Structure and activity of PPX/GppA homologs from Escherichia coli and Helicobacter pylori

Song, He; Dharmasena, Madushini N.; Wang, Chao; Shaw, Gary X.; Cherry, Scott; Tropea, Joseph E.; Jin, Ding J.; Ji, Xinhua

doi:10.1111/febs.15120

Title: Structure and activity of PPX/GppA homologs from Escherichia coli and Helicobacter pylori

Authors:

Song, He ^[1]; Dharmasena, Madushini N. ^[2]; Wang, Chao ^[1]; Shaw, Gary X. ^[1]; Cherry, Scott ^[1]; Tropea, Joseph E. ^[1]; Jin, Ding J. ^[2];

^[1]

Macromolecular Crystallography Laboratory National Cancer Institute Frederick MD USA
RNA Biology Laboratory National Cancer Institute Frederick MD USA

Publication Date:: 2019-11-23

Sponsoring Org.:: USDOE

OSTI Identifier:: 1575312

Grant/Contract Number:: DE‐AC02‐06CH11357

Resource Type:: Publisher's Accepted Manuscript

Journal Name:: Federation of European Biochemical Societies (FEBS) Journal

Additional Journal Information:: Journal Name: Federation of European Biochemical Societies (FEBS) Journal Journal Volume: 287 Journal Issue: 9; Journal ID: ISSN 1742-464X

Publisher:: Wiley-Blackwell

Country of Publication:: United Kingdom

Language:: English

Citation Formats


                    Song, He, Dharmasena, Madushini N., Wang, Chao, Shaw, Gary X., Cherry, Scott, Tropea, Joseph E., Jin, Ding J., and Ji, Xinhua. Structure and activity of PPX/GppA homologs from Escherichia coli and Helicobacter pylori.  United Kingdom: N. p., 2019. 
Web.  doi:10.1111/febs.15120.

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                    Song, He, Dharmasena, Madushini N., Wang, Chao, Shaw, Gary X., Cherry, Scott, Tropea, Joseph E., Jin, Ding J., & Ji, Xinhua. Structure and activity of PPX/GppA homologs from Escherichia coli and Helicobacter pylori.  United Kingdom.  https://doi.org/10.1111/febs.15120

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                    Song, He, Dharmasena, Madushini N., Wang, Chao, Shaw, Gary X., Cherry, Scott, Tropea, Joseph E., Jin, Ding J., and Ji, Xinhua. Sat .  
"Structure and activity of PPX/GppA homologs from Escherichia coli and Helicobacter pylori".  United Kingdom.  https://doi.org/10.1111/febs.15120.

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@article{osti_1575312,

  title        = {Structure and activity of PPX/GppA homologs from Escherichia coli and Helicobacter pylori},

  author       = {Song, He and Dharmasena, Madushini N. and Wang, Chao and Shaw, Gary X. and Cherry, Scott and Tropea, Joseph E. and Jin, Ding J. and Ji, Xinhua},

  abstractNote = {},

  doi          = {10.1111/febs.15120},

  journal      = {Federation of European Biochemical Societies (FEBS) Journal},

  number       = 9,

  volume       = 287,

  place        = {United Kingdom},

  year         = {2019},

  month        = {11}

}

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https://doi.org/10.1111/febs.15120

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Title: Structure and activity of PPX/GppA homologs from Escherichia coli and Helicobacter pylori

Citation Formats

Recent functional insights into the role of (p)ppGpp in bacterial physiology journal, April 2015

Uniqueness of ab initio shape determination in small-angle scattering journal, April 2003

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences journal, November 2015

Hit the right spots: cell cycle control by phosphorylated guanosines in alphaproteobacteria journal, January 2017

Novel Assay Reveals Multiple Pathways Regulating Stress-Induced Accumulations of Inorganic Polyphosphate in Escherichia coli journal, April 1998

A Magic Spot in Genome Maintenance journal, January 2017

Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard journal, December 2007

CRYSOL – a Program to Evaluate X-ray Solution Scattering of Biological Macromolecules from Atomic Coordinates journal, December 1995

Determination of the regularization parameter in indirect-transform methods using perceptual criteria journal, August 1992

ppGpp couples transcription to DNA repair in E. coli journal, May 2016

Guanosine pentaphosphate phosphohydrolase of Escherichia coli is a long-chain exopolyphosphatase. journal, August 1993

Functional characterization of exopolyphosphatase/guanosine pentaphosphate phosphohydrolase (PPX/GPPA) of Campylobacter jejuni journal, February 2014

A polyphosphate kinase (PPK2) widely conserved in bacteria journal, December 2002

PRIMUS: a Windows PC-based system for small-angle scattering data analysis journal, September 2003

Bacterial nucleotide-based second messengers journal, April 2009

Two exopolyphosphatases with distinct molecular architectures and substrate specificities from the thermophilic green-sulfur bacterium Chlorobium tepidum TLS journal, June 2014

Inorganic Polyphosphate: A Molecule of Many Functions journal, June 1999

Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard journal, May 2009

The magic dance of the alarmones (p)ppGpp: The structural biology of the alarmones (p)ppGpp journal, June 2016

