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Title: X-ray crystallography–based structural elucidation of enzyme-bound intermediates along the 1-deoxy-d-xylulose 5-phosphate synthase reaction coordinate

Authors:
ORCiD logo; ; ORCiD logo; ORCiD logo
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
Sponsoring Org.:
National Institutes of Health (NIH)
OSTI Identifier:
1561288
Resource Type:
Journal Article
Journal Name:
Journal of Biological Chemistry
Additional Journal Information:
Journal Volume: 294; Journal Issue: 33; Journal ID: ISSN 0021-9258
Publisher:
American Society for Biochemistry and Molecular Biology
Country of Publication:
United States
Language:
ENGLISH

Citation Formats

Chen, Percival Yang-Ting, DeColli, Alicia A., Freel Meyers, Caren L., and Drennan, Catherine L. X-ray crystallography–based structural elucidation of enzyme-bound intermediates along the 1-deoxy-d-xylulose 5-phosphate synthase reaction coordinate. United States: N. p., 2019. Web. doi:10.1074/jbc.RA119.009321.
Chen, Percival Yang-Ting, DeColli, Alicia A., Freel Meyers, Caren L., & Drennan, Catherine L. X-ray crystallography–based structural elucidation of enzyme-bound intermediates along the 1-deoxy-d-xylulose 5-phosphate synthase reaction coordinate. United States. doi:10.1074/jbc.RA119.009321.
Chen, Percival Yang-Ting, DeColli, Alicia A., Freel Meyers, Caren L., and Drennan, Catherine L. Tue . "X-ray crystallography–based structural elucidation of enzyme-bound intermediates along the 1-deoxy-d-xylulose 5-phosphate synthase reaction coordinate". United States. doi:10.1074/jbc.RA119.009321.
@article{osti_1561288,
title = {X-ray crystallography–based structural elucidation of enzyme-bound intermediates along the 1-deoxy-d-xylulose 5-phosphate synthase reaction coordinate},
author = {Chen, Percival Yang-Ting and DeColli, Alicia A. and Freel Meyers, Caren L. and Drennan, Catherine L.},
abstractNote = {},
doi = {10.1074/jbc.RA119.009321},
journal = {Journal of Biological Chemistry},
issn = {0021-9258},
number = 33,
volume = 294,
place = {United States},
year = {2019},
month = {6}
}

Works referenced in this record:

Crystal Structure of 1-Deoxy-d-xylulose 5-Phosphate Synthase, a Crucial Enzyme for Isoprenoids Biosynthesis
journal, November 2006

  • Xiang, Song; Usunow, Gerlinde; Lange, Gudrun
  • Journal of Biological Chemistry, Vol. 282, Issue 4
  • DOI: 10.1074/jbc.M610235200

1-Deoxy-d-xylulose 5-Phosphate Synthase Catalyzes a Novel Random Sequential Mechanism
journal, August 2011

  • Brammer, Leighanne A.; Smith, Jessica M.; Wade, Herschel
  • Journal of Biological Chemistry, Vol. 286, Issue 42
  • DOI: 10.1074/jbc.M111.259747

Determination of Pre-Steady-State Rate Constants on the Escherichia coli Pyruvate Dehydrogenase Complex Reveals That Loop Movement Controls the Rate-Limiting Step
journal, November 2012

  • Balakrishnan, Anand; Nemeria, Natalia S.; Chakraborty, Sumit
  • Journal of the American Chemical Society, Vol. 134, Issue 45
  • DOI: 10.1021/ja3062375

Radical reactions of thiamin pyrophosphate in 2-oxoacid oxidoreductases
journal, November 2012

  • Reed, George H.; Ragsdale, Stephen W.; Mansoorabadi, Steven O.
  • Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, Vol. 1824, Issue 11
  • DOI: 10.1016/j.bbapap.2011.11.010

Collaboration gets the most out of software
journal, September 2013


Pyridoxal phosphate: Biosynthesis and catabolism
journal, November 2011

  • Mukherjee, Tathagata; Hanes, Jeremiah; Tews, Ivo
  • Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, Vol. 1814, Issue 11
  • DOI: 10.1016/j.bbapap.2011.06.018

Evolutionary Analysis of the TPP-Dependent Enzyme Family
journal, November 2007

  • Costelloe, Seán J.; Ward, John M.; Dalby, Paul A.
  • Journal of Molecular Evolution, Vol. 66, Issue 1
  • DOI: 10.1007/s00239-007-9056-2

