Skip to main content
U.S. Department of Energy
Office of Scientific and Technical Information

X-ray free-electron laser studies reveal correlated motion during isopenicillin N synthase catalysis

Journal Article · · Science Advances
 [1];  [2];  [3];  [1];  [4];  [3];  [3];  [1];  [1];  [1];  [1];  [1];  [4];  [1];  [3];  [5];  [3];  [6];  [7];  [3] more »;  [8];  [3];  [3];  [1];  [3];  [9];  [9];  [9];  [5];  [5];  [5];  [10];  [11];  [3];  [1];  [1];  [3];  [3];  [3];  [4];  [1] « less
  1. Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK.
  2. Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK., Diamond Light Source, Diamond House, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK., Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, Oxfordshire OX11 0FA, UK.
  3. Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.
  4. Diamond Light Source, Diamond House, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK., Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, Oxfordshire OX11 0FA, UK.
  5. Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.
  6. Department of Chemistry - Ångström, Molecular Biomimetics, Uppsala University, SE 751 20 Uppsala, Sweden.
  7. Interdisciplinary Center for Scientific Computing, University of Heidelberg, 69120 Heidelberg, Germany.
  8. Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA., Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, 600 16th Street, San Francisco, CA 94158, USA.
  9. Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan., RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.
  10. Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA., Department of Physics, University of Wisconsin–Madison, 1150 University Avenue, Madison, WI 53706, USA.
  11. Diamond Light Source, Diamond House, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK.

Complementary XFEL methods reveal O 2 reaction intermediates and global protein dynamics during Isopenicillin N synthase catalysis.

Research Organization:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Organization:
Biotechnology and Biological Sciences Research Council (BBSRC); Cancer Research UK; Deutsche Akademie für Naturforscher Leopoldina, Germany; Engineering and Physical Sciences Research Council (EPSRC); Ineos Oxford Institute; Medical Research Foundation (MRF); National Institutes of Health (NIH); St. John’s College; USDOE; USDOE Office of Science (SC), Basic Energy Sciences (BES); Wellcome Trust
Grant/Contract Number:
AC02-05CH11231; AC02-76SF00515
OSTI ID:
1814520
Alternate ID(s):
OSTI ID: 1825707
Journal Information:
Science Advances, Journal Name: Science Advances Journal Issue: 34 Vol. 7; ISSN 2375-2548
Publisher:
American Association for the Advancement of Science (AAAS)Copyright Statement
Country of Publication:
United States
Language:
English

References (71)