Inorganic Polyphosphate: Essential for Growth and Survival journal, June 2009

Guanosine Tetra- and Pentaphosphate Promote Accumulation of Inorganic Polyphosphate in Escherichia coli journal, August 1997

Structural Characterization of the Stringent Response Related Exopolyphosphatase/Guanosine Pentaphosphate Phosphohydrolase Protein Family † , ‡ journal, July 2004

ExPASy: the proteomics server for in-depth protein knowledge and analysis journal, July 2003

The complete genome of the hyperthermophilic bacterium Aquifex aeolicus journal, March 1998

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees journal, April 2016

The mechanism of RNA duplex recognition and unwinding by DEAD-box helicase DDX3X journal, July 2019

Direct binding targets of the stringent response alarmone (p)ppGpp journal, August 2012

HKL -3000: the integration of data reduction and structure solution – from diffraction images to an initial model in minutes journal, July 2006

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

Structure of the PPX/GPPA Phosphatase from Aquifex aeolicus in Complex with the Alarmone ppGpp journal, February 2008

Restoring Low Resolution Structure of Biological Macromolecules from Solution Scattering Using Simulated Annealing journal, June 1999

New developments in the ATSAS program package for small-angle scattering data analysis journal, March 2012

Living dangerously: how Helicobacter pylori survives in the human stomach journal, June 2001

Helicobacter pylori Initiates the Stringent Response upon Nutrient and pH Downshift journal, May 2006

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

The Functional Cycle of Rnt1p: Five Consecutive Steps of Double-Stranded RNA Processing by a Eukaryotic RNase III journal, February 2017

Automated matching of high- and low-resolution structural models journal, February 2001

The Structure of the Exopolyphosphatase (PPX) from Escherichia coli O157:H7 Suggests a Binding Mode for Long Polyphosphate Chains journal, June 2006

An exopolyphosphatase of Escherichia coli. The enzyme and its ppx gene in a polyphosphate operon. journal, January 1993

Determination of the molecular weight of proteins in solution from a single small-angle X-ray scattering measurement on a relative scale journal, December 2009

(p)ppGpp: Still Magical? journal, October 2008

The Protein Data Bank journal, January 2000

Differential regulation by ppGpp versus pppGpp in Escherichia coli journal, April 2013

Origin of Exopolyphosphatase Processivity: Fusion of an ASKHA Phosphotransferase and a Cyclic Nucleotide Phosphodiesterase Homolog journal, August 2006

Jalview Version 2--a multiple sequence alignment editor and analysis workbench journal, January 2009

The RelA/SpoT Homolog (RSH) Superfamily: Distribution and Functional Evolution of ppGpp Synthetases and Hydrolases across the Tree of Life journal, August 2011

Phaser crystallographic software journal, July 2007

Recent functional insights into the role of (p)ppGpp in bacterial physiology
journal, April 2015

Uniqueness of ab initio shape determination in small-angle scattering
journal, April 2003

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences
journal, November 2015

Hit the right spots: cell cycle control by phosphorylated guanosines in alphaproteobacteria
journal, January 2017

Novel Assay Reveals Multiple Pathways Regulating Stress-Induced Accumulations of Inorganic Polyphosphate in Escherichia coli
journal, April 1998

A Magic Spot in Genome Maintenance
journal, January 2017

Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard
journal, December 2007

CRYSOL – a Program to Evaluate X-ray Solution Scattering of Biological Macromolecules from Atomic Coordinates
journal, December 1995

Determination of the regularization parameter in indirect-transform methods using perceptual criteria
journal, August 1992

ppGpp couples transcription to DNA repair in E. coli
journal, May 2016

Guanosine pentaphosphate phosphohydrolase of Escherichia coli is a long-chain exopolyphosphatase.
journal, August 1993

Functional characterization of exopolyphosphatase/guanosine pentaphosphate phosphohydrolase (PPX/GPPA) of Campylobacter jejuni
journal, February 2014

A polyphosphate kinase (PPK2) widely conserved in bacteria
journal, December 2002

PRIMUS: a Windows PC-based system for small-angle scattering data analysis
journal, September 2003

Bacterial nucleotide-based second messengers
journal, April 2009

Two exopolyphosphatases with distinct molecular architectures and substrate specificities from the thermophilic green-sulfur bacterium Chlorobium tepidum TLS
journal, June 2014

Inorganic Polyphosphate: A Molecule of Many Functions
journal, June 1999

Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard
journal, May 2009

The magic dance of the alarmones (p)ppGpp: The structural biology of the alarmones (p)ppGpp
journal, June 2016

Inorganic Polyphosphate: Essential for Growth and Survival
journal, June 2009

Guanosine Tetra- and Pentaphosphate Promote Accumulation of Inorganic Polyphosphate in Escherichia coli
journal, August 1997

Structural Characterization of the Stringent Response Related Exopolyphosphatase/Guanosine Pentaphosphate Phosphohydrolase Protein Family ^† ^, ^‡
journal, July 2004

ExPASy: the proteomics server for in-depth protein knowledge and analysis
journal, July 2003

The complete genome of the hyperthermophilic bacterium Aquifex aeolicus
journal, March 1998

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees
journal, April 2016

The mechanism of RNA