Oxidative decarboxylation of pyruvate by 1-deoxy-d-xyulose 5-phosphate synthase, a central metabolic enzyme in bacteria
journal, May 2018

  • DeColli, Alicia A.; Nemeria, Natalia S.; Majumdar, Ananya
  • Journal of Biological Chemistry, Vol. 293, Issue 28
  • DOI: 10.1074/jbc.RA118.001980

Structure of the Pyruvate Dehydrogenase Multienzyme Complex E1 Component from Escherichia coli at 1.85 Å Resolution ,
journal, April 2002

  • Arjunan, Palaniappa; Nemeria, Natalia; Brunskill, Andrew
  • Biochemistry, Vol. 41, Issue 16
  • DOI: 10.1021/bi0118557

Selective inhibition of E. coli1-deoxy- d -xylulose-5-phosphate synthase by acetylphosphonates
journal, January 2012

  • Smith, Jessica M.; Vierling, Ryan J.; Meyers, Caren Freel
  • Med. Chem. Commun., Vol. 3, Issue 1
  • DOI: 10.1039/c1md00233c

Targeting the Unique Mechanism of Bacterial 1-Deoxy- d -xylulose-5-phosphate Synthase
journal, June 2018


Identification of Charge Transfer Transitions Related to Thiamin-Bound Intermediates on Enzymes Provides a Plethora of Signatures Useful in Mechanistic Studies
journal, March 2014

  • Patel, Hetalben; Nemeria, Natalia S.; Andrews, Forest H.
  • Biochemistry, Vol. 53, Issue 13
  • DOI: 10.1021/bi4015743

Spectroscopic Evidence for Participation of the 1′,4′-Imino Tautomer of Thiamin Diphosphate in Catalysis by Yeast Pyruvate Decarboxylase
journal, June 2002

  • Jordan, Frank; Zhang, Zhen; Sergienko, Eduard
  • Bioorganic Chemistry, Vol. 30, Issue 3
  • DOI: 10.1006/bioo.2002.1249

DXP Synthase-Catalyzed CN Bond Formation: Nitroso Substrate Specificity Studies Guide Selective Inhibitor Design
journal, July 2013

  • Morris, Francine; Vierling, Ryan; Boucher, Lauren
  • ChemBioChem, Vol. 14, Issue 11
  • DOI: 10.1002/cbic.201300187

Reaction mechanisms of thiamin diphosphate enzymes: defining states of ionization and tautomerization of the cofactor at individual steps
journal, May 2009


Phosphonate analogues of pyruvate. Probes of substrate binding to pyruvate oxidase and other thiamin pyrophosphate-dependent decarboxylases
journal, May 1980

  • O'Brien, Thomas A.; Kluger, Ronald; Pike, David C.
  • Biochimica et Biophysica Acta (BBA) - Enzymology, Vol. 613, Issue 1
  • DOI: 10.1016/0005-2744(80)90186-2

Identification of a thiamin-dependent synthase in Escherichia coli required for the formation of the 1-deoxy-D-xylulose 5-phosphate precursor to isoprenoids, thiamin, and pyridoxol
journal, November 1997

  • Sprenger, G. A.; Schorken, U.; Wiegert, T.
  • Proceedings of the National Academy of Sciences, Vol. 94, Issue 24
  • DOI: 10.1073/pnas.94.24.12857

One-carbon chemistry of oxalate oxidoreductase captured by X-ray crystallography
journal, December 2015

  • Gibson, Marcus I.; Chen, Percival Yang-Ting; Johnson, Aileen C.
  • Proceedings of the National Academy of Sciences, Vol. 113, Issue 2
  • DOI: 10.1073/pnas.1518537113

A Reverse TCA Cycle 2-Oxoacid:Ferredoxin Oxidoreductase that Makes C-C Bonds from CO2
journal, February 2019


The Methylerythritol Phosphate Pathway: Promising Drug Targets in the Fight against Tuberculosis
journal, February 2018


Revealing Substrate Promiscuity of 1-Deoxy- d -xylulose 5-Phosphate Synthase
journal, October 2009

  • Brammer, Leighanne A.; Meyers, Caren Freel
  • Organic Letters, Vol. 11, Issue 20
  • DOI: 10.1021/ol901961q

Rhodobacter capsulatus 1-Deoxy- d -xylulose 5-Phosphate Synthase:  Steady-State Kinetics and Substrate Binding
journal, February 2003

  • Eubanks, Lisa M.; Poulter, C. Dale
  • Biochemistry, Vol. 42, Issue 4
  • DOI: 10.1021/bi0205303

