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Crystal structure of the integral membrane diacylglycerol kinase

Diacylglycerol kinase catalyses the ATP-dependent phosphorylation of diacylglycerol to phosphatidic acid for use in shuttling water-soluble components to membrane-derived oligosaccharide and lipopolysaccharide in the cell envelope of Gram-negative bacteria^sup 1^. For half a century, this 121-residu... Full description

Journal Title: Nature 2013, Vol.497(7450), p.521
Main Author: Dianfan Li
Other Authors: Joseph A. Lyons , Valerie E. Pye , Lutz Vogeley , David Aragão , Colin P. Kenyon , Syed T. A. Shah , Christine Doherty , Margaret Aherne , Martin Caffrey
Format: Electronic Article Electronic Article
Language:
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ID: ISSN: 0028-0836 ; E-ISSN: 1476-4687 ; DOI: 10.1038/nature12179
Link: http://dx.doi.org/10.1038/nature12179
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recordid: nature_a10.1038/nature12179
title: Crystal structure of the integral membrane diacylglycerol kinase
format: Article
creator:
  • Dianfan Li
  • Joseph A. Lyons
  • Valerie E. Pye
  • Lutz Vogeley
  • David Aragão
  • Colin P. Kenyon
  • Syed T. A. Shah
  • Christine Doherty
  • Margaret Aherne
  • Martin Caffrey
subjects:
  • Adenosine Triphosphate–Metabolism
  • Bacterial Proteins–Chemistry
  • Bacterial Proteins–Genetics
  • Bacterial Proteins–Metabolism
  • Catalytic Domain–Metabolism
  • Cell Membrane–Chemistry
  • Crystallography, X-Ray–Genetics
  • Diacylglycerol Kinase–Metabolism
  • Diacylglycerol Kinase–Drug Effects
  • Diacylglycerol Kinase–Metabolism
  • Enzyme Activation–Chemistry
  • Enzyme Stability–Genetics
  • Lipids–Metabolism
  • Magnesium–Chemistry
  • Membrane Proteins–Genetics
  • Membrane Proteins–Metabolism
  • Membrane Proteins–Pharmacology
  • Models, Molecular–Pharmacology
  • Mutant Proteins–Pharmacology
  • Mutant Proteins–Pharmacology
  • Mutant Proteins–Pharmacology
  • Nuclear Magnetic Resonance, Biomolecular–Pharmacology
  • Protein Conformation–Pharmacology
  • Zinc–Pharmacology
  • Crystal Structure
  • Enzymes
  • Binding Sites
  • Proteins
  • Kinases
  • Bacterial Proteins
  • Lipids
  • Membrane Proteins
  • Mutant Proteins
  • Adenosine Triphosphate
  • Diacylglycerol Kinase
  • Magnesium
  • Zinc
ispartof: Nature, 2013, Vol.497(7450), p.521
description: Diacylglycerol kinase catalyses the ATP-dependent phosphorylation of diacylglycerol to phosphatidic acid for use in shuttling water-soluble components to membrane-derived oligosaccharide and lipopolysaccharide in the cell envelope of Gram-negative bacteria^sup 1^. For half a century, this 121-residue kinase has served as a model for investigating membrane protein enzymology^sup 1-6^, folding^sup 7,8^, assembly^sup 9-12^ and stability^sup 1,13^. Here we present crystal structures for three functional forms of this unique and paradigmatic kinase, one of which is wild type. These reveal a homo-trimeric enzyme with three transmembrane helices and an amino-terminal amphiphilic helix per monomer. Bound lipid substrate and docked ATP identify the putative active site that is of the composite, shared site type. The crystal structures rationalize extensive biochemical and biophysical data on the enzyme. They are, however, at variance with a published solution NMR model^sup 14^ in that domain swapping, a key feature of the solution form, is not observed in the crystal structures. [PUBLICATION ]
language:
source:
identifier: ISSN: 0028-0836 ; E-ISSN: 1476-4687 ; DOI: 10.1038/nature12179
fulltext: fulltext
issn:
  • 0028-0836
  • 00280836
  • 1476-4687
  • 14764687
url: Link


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titleCrystal structure of the integral membrane diacylglycerol kinase
creatorDianfan Li ; Joseph A. Lyons ; Valerie E. Pye ; Lutz Vogeley ; David Aragão ; Colin P. Kenyon ; Syed T. A. Shah ; Christine Doherty ; Margaret Aherne ; Martin Caffrey
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subjectAdenosine Triphosphate–Metabolism ; Bacterial Proteins–Chemistry ; Bacterial Proteins–Genetics ; Bacterial Proteins–Metabolism ; Catalytic Domain–Metabolism ; Cell Membrane–Chemistry ; Crystallography, X-Ray–Genetics ; Diacylglycerol Kinase–Metabolism ; Diacylglycerol Kinase–Drug Effects ; Diacylglycerol Kinase–Metabolism ; Enzyme Activation–Chemistry ; Enzyme Stability–Genetics ; Lipids–Metabolism ; Magnesium–Chemistry ; Membrane Proteins–Genetics ; Membrane Proteins–Metabolism ; Membrane Proteins–Pharmacology ; Models, Molecular–Pharmacology ; Mutant Proteins–Pharmacology ; Mutant Proteins–Pharmacology ; Mutant Proteins–Pharmacology ; Nuclear Magnetic Resonance, Biomolecular–Pharmacology ; Protein Conformation–Pharmacology ; Zinc–Pharmacology ; Crystal Structure ; Enzymes ; Binding Sites ; Proteins ; Kinases ; Bacterial Proteins ; Lipids ; Membrane Proteins ; Mutant Proteins ; Adenosine Triphosphate ; Diacylglycerol Kinase ; Magnesium ; Zinc;
descriptionDiacylglycerol kinase catalyses the ATP-dependent phosphorylation of diacylglycerol to phosphatidic acid for use in shuttling water-soluble components to membrane-derived oligosaccharide and lipopolysaccharide in the cell envelope of Gram-negative bacteria^sup 1^. For half a century, this 121-residue kinase has served as a model for investigating membrane protein enzymology^sup 1-6^, folding^sup 7,8^, assembly^sup 9-12^ and stability^sup 1,13^. Here we present crystal structures for three functional forms of this unique and paradigmatic kinase, one of which is wild type. These reveal a homo-trimeric enzyme with three transmembrane helices and an amino-terminal amphiphilic helix per monomer. Bound lipid substrate and docked ATP identify the putative active site that is of the composite, shared site type. The crystal structures rationalize extensive biochemical and biophysical data on the enzyme. They are, however, at variance with a published solution NMR model^sup 14^ in that domain swapping, a key feature of the solution form, is not observed in the crystal structures. [PUBLICATION ]
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