skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: The predominance of nucleotidyl activation in bacterial phosphonate biosynthesis

ORCiD logo; ; ORCiD logo; ORCiD logo; ORCiD logo; ORCiD logo; ORCiD logo; ORCiD logo; ORCiD logo; ORCiD logo; ORCiD logo; ORCiD logo; ORCiD logo; ORCiD logo; ORCiD logo
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
Sponsoring Org.:
OSTI Identifier:
Resource Type:
Journal Article
Journal Name:
Nature Communications
Additional Journal Information:
Journal Volume: 10; Journal Issue: 1; Journal ID: ISSN 2041-1723
Nature Publishing Group
Country of Publication:
United States

Citation Formats

Rice, Kyle, Batul, Kissa, Whiteside, Jacqueline, Kelso, Jayne, Papinski, Monica, Schmidt, Edward, Pratasouskaya, Alena, Wang, Dacheng, Sullivan, Rebecca, Bartlett, Christopher, Weadge, Joel T., Van der Kamp, Marc W., Moreno-Hagelsieb, Gabriel, Suits, Michael D., and Horsman, Geoff P. The predominance of nucleotidyl activation in bacterial phosphonate biosynthesis. United States: N. p., 2019. Web. doi:10.1038/s41467-019-11627-6.
Rice, Kyle, Batul, Kissa, Whiteside, Jacqueline, Kelso, Jayne, Papinski, Monica, Schmidt, Edward, Pratasouskaya, Alena, Wang, Dacheng, Sullivan, Rebecca, Bartlett, Christopher, Weadge, Joel T., Van der Kamp, Marc W., Moreno-Hagelsieb, Gabriel, Suits, Michael D., & Horsman, Geoff P. The predominance of nucleotidyl activation in bacterial phosphonate biosynthesis. United States. doi:10.1038/s41467-019-11627-6.
Rice, Kyle, Batul, Kissa, Whiteside, Jacqueline, Kelso, Jayne, Papinski, Monica, Schmidt, Edward, Pratasouskaya, Alena, Wang, Dacheng, Sullivan, Rebecca, Bartlett, Christopher, Weadge, Joel T., Van der Kamp, Marc W., Moreno-Hagelsieb, Gabriel, Suits, Michael D., and Horsman, Geoff P. Fri . "The predominance of nucleotidyl activation in bacterial phosphonate biosynthesis". United States. doi:10.1038/s41467-019-11627-6.
title = {The predominance of nucleotidyl activation in bacterial phosphonate biosynthesis},
author = {Rice, Kyle and Batul, Kissa and Whiteside, Jacqueline and Kelso, Jayne and Papinski, Monica and Schmidt, Edward and Pratasouskaya, Alena and Wang, Dacheng and Sullivan, Rebecca and Bartlett, Christopher and Weadge, Joel T. and Van der Kamp, Marc W. and Moreno-Hagelsieb, Gabriel and Suits, Michael D. and Horsman, Geoff P.},
abstractNote = {},
doi = {10.1038/s41467-019-11627-6},
journal = {Nature Communications},
issn = {2041-1723},
number = 1,
volume = 10,
place = {United States},
year = {2019},
month = {8}

Works referenced in this record:

The Kennedy pathway-De novo synthesis of phosphatidylethanolamine and phosphatidylcholine
journal, June 2010

  • Gibellini, Federica; Smith, Terry K.
  • IUBMB Life, Vol. 62, Issue 6
  • DOI: 10.1002/iub.354

Phosphonate Biochemistry
journal, October 2016

The licC Gene of Streptococcus pneumoniae Encodes a CTP:Phosphocholine Cytidylyltransferase
journal, August 2001

Evaporative light scattering quantification of natural products possessing a carbon–phosphorus bond
journal, May 2015

  • Chi, Matthew C.; Horsman, Geoff P.
  • The Journal of Antibiotics, Vol. 68, Issue 12
  • DOI: 10.1038/ja.2015.62

The Renaissance of Bacillosamine and Its Derivatives: Pathway Characterization and Implications in Pathogenicity
journal, January 2014

  • Morrison, Michael J.; Imperiali, Barbara
  • Biochemistry, Vol. 53, Issue 4
  • DOI: 10.1021/bi401546r

The Phosphonopyruvate Decarboxylase from Bacteroides fragilis
journal, August 2003