Mechanistic Studies of 1-Deoxy-D-Xylulose-5-Phosphate Synthase from Deinococcus radiodurans
journal, January 2018

  • Handa, Sumit; Dempsey, Daniel R.; Ramamoorthy, Divya
  • Biochemistry & Molecular Biology Journal, Vol. 04, Issue 01
  • DOI: 10.21767/2471-8084.100051

Features and development of Coot
journal, March 2010

  • Emsley, P.; Lohkamp, B.; Scott, W. G.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4
  • DOI: 10.1107/S0907444910007493

Binding site for coenzyme A revealed in the structure of pyruvate:ferredoxin oxidoreductase from Moorella thermoacetica
journal, March 2018

  • Chen, Percival Yang-Ting; Aman, Heather; Can, Mehmet
  • Proceedings of the National Academy of Sciences, Vol. 115, Issue 15
  • DOI: 10.1073/pnas.1722329115

Active site generated analogs of reactive intermediates in enzymic reactions. Potent inhibition of pyruvate dehydrogenase by a phosphonate analog of pyruvate
journal, June 1977

  • Kluger, Ronald; Pike, David C.
  • Journal of the American Chemical Society, Vol. 99, Issue 13
  • DOI: 10.1021/ja00455a052

A structural phylogeny for understanding 2-oxoacid oxidoreductase function
journal, December 2016

  • Gibson, Marcus I.; Chen, Percival Yang-Ting; Drennan, Catherine L.
  • Current Opinion in Structural Biology, Vol. 41
  • DOI: 10.1016/j.sbi.2016.05.011

PHENIX: a comprehensive Python-based system for macromolecular structure solution
journal, January 2010

  • Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221
  • DOI: 10.1107/S0907444909052925

Catalytically Important Residues in E. coli 1-Deoxy-D-Xylulose 5-Phosphate Synthase
journal, January 2014

  • Querol-Audí, Jordi; Boronat, Albert; Centelles, Josep J.
  • Journal of Biosciences and Medicines, Vol. 02, Issue 04
  • DOI: 10.4236/jbm.2014.24006

NMRPipe: A multidimensional spectral processing system based on UNIX pipes
journal, November 1995

  • Delaglio, Frank; Grzesiek, Stephan; Vuister, GeertenW.
  • Journal of Biomolecular NMR, Vol. 6, Issue 3
  • DOI: 10.1007/BF00197809

Thiamin (Vitamin B1) Biosynthesis and Regulation: A Rich Source of Antimicrobial Drug Targets?
journal, January 2011

  • Du, Qinglin; Wang, Honghai; Xie, Jianping
  • International Journal of Biological Sciences, Vol. 7, Issue 1
  • DOI: 10.7150/ijbs.7.41

Thiamin Diphosphate Activation in 1-Deoxy- d -xylulose 5-Phosphate Synthase: Insights into the Mechanism and Underlying Intermolecular Interactions
journal, August 2016

  • White, Justin K.; Handa, Sumit; Vankayala, Sai Lakshmana
  • The Journal of Physical Chemistry B, Vol. 120, Issue 37
  • DOI: 10.1021/acs.jpcb.6b07248

Targeting DXP synthase in human pathogens: enzyme inhibition and antimicrobial activity of butylacetylphosphonate
journal, October 2013

  • Smith, Jessica M.; Warrington, Nicole V.; Vierling, Ryan J.
  • The Journal of Antibiotics, Vol. 67, Issue 1
  • DOI: 10.1038/ja.2013.105

Challenges and Hallmarks of Establishing Alkylacetylphosphonates as Probes of Bacterial 1-Deoxy- d -xylulose 5-Phosphate Synthase
journal, March 2017


Conformational dynamics of 1-deoxy-d-xylulose 5-phosphate synthase on ligand binding revealed by H/D exchange MS
journal, August 2017

  • Zhou, Jieyu; Yang, Luying; DeColli, Alicia
  • Proceedings of the National Academy of Sciences, Vol. 114, Issue 35
  • DOI: 10.1073/pnas.1619981114

Phaser crystallographic software
journal, July 2007

  • McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D.
  • Journal of Applied Crystallography, Vol. 40, Issue 4
  • DOI: 10.1107/S0021889807021206

Unleashing Hydrogenase Activity in Carbon Monoxide Dehydrogenase/Acetyl-CoA Synthase and Pyruvate:Ferredoxin Oxidoreductase
journal, January 1996

  • Menon, Saurabh; Ragsdale, Stephen W.
  • Biochemistry, Vol. 35, Issue 49
  • DOI: 10.1021/bi9615598