. The acyl chain of the bound stearoyl-CoA is enclosed in a tunnel buried in the cytosolic domain, and the geometry of the tunnel and the conformation of the bound acyl chain provide a structural basis for the regioselectivity and stereospecificity of the desaturation reaction. The dimetal centre is coordinated by a unique spacial arrangement of nine conserved histidine residues that implies a potentially novel mechanism for oxygen activation. The structure also illustrates a possible route for electron transfer from cytochrome b5 to the di-iron centre.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4689147/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4689147/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bai, Yonghong -- McCoy, Jason G -- Levin, Elena J -- Sobrado, Pablo -- Rajashankar, Kanagalaghatta R -- Fox, Brian G -- Zhou, Ming -- P41 GM103403/GM/NIGMS NIH HHS/ -- P41GM103403/GM/NIGMS NIH HHS/ -- R01 DK088057/DK/NIDDK NIH HHS/ -- R01 GM098878/GM/NIGMS NIH HHS/ -- R01 HL086392/HL/NHLBI NIH HHS/ -- R01DK088057/DK/NIDDK NIH HHS/ -- R01GM050853/GM/NIGMS NIH HHS/ -- R01GM098878/GM/NIGMS NIH HHS/ -- R01HL086392/HL/NHLBI NIH HHS/ -- U54 GM094584/GM/NIGMS NIH HHS/ -- U54GM094584/GM/NIGMS NIH HHS/ -- U54GM095315/GM/NIGMS NIH HHS/ -- England -- Nature. 2015 Aug 13;524(7564):252-6. doi: 10.1038/nature14549. Epub 2015 Jun 22.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA. ; Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA. ; NE-CAT and Department of Chemistry and Chemical Biology, Cornell University, Argonne National Laboratory, Argonne, Illinois 60439, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26098370" target="_blank"〉PubMed〈/a〉
    Keywords: Acyl Coenzyme A/chemistry/metabolism ; Animals ; Binding Sites ; Crystallography, X-Ray ; Cytochromes b5/chemistry/metabolism ; Electron Transport ; Histidine/chemistry/metabolism ; Iron/metabolism ; Mice ; Models, Molecular ; Oxygen/metabolism ; Protein Structure, Tertiary ; Static Electricity ; Stearoyl-CoA Desaturase/*chemistry/metabolism ; Structure-Activity Relationship
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  • 7
    Publication Date: 2011-02-26
    Description: Gram-negative bacteria, such as Escherichia coli, expel toxic chemicals through tripartite efflux pumps that span both the inner and outer membrane. The three parts are an inner membrane, substrate-binding transporter; a membrane fusion protein; and an outer-membrane-anchored channel. The fusion protein connects the transporter to the channel within the periplasmic space. A crystallographic model of this tripartite efflux complex has been unavailable because co-crystallization of the various components of the system has proven to be extremely difficult. We previously described the crystal structures of both the inner membrane transporter CusA and the membrane fusion protein CusB of the CusCBA efflux system of E. coli. Here we report the co-crystal structure of the CusBA efflux complex, showing that the transporter (or pump) CusA, which is present as a trimer, interacts with six CusB protomers and that the periplasmic domain of CusA is involved in these interactions. The six CusB molecules seem to form a continuous channel. The affinity of the CusA and CusB interaction was found to be in the micromolar range. Finally, we have predicted a three-dimensional structure for the trimeric CusC outer membrane channel and developed a model of the tripartite efflux assemblage. This CusC(3)-CusB(6)-CusA(3) model shows a 750-kilodalton efflux complex that spans the entire bacterial cell envelope and exports Cu I and Ag I ions.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3078058/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3078058/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Su, Chih-Chia -- Long, Feng -- Zimmermann, Michael T -- Rajashankar, Kanagalaghatta R -- Jernigan, Robert L -- Yu, Edward W -- R01 GM072014/GM/NIGMS NIH HHS/ -- R01 GM074027/GM/NIGMS NIH HHS/ -- R01 GM074027-05/GM/NIGMS NIH HHS/ -- R01 GM086431/GM/NIGMS NIH HHS/ -- R01 GM086431-01A2/GM/NIGMS NIH HHS/ -- R01GM072014/GM/NIGMS NIH HHS/ -- R01GM074027/GM/NIGMS NIH HHS/ -- R01GM081680/GM/NIGMS NIH HHS/ -- R01GM086431/GM/NIGMS NIH HHS/ -- RR-15301/RR/NCRR NIH HHS/ -- England -- Nature. 2011 Feb 24;470(7335):558-62. doi: 10.1038/nature09743.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Iowa State University, Ames, Iowa 50011, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21350490" target="_blank"〉PubMed〈/a〉