  • Zhang, Guofeng; Dai, Jiaying; Lu, Zhibing
  • Journal of Biological Chemistry, Vol. 278, Issue 42
  • DOI: 10.1074/jbc.M305976200

Continuous enzyme-coupled assay of phosphate- or pyrophosphate-releasing enzymes
journal, August 2012

  • Suárez, Antonio S. Guillén; Stefan, Alessandra; Lemma, Silvia
  • BioTechniques, Vol. 53, Issue 2
  • DOI: 10.2144/000113905

Role of Teichoic Acid Choline Moieties in the Virulence of Streptococcus pneumoniae
journal, May 2009

  • Gehre, F.; Spisek, R.; Kharat, A. S.
  • Infection and Immunity, Vol. 77, Issue 7
  • DOI: 10.1128/IAI.00986-08

Phosphoethanolamine Modification of Neisseria gonorrhoeae Lipid A Reduces Autophagy Flux in Macrophages
journal, December 2015

PHENIX : building new software for automated crystallographic structure determination
journal, October 2002

  • Adams, Paul D.; Grosse-Kunstleve, Ralf W.; Hung, Li-Wei
  • Acta Crystallographica Section D Biological Crystallography, Vol. 58, Issue 11
  • DOI: 10.1107/S0907444902016657

Structure-based Mechanism of CMP-2-keto-3-deoxymanno-octulonic Acid Synthetase: CONVERGENT EVOLUTION OF A SUGAR-ACTIVATING ENZYME WITH DNA/RNA POLYMERASES
journal, October 2009

  • Heyes, Derren J.; Levy, Colin; Lafite, Pierre
  • Journal of Biological Chemistry, Vol. 284, Issue 51
  • DOI: 10.1074/jbc.M109.056630

NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins
journal, January 2007

  • Pruitt, K. D.; Tatusova, T.; Maglott, D. R.
  • Nucleic Acids Research, Vol. 35, Issue Database
  • DOI: 10.1093/nar/gkl842

Genomics-enabled discovery of phosphonate natural products and their biosynthetic pathways
journal, November 2013

  • Ju, Kou-San; Doroghazi, James R.; Metcalf, William W.
  • Journal of Industrial Microbiology & Biotechnology, Vol. 41, Issue 2
  • DOI: 10.1007/s10295-013-1375-2

Composite Aromatic Boxes for Enzymatic Transformations of Quaternary Ammonium Substrates
journal, October 2014

  • Nagy, Gergely N.; Marton, Lívia; Contet, Alicia
  • Angewandte Chemie International Edition, Vol. 53, Issue 49
  • DOI: 10.1002/anie.201408246

Phosphoethanolamine cellulose: A naturally produced chemically modified cellulose
journal, January 2018

  • Thongsomboon, Wiriya; Serra, Diego O.; Possling, Alexandra
  • Science, Vol. 359, Issue 6373
  • DOI: 10.1126/science.aao4096

Phosphorylcholine Allows for Evasion of Bactericidal Antibody by Haemophilus influenzae
journal, March 2012

Isolation of 2-Aminoethane Phosphonic Acid from Rumen Protozoa
journal, September 1959

  • Horiguchi, Masaaki; Kandatstu, Makoto
  • Nature, Vol. 184, Issue 4690
  • DOI: 10.1038/184901b0

The 2-Aminoethylphosphonate-Specific Transaminase of the 2-Aminoethylphosphonate Degradation Pathway
journal, August 2002

Development and testing of a general amber force field
journal, January 2004

  • Wang, Junmei; Wolf, Romain M.; Caldwell, James W.
  • Journal of Computational Chemistry, Vol. 25, Issue 9
  • DOI: 10.1002/jcc.20035

Structural elucidation of two capsular polysaccharides from one strain of Bacteroides fragilis using high-resolution NMR spectroscopy
journal, April 1992

  • Baumann, H.; Tzianabos, A. O.; Brisson, J. R.
  • Biochemistry, Vol. 31, Issue 16
  • DOI: 10.1021/bi00131a026

The I-TASSER Suite: protein structure and function prediction
journal, December 2014

  • Yang, Jianyi; Yan, Renxiang; Roy, Ambrish
  • Nature Methods, Vol. 12, Issue 1
  • DOI: 10.1038/nmeth.3213

Kinetic Analysis of Escherichia coli 2-C-Methyl- d -erythritol-4-phosphate Cytidyltransferase, Wild Type and Mutants, Reveals Roles of Active Site Amino Acids
journal, September 2004

