scholarly journals Structure of theDietziaMrp complex reveals molecular mechanism of this giant bacterial sodium proton pump

2020 ◽  
Vol 117 (49) ◽  
pp. 31166-31176
Author(s):  
Bin Li ◽  
Kaiduan Zhang ◽  
Yong Nie ◽  
Xianping Wang ◽  
Yan Zhao ◽  
...  
Keyword(s):  
Complex I ◽  
Three Dimensional ◽  
Transport Processes ◽  
Dimensional Structure ◽  
Multiple Resistance ◽  
Sodium Ions ◽  
Microscopy Method ◽  
Functional Analyses ◽  
Ph Adaptation ◽  
Shed Light

Multiple resistance and pH adaptation (Mrp) complexes are sophisticated cation/proton exchangers found in a vast variety of alkaliphilic and/or halophilic microorganisms, and are critical for their survival in highly challenging environments. This family of antiporters is likely to represent the ancestor of cation pumps found in many redox-driven transporter complexes, including the complex I of the respiratory chain. Here, we present the three-dimensional structure of the Mrp complex from aDietziasp. strain solved at 3.0-Å resolution using the single-particle cryoelectron microscopy method. Our structure-based mutagenesis and functional analyses suggest that the substrate translocation pathways for the driving substance protons and the substrate sodium ions are separated in two modules and that symmetry-restrained conformational change underlies the functional cycle of the transporter. Our findings shed light on mechanisms of redox-driven primary active transporters, and explain how driving substances of different electric charges may drive similar transport processes.

scholarly journals The three-dimensional structure of complex I from Yarrowia lipolytica: A highly dynamic enzyme

2006 ◽  
Vol 154 (3) ◽  
pp. 269-279 ◽  
Author(s):  
M. Radermacher ◽  
T. Ruiz ◽  
T. Clason ◽  
S. Benjamin ◽  
U. Brandt ◽  
...  
Keyword(s):  
Yarrowia Lipolytica ◽  
Complex I ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Three Dimensional Structure

scholarly journals Tetrahydrolipstatin Inhibition, Functional Analyses, and Three-dimensional Structure of a Lipase Essential for Mycobacterial Viability

2010 ◽  
Vol 285 (39) ◽  
pp. 30050-30060 ◽  
Author(s):  
Paul K. Crellin ◽  
Julian P. Vivian ◽  
Judith Scoble ◽  
Frances M. Chow ◽  
Nicholas P. West ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Dimensional Structure ◽  
Three Dimensional Structure ◽  
Functional Analyses

Central role of the Na+-translocating NADH:quinone oxidoreductase (Na+-NQR) in sodium bioenergetics of Vibrio cholerae

2014 ◽  
Vol 395 (12) ◽  
pp. 1389-1399 ◽  
Author(s):  
Julia Steuber ◽  
Petra Halang ◽  
Thomas Vorburger ◽  
Wojtek Steffen ◽  
Georg Vohl ◽  
...  
Keyword(s):  
Vibrio Cholerae ◽  
Cytoplasmic Membrane ◽  
Sea Water ◽  
Three Dimensional ◽  
Transport Processes ◽  
Dimensional Structure ◽  
Substrate Uptake ◽  
Molecular Architecture ◽  
Nadh:Quinone Oxidoreductase

Abstract Vibrio cholerae is a Gram-negative bacterium that lives in brackish or sea water environments. Strains of V. cholerae carrying the pathogenicity islands infect the human gut and cause the fatal disease cholera. Vibrio cholerae maintains a Na+ gradient at its cytoplasmic membrane that drives substrate uptake, motility, and efflux of antibiotics. Here, we summarize the major Na+-dependent transport processes and describe the central role of the Na+-translocating NADH:quinone oxidoreductase (Na+-NQR), a primary Na+ pump, in maintaining a Na+-motive force. The Na+-NQR is a membrane protein complex with a mass of about 220 kDa that couples the exergonic oxidation of NADH to the transport of Na+ across the cytoplasmic membrane. We describe the molecular architecture of this respiratory complex and summarize the findings how electron transport might be coupled to Na+-translocation. Moreover, recent advances in the determination of the three-dimensional structure of this complex are reported.

scholarly journals Three-dimensional Structure of Eukaryotic Complex I

2006 ◽  
Vol 12 (S02) ◽  
pp. 380-381 ◽  
Author(s):  
TA Clason ◽  
T Ruiz ◽  
H Schägger ◽  
M Radermacher
Keyword(s):  
Complex I ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Three Dimensional Structure

Extended abstract of a paper presented at Microscopy and Microanalysis 2006 in Chicago, Illinois, USA, July 30 – August 3, 2005

scholarly journals Structural and Functional Analyses of PolyProline-II helices in Globular Proteins

2016 ◽  
Author(s):  
Prasun Kumar ◽  
Manju Bansal
Keyword(s):  
Protein Structures ◽  
Three Dimensional ◽  
Aromatic Amino Acids ◽  
Dimensional Structure ◽  
Protein Chain ◽  
Left Handed ◽  
Polyproline Ii ◽  
Backbone Torsion Angle ◽  
Functional Analyses ◽  
Flanking Regions