    Keywords: Copper/metabolism ; Crystallization ; Crystallography, X-Ray ; Escherichia coli/*chemistry ; Escherichia coli Proteins/*chemistry/metabolism ; Membrane Transport Proteins/*chemistry/metabolism ; Metals, Heavy/*metabolism ; Models, Molecular ; Multiprotein Complexes/*chemistry/metabolism ; Protein Binding ; Protein Multimerization ; Protein Structure, Quaternary ; Protein Structure, Tertiary ; Silver/metabolism ; Static Electricity
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  • 8
    Publication Date: 2011-02-15
    Description: The TrkH/TrkG/KtrB proteins mediate K(+) uptake in bacteria and probably evolved from simple K(+) channels by multiple gene duplications or fusions. Here we present the crystal structure of a TrkH from Vibrio parahaemolyticus. TrkH is a homodimer, and each protomer contains an ion permeation pathway. A selectivity filter, similar in architecture to those of K(+) channels but significantly shorter, is lined by backbone and side-chain oxygen atoms. Functional studies showed that TrkH is selective for permeation of K(+) and Rb(+) over smaller ions such as Na(+) or Li(+). Immediately intracellular to the selectivity filter are an intramembrane loop and an arginine residue, both highly conserved, which constrict the permeation pathway. Substituting the arginine with an alanine significantly increases the rate of K(+) flux. These results reveal the molecular basis of K(+) selectivity and suggest a novel gating mechanism for this large and important family of membrane transport proteins.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3077569/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3077569/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cao, Yu -- Jin, Xiangshu -- Huang, Hua -- Derebe, Mehabaw Getahun -- Levin, Elena J -- Kabaleeswaran, Venkataraman -- Pan, Yaping -- Punta, Marco -- Love, James -- Weng, Jun -- Quick, Matthias -- Ye, Sheng -- Kloss, Brian -- Bruni, Renato -- Martinez-Hackert, Erik -- Hendrickson, Wayne A -- Rost, Burkhard -- Javitch, Jonathan A -- Rajashankar, Kanagalaghatta R -- Jiang, Youxing -- Zhou, Ming -- DK088057/DK/NIDDK NIH HHS/ -- GM05026/GM/NIGMS NIH HHS/ -- GM05026-SUB0007/GM/NIGMS NIH HHS/ -- HL086392/HL/NHLBI NIH HHS/ -- K05 DA022413/DA/NIDA NIH HHS/ -- P30 EB009998/EB/NIBIB NIH HHS/ -- R01 DK088057/DK/NIDDK NIH HHS/ -- R01 DK088057-01/DK/NIDDK NIH HHS/ -- R01 HL086392/HL/NHLBI NIH HHS/ -- R01 HL086392-05/HL/NHLBI NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2011 Mar 17;471(7338):336-40. doi: 10.1038/nature09731. Epub 2011 Feb 13.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physiology & Cellular Biophysics, College of Physicians and Surgeons, Columbia University, 630 West 168th Street, New York, New York 10032, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21317882" target="_blank"〉PubMed〈/a〉
    Keywords: ATP-Binding Cassette Transporters/chemistry ; Amino Acid Sequence ; Crystallography, X-Ray ; Escherichia coli Proteins/chemistry ; Ion Channel Gating ; Ion Transport ; Models, Molecular ; Molecular Sequence Data ; Potassium/metabolism ; Potassium Channels/*chemistry/*metabolism ; Structure-Activity Relationship ; Substrate Specificity ; Vibrio parahaemolyticus/*chemistry
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    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 9
    Publication Date: 2012-06-09
    Description: Significant advances in our understanding of RNA architecture, folding and recognition have emerged from structure-function studies on riboswitches, non-coding RNAs whose sensing domains bind small ligands and whose adjacent expression platforms contain RNA elements involved in the control of gene regulation. We now report on the ligand-bound structure of the Thermotoga petrophila fluoride riboswitch, which adopts a higher-order RNA architecture stabilized by pseudoknot and long-range reversed Watson-Crick and Hoogsteen A*U pair formation. The bound fluoride ion is encapsulated within the junctional architecture, anchored in place through direct coordination to three Mg(2+) ions, which in turn are octahedrally coordinated to water molecules and five inwardly pointing backbone phosphates. Our structure of the fluoride riboswitch in the bound state shows how RNA can form a binding pocket selective for fluoride, while discriminating against larger halide ions. The T. petrophila fluoride riboswitch probably functions in gene regulation through a transcription termination mechanism.