  • Richard, Stéphane B.; Lillo, Antonietta M.; Tetzlaff, Charles N.
  • Biochemistry, Vol. 43, Issue 38
  • DOI: 10.1021/bi0487241

Degradation Pathway of the Phosphonate Ciliatine:  Crystal Structure of 2-Aminoethylphosphonate Transaminase ,
journal, November 2002

  • Chen, Celia C. H.; Zhang, H.; Kim, A. D.
  • Biochemistry, Vol. 41, Issue 44
  • DOI: 10.1021/bi026231v

A continuous spectrophotometric assay for inorganic phosphate and for measuring phosphate release kinetics in biological systems.
journal, June 1992

Unusual transformations in the biosynthesis of the antibiotic phosphinothricin tripeptide
journal, July 2007

  • Blodgett, Joshua A. V.; Thomas, Paul M.; Li, Gongyong
  • Nature Chemical Biology, Vol. 3, Issue 8
  • DOI: 10.1038/nchembio.2007.9

Diversity and abundance of phosphonate biosynthetic genes in nature
journal, December 2013

  • Yu, X.; Doroghazi, J. R.; Janga, S. C.
  • Proceedings of the National Academy of Sciences, Vol. 110, Issue 51
  • DOI: 10.1073/pnas.1315107110

Biosynthesis of Teichoic Acids in Streptococcus pneumoniae and Closely Related Species: Lessons from Genomes
journal, June 2012

  • Denapaite, Dalia; Brückner, Reinhold; Hakenbeck, Regine
  • Microbial Drug Resistance, Vol. 18, Issue 3
  • DOI: 10.1089/mdr.2012.0026

Accumulation of Peptidoglycan O -Acetylation Leads to Altered Cell Wall Biochemistry and Negatively Impacts Pathogenesis Factors of Campylobacter jejuni
journal, July 2016

  • Ha, Reuben; Frirdich, Emilisa; Sychantha, David
  • Journal of Biological Chemistry, Vol. 291, Issue 43
  • DOI: 10.1074/jbc.M116.746404

Functional Characterization of Enzymatic Steps Involved in Pyruvylation of Bacterial Secondary Cell Wall Polymer Fragments
journal, June 2018

  • Hager, Fiona F.; López-Guzmán, Arturo; Krauter, Simon
  • Frontiers in Microbiology, Vol. 9
  • DOI: 10.3389/fmicb.2018.01356

Fosfomycin Biosynthesis via Transient Cytidylylation of 2-Hydroxyethylphosphonate by the Bifunctional Fom1 Enzyme
journal, July 2017

Phylogenomic clustering for selecting non-redundant genomes for comparative genomics
journal, February 2013

Structural and Chemical Biology of Terpenoid Cyclases
journal, August 2017

Clonality of bacterial consortia in root canals and subjacent gingival crevices
journal, August 2014

  • Parahitiyawa, Nipuna B.; Chu, Frederick C. S.; Leung, Wai K.
  • Journal of Investigative and Clinical Dentistry, Vol. 6, Issue 1
  • DOI: 10.1111/jicd.12070

Structural Basis of Perturbed pKa Values of Catalytic Groups in Enzyme Active Sites
journal, February 2002

  • Harris, Thomas K.; Turner, George J.
  • IUBMB Life (International Union of Biochemistry and Molecular Biology: Life), Vol. 53, Issue 2
  • DOI: 10.1080/15216540211468

The Pfam protein families database: towards a more sustainable future
journal, December 2015

  • Finn, Robert D.; Coggill, Penelope; Eberhardt, Ruth Y.
  • Nucleic Acids Research, Vol. 44, Issue D1
  • DOI: 10.1093/nar/gkv1344

Biosynthesis of Phosphonic and Phosphinic Acid Natural Products
journal, June 2009

Kinetic Mechanism of DNA Polymerases: Contributions of Conformational Dynamics and a Third Divalent Metal Ion
journal, June 2018

Review of phosphocholine substituents on bacterial pathogen glycans: Synthesis, structures and interactions with host proteins
journal, December 2013

Crystal structure of an alanine-glyoxylate aminotransferase from Anabaena sp. at 1.70 Å resolution reveals a noncovalently linked PLP cofactor
journal, January 2005