Monitoring Conformational Changes in the NDM-1 Metallo-β-lactamase by 19 F NMR Spectroscopy journal February 2014
Terminally Truncated Isopenicillin N Synthase Generates a Dithioester Product: Evidence for a Thioaldehyde Intermediate during Catalysis and a New Mode of Reaction for Non-Heme Iron Oxidases journal August 2017
19 F NMR Monitoring of Reversible Protein Post‐Translational Modifications: Class D β‐Lactamase Carbamylation and Inhibition journal August 2019
Studies of isopenicillin N synthase enzymatic properties using a continuous spectrophotometric assay journal November 2000
Spectroscopic Studies of Isopenicillin N Synthase journal December 1989
Basic local alignment search tool journal October 1990
High-level soluble expression of isopenicillin N synthase isozymes in E. coli journal July 1991
Structural Basis for Binding of Hypoxia-Inducible Factor to the Oxygen-Sensing Prolyl Hydroxylases journal July 2009
Amazing Diversity in Biochemical Roles of Fe(II)/2-Oxoglutarate Oxygenases journal July 2018
X-ray Emission Spectroscopy as an in Situ Diagnostic Tool for X-ray Crystallography of Metalloproteins Using an X-ray Free-Electron Laser journal April 2018
Chemical Sensitivity of Kβ and Kα X-ray Emission from a Systematic Investigation of Iron Compounds journal August 2020
Dynamically Achieved Active Site Precision in Enzyme Catalysis journal December 2014
X-ray absorption studies of the ferrous active site of isopenicillin N synthase and related model complexes journal July 1993
Thiolate ligation of the active site iron(II) of isopenicillin N synthase derives from substrate rather than endogenous cysteine: spectroscopic studies of site-specific Cys .fwdarw. Ser mutated enzymes journal May 1992
19 F NMR of Trifluoroacetyl-Labeled Cysteine Mutants of Myoglobin:  Structural Probes of Nitric Oxide Bound to the H93G Cavity Mutant journal June 2001
The Mechanism for Isopenicillin N Synthase from Density-Functional Modeling Highlights the Similarities with Other Enzymes in the 2-His-1-carboxylate Family journal January 2008
Reaction Coordinate of Isopenicillin N Synthase: Oxidase versus Oxygenase Activity journal February 2010
Isopenicillin N synthase: mechanistic studies journal November 1990
Transition States in a Protein Environment − ONIOM QM:MM Modeling of Isopenicillin N Synthesis journal December 2008
VTVH-MCD and DFT Studies of Thiolate Bonding to {FeNO} 7 /{FeO 2 } 8 Complexes of Isopenicillin N Synthase:  Substrate Determination of Oxidase versus Oxygenase Activity in Nonheme Fe Enzymes journal June 2007
Structural Characterization of the Fleeting Ferric Peroxo Species in Myoglobin:  Experiment and Theory journal November 2007
High-Resolution XFEL Structure of the Soluble Methane Monooxygenase Hydroxylase Complex with its Regulatory Component at Ambient Temperature in Two Oxidation States journal July 2020
Spectroscopic Evidence for the Two C–H-Cleaving Intermediates of Aspergillus nidulans Isopenicillin N Synthase journal July 2016
Formation of a Reactive, Alkyl Thiolate-Ligated Fe III -Superoxo Intermediate Derived from Dioxygen journal January 2019
Probing the 3d Spin Momentum with X-ray Emission Spectroscopy:  The Case of Molecular-Spin Transitions journal June 2006
Protein Environment Facilitates O 2 Binding in Non-Heme Iron Enzyme. An Insight from ONIOM Calculations on Isopenicillin N Synthase (IPNS) journal July 2007
Comprehensive Analysis of Protein Digestion Using Six Trypsins Reveals the Origin of Trypsin As a Significant Source of Variability in Proteomics journal November 2013
Structure of a cephalosporin synthase journal August 1998
Crystal structure of isopenicillin N synthase is the first from a new structural family of enzymes journal June 1995
Structure of isopenicillinN synthase complexed with substrate and the mechanism ofpenicillin formation journal June 1997
The reaction cycle of isopenicillin N synthase observed by X-ray diffraction journal October 1999
Crystal structures of DNA/RNA repair enzymes AlkB and ABH2 bound to dsDNA journal April 2008
Structure of a Naegleria Tet-like dioxygenase in complex with 5-methylcytosine DNA journal December 2013
Structure of photosystem II and substrate binding at room temperature journal November 2016
Structural basis for oxygen degradation domain selectivity of the HIF prolyl hydroxylases journal August 2016
Accurate macromolecular structures using minimal measurements from X-ray free-electron lasers journal March 2014
Grease matrix as a versatile carrier of proteins for serial crystallography journal November 2014
High-resolution mass spectrometry of small molecules bound to membrane proteins journal February 2016
Drop-on-demand sample delivery for studying biocatalysts in action at X-ray free-electron lasers journal February 2017
First lasing and operation of an ångstrom-wavelength free-electron laser journal August 2010
Oxygen sensing by HIF hydroxylases journal May 2004
Enzymatic and structural insights for substrate specificity of a family of jumonji histone lysine demethylases journal December 2009
Membrane protein megahertz crystallography at the European XFEL journal November 2019
Structural dynamics in proteins induced by and probed with X-ray free-electron laser pulses journal April 2020
Structures of the intermediates of Kok’s photosynthetic water oxidation clock journal November 2018
Roles of 2-oxoglutarate oxygenases and isopenicillin N synthase in β-lactam biosynthesis journal January 2018
19 F NMR studies on γ-butyrobetaine hydroxylase provide mechanistic insights and suggest a dual inhibition mode journal January 2019
The structure of a peptide, containing α-aminoadipic acid, cystine and valine, present in the mycelium of Penicillium chrysogenum journal August 1960
Structure of Human Phytanoyl-CoA 2-Hydroxylase Identifies Molecular Mechanisms of Refsum Disease journal September 2005
The New Macromolecular Femtosecond Crystallography (MFX) Instrument at LCLS journal January 2016
A Functional Isopenicillin N Synthase in an Animal Genome journal November 2012
ESPript/ENDscript: extracting and rendering sequence and 3D information from atomic structures of proteins journal July 2003
Phaser crystallographic software journal July 2007
PHENIX : building new software for automated crystallographic structure determination journal October 2002
Features and development of Coot journal March 2010
New Python-based methods for data processing journal June 2013
Decision making in xia 2 journal June 2013
Improved crystal orientation and physical properties from single-shot XFEL stills journal November 2014
MAP_CHANNELS : a computation tool to aid in the visualization and characterization of solvent channels in macromolecular crystals journal November 2014
XFEL diffraction: developing processing methods to optimize data quality journal January 2015
Anaerobic fixed-target serial crystallography journal August 2020
Diffraction-geometry refinement in the DIALS framework journal March 2016
Polder maps: improving OMIT maps by excluding bulk solvent journal February 2017
Low-dose fixed-target serial synchrotron crystallography journal March 2017
DIALS : implementation and evaluation of a new integration package journal February 2018
Improving signal strength in serial crystallography with DIALS geometry refinement journal September 2018
Anaerobic Crystallisation of an Isopenicillin N Synthase . Fe(II) . Substrate Complex Demonstrated by X-Ray Studies journal December 1996
Simultaneous Femtosecond X-ray Spectroscopy and Diffraction of Photosystem II at Room Temperature journal February 2013
Diffusion Coefficient of Oxygen in Propylene Glycol-Water Mixtures and Glycerol-Water Mixtures [Propylene Glycol-H2O混液およびGlycerol-H2O混液中酸素の拡散係数について] journal January 1962
Enabling X-ray free electron laser crystallography for challenging biological systems from a limited number of crystals journal March 2015
Biosynthesis of histone messenger RNA employs a specific 3' end endonuclease journal December 2018

Similar Records

Cloning, expression, purification, crystallization and X-ray diffraction analysis of dihydrodipicolinate synthase from the human pathogenic bacterium Bartonella henselae strain Houston-1 at 2.1 Å resolution
Journal Article · Thu Dec 31 23:00:00 EST 2015 · Acta Crystallographica. Section F, Structural Biology Communications · OSTI ID:1378764

Electron spin echo envelope modulation studies of the Cu(II)-substituted derivative of isopenicillin N synthase: A structural and spectroscopic model
Journal Article · Mon Dec 02 23:00:00 EST 1991 · Biochemistry; (United States) · OSTI ID:5487358