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3744881/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3744881/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ren, Aiming -- Rajashankar, Kanagalaghatta R -- Patel, Dinshaw J -- GM34504/GM/NIGMS NIH HHS/ -- R01 GM034504/GM/NIGMS NIH HHS/ -- England -- Nature. 2012 May 13;486(7401):85-9. doi: 10.1038/nature11152.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Structural Biology Program, Memorial Sloan-Kettering Center, New York, New York 10065, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22678284" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Binding Sites ; Cations, Divalent/*chemistry ; Fluorides/*chemistry/*metabolism ; Gene Expression Regulation, Bacterial ; Gram-Negative Anaerobic Straight, Curved, and Helical Rods/*genetics ; Ligands ; Magnesium/*chemistry ; Models, Molecular ; Nucleic Acid Conformation ; Nucleotide Motifs ; Phosphates/*chemistry/metabolism ; Riboswitch/*genetics ; Structure-Activity Relationship ; Substrate Specificity ; Water/chemistry/metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 10
    Publication Date: 2016-02-26
    Description: Polymyxins are antibiotics used in the last line of defense to combat multidrug-resistant infections by Gram-negative bacteria. Polymyxin resistance arises through charge modification of the bacterial outer membrane with the attachment of the cationic sugar 4-amino-4-deoxy-l-arabinose to lipid A, a reaction catalyzed by the integral membrane lipid-to-lipid glycosyltransferase 4-amino-4-deoxy-L-arabinose transferase (ArnT). Here, we report crystal structures of ArnT from Cupriavidus metallidurans, alone and in complex with the lipid carrier undecaprenyl phosphate, at 2.8 and 3.2 angstrom resolution, respectively. The structures show cavities for both lipidic substrates, which converge at the active site. A structural rearrangement occurs on undecaprenyl phosphate binding, which stabilizes the active site and likely allows lipid A binding. Functional mutagenesis experiments based on these structures suggest a mechanistic model for ArnT family enzymes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Petrou, Vasileios I -- Herrera, Carmen M -- Schultz, Kathryn M -- Clarke, Oliver B -- Vendome, Jeremie -- Tomasek, David -- Banerjee, Surajit -- Rajashankar, Kanagalaghatta R -- Belcher Dufrisne, Meagan -- Kloss, Brian -- Kloppmann, Edda -- Rost, Burkhard -- Klug, Candice S -- Trent, M Stephen -- Shapiro, Lawrence -- Mancia, Filippo -- AI064184/AI/NIAID NIH HHS/ -- AI076322/AI/NIAID NIH HHS/ -- P41 GM103403/GM/NIGMS NIH HHS/ -- R01 GM111980/GM/NIGMS NIH HHS/ -- S10 RR029205/RR/NCRR NIH HHS/ -- U54 GM095315/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2016 Feb 5;351(6273):608-12. doi: 10.1126/science.aad1172.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA. ; Department of Infectious Diseases, University of Georgia, College of Veterinary Medicine, Athens, GA 30602, USA. ; Department of Biophysics, Medical College of Wisconsin, Milwaukee, WI 53226, USA. ; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA. ; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA. Department of Systems Biology, Columbia University, New York, NY 10032, USA. ; Department of Chemistry and Chemical Biology, Cornell University, Northeastern Collaborative Access Team, Advanced Photon Source, Argonne, IL 60439, USA. ; New York Consortium on Membrane Protein Structure, New York Structural Biology Center, 89 Convent Avenue, New York, NY 10027, USA. ; Department of Informatics, Bioinformatics and Computational Biology, Technische Universitat Munchen, Boltzmannstrasse 3, 85748 Garching, Germany. ; Department of Informatics, Bioinformatics and Computational Biology, Technische Universitat Munchen, Boltzmannstrasse 3, 85748 Garching, Germany. Institute for Advanced Study (TUM-IAS), Technische Universitat Munchen, Boltzmannstrasse 3, 85748 Garching, Germany. ; Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA. fm123@cumc.columbia.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26912703" target="_blank"〉PubMed〈/a〉
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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