  • Won Han, Gye; Schwarzenbacher, Robert; Page, Rebecca
  • Proteins: Structure, Function, and Bioinformatics, Vol. 58, Issue 4
  • DOI: 10.1002/prot.20360

Structure and Mechanism of CTP:Phosphocholine Cytidylyltransferase (LicC) from Streptococcus pneumoniae
journal, November 2001

  • Kwak, Bo-Yeon; Zhang, Yong-Mei; Yun, Mikyung
  • Journal of Biological Chemistry, Vol. 277, Issue 6
  • DOI: 10.1074/jbc.M109163200

Coot model-building tools for molecular graphics
journal, November 2004

  • Emsley, Paul; Cowtan, Kevin
  • Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 12, p. 2126-2132
  • DOI: 10.1107/S0907444904019158

p K a Calculations of Aliphatic Amines, Diamines, and Aminoamides via Density Functional Theory with a Poisson−Boltzmann Continuum Solvent Model
journal, May 2007

  • Bryantsev, Vyacheslav S.; Diallo, Mamadou S.; Goddard, William A.
  • The Journal of Physical Chemistry A, Vol. 111, Issue 20
  • DOI: 10.1021/jp071040t

Discovery of phosphonic acid natural products by mining the genomes of 10,000 actinomycetes
journal, August 2015

  • Ju, Kou-San; Gao, Jiangtao; Doroghazi, James R.
  • Proceedings of the National Academy of Sciences, Vol. 112, Issue 39
  • DOI: 10.1073/pnas.1500873112

Complete genome sequence of Olsenella uli type strain (VPI D76D-27CT)
journal, August 2010

  • Göker, Markus; Held, Brittany; Lucas, Susan
  • Standards in Genomic Sciences, Vol. 3, Issue 1
  • DOI: 10.4056/sigs.1082860

Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega
journal, January 2011

  • Sievers, Fabian; Wilm, Andreas; Dineen, David
  • Molecular Systems Biology, Vol. 7, Issue 1
  • DOI: 10.1038/msb.2011.75

Whole-Cell Detection of C–P Bonds in Bacteria
journal, October 2017

Molecular Signaling Mechanisms of the Periopathogen, Treponema denticola
journal, March 2011

  • Frederick, J. R.; Sarkar, J.; McDowell, J. V.
  • Journal of Dental Research, Vol. 90, Issue 10
  • DOI: 10.1177/0022034511402994

Phosphonate biosynthesis and catabolism: a treasure trove of unusual enzymology
journal, August 2013

  • Peck, Spencer C.; van der Donk, Wilfred A.
  • Current Opinion in Chemical Biology, Vol. 17, Issue 4
  • DOI: 10.1016/j.cbpa.2013.06.018

Microbial Modulation of Host Immunity with the Small Molecule Phosphorylcholine
journal, December 2012

  • Clark, Sarah E.; Weiser, Jeffrey N.
  • Infection and Immunity, Vol. 81, Issue 2
  • DOI: 10.1128/IAI.01168-12

Distinct Properties of the Two Isoforms of CDP-Diacylglycerol Synthase
journal, November 2014

  • D’Souza, Kenneth; Kim, Yeun Ju; Balla, Tamas
  • Biochemistry, Vol. 53, Issue 47
  • DOI: 10.1021/bi501250m

HMMER web server: interactive sequence similarity searching
journal, May 2011

  • Finn, R. D.; Clements, J.; Eddy, S. R.
  • Nucleic Acids Research, Vol. 39, Issue suppl
  • DOI: 10.1093/nar/gkr367

Catalysis and thermodynamics of the phosphoenolpyruvate/phosphonopyruvate rearrangement. Entry into the phosphonate class of naturally occurring organophosphorus compounds
journal, August 1988

  • Bowman, Elise.; McQueney, Michael.; Barry, Robert J.
  • Journal of the American Chemical Society, Vol. 110, Issue 16
  • DOI: 10.1021/ja00224a054

A C-terminal truncated mutation of licC attenuates the virulence of Streptococcus pneumoniae
journal, October 2014

Roll: a new algorithm for the detection of protein pockets and cavities with a rolling probe sphere
journal, October 2009

Deciphering the Late Biosynthetic Steps of Antimalarial Compound FR-900098
journal, January 2010

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

PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data
journal, June 2013

  • Roe, Daniel R.; Cheatham, Thomas E.
  • Journal of Chemical Theory and Computation, Vol. 9, Issue 7
  • DOI: 10.1021/ct400341p