PolyProline-II (PPII) helices are defined as a continuous stretch of a protein chain in which the constituent residues have the backbone torsion angle (φ,ψ) values of (-75°, 145°) and take up extended left handed conformation, lacking any intra-helical hydrogen bonds. They are found to occur very frequently in protein structures with their number exceeding that of π-helices, though it is considerably less than that of α-helices and β-strands. A relatively new procedure, ASSP, for the identification of regular secondary structures using Cα trace identifies 3597 PPII helices in 3582 protein chains, solved at resolution ≤ 2.5Å. Taking advantage of this significantly expanded database of PPII-helices, we have analyzed the functional and structural roles of PPII helices as well as determined the amino acid propensity within and around them. Though Pro residues are highly preferred, it is not a mandatory condition for the formation of PPII-helices, since ~40% PPII-helices were found to contain no Proline residues. Aromatic amino acids are avoided within this helix, while Gly, Asn and Asp residues are preferred in the proximal flanking regions. These helices range from 3 to 13 residues in length with the average twist and rise being -121.2°±9.2° and 3.0ű0.1Å respectively. A majority (~72%) of PPII-helices were found to occur in conjunction with α-helices and β-strands, and serve as linkers as well. The analysis of various intra-helical non-bonded interactions revealed frequent presence of C-H...O H-bonds. PPII-helices participate in maintaining the three-dimensional structure of proteins and are important constituents of binding motifs involved in various biological functions.

The crystal and molecular structure of adenosine triphosphate

1971 ◽  
Vol 325 (1562) ◽  
pp. 401-436 ◽  
Keyword(s):  
Adenosine Triphosphate ◽  
Three Dimensional ◽  
Direct Methods ◽  
Disodium Salt ◽  
Dimensional Structure ◽  
Water Molecules ◽  
Sodium Ions ◽  
X Ray Diffraction ◽  
Orthorhombic Space Group ◽  
Centrosymmetric Dimer

The three-dimensional structure of the hydrated disodium salt of adenosine triphosphate (Na 2 ATP) has been determined from an X-ray diffraction study to a resolution of 0.9 Å. The crystals are orthorhombic, space group P 2 1 2 1 2 1 , with a = 30.45(4), b = 20.88(3), c = 7.07(1) Å. There are two molecules of ATP, four sodium ions, and six water molecules in the asymmetric unit. The structure was solved by direct methods and refined to R = 12.3 % using 1118 intensities measured on an automatic diffractometer. The triphosphate chain is in the folded conformation in each of the two crystallographically independent molecules. However, in one molecule (A) it is folded so as to form part of a lefthanded helix, while in the other part of a right-handed helix. There are corresponding differences in the conformations of the ribose rings. The ring is in the envelope conformation with C3' endo in molecule A and C2' endo in molecule B. Two of the sodium ions coordinate the two molecules through the phosphate oxygens and N7 to form an almost centrosymmetric ‘dimer’ which is the fundamental structural unit. The adenine bases show considerable overlap and are stacked in the c axis direction. Details of the hydrogen bonding and the role of water molecules in the structure are discussed.

scholarly journals Crystal structures of binary compounds of meldonium 3-(1,1,1-trimethylhydrazin-1-ium-2-yl)propanoate with sodium bromide and sodium iodide

2018 ◽  
Vol 74 (6) ◽  
pp. 829-834 ◽  
Author(s):  
Alexander Y Nazarenko
Keyword(s):  
Electrostatic Interactions ◽  
Sodium Iodide ◽  
Three Dimensional ◽  
Sodium Bromide ◽  
Dimensional Structure ◽  
Sodium Ions ◽  
Coordination Polyhedra ◽  
Coordination Numbers ◽  
Distorted Octahedra ◽  
Binary Compounds

3-(1,1,1-Trimethylhydrazin-1-ium-2-yl)propanoate (C6H14N2O2,M, more commonly known under its commercial namesMeldoniumorMildronate) co-crystalizes with sodium bromide and sodium iodide forming polymeric hydrates poly[[tetra-μ-aqua-diaquabis[3-(1,1,1-trimethylhydrazin-1-ium-2-yl)propanoate]disodium] dibromide tetrahydrate], [Na2(C6H14N2O2)2(H2O)6]Br2·4H2O, and poly[[di-μ-aqua-diaqua[μ-3-(1,1,1-trimethylhydrazin-1-ium-2-yl)propanoate]disodium] diiodide], [Na2(C6H14N2O2)2(H2O)4]I2. The coordination numbers of the sodium ions are 6; the coordination polyhedra can be described as distorted octahedra. Metal ions andMzwitterions are assembled into infinite layersviaelectrostatic interactions and hydrogen-bonded networks. These layers are connectedviaelectrostatic attraction between halogenide ions and positive trimethylhydrazinium groups into a three-dimensional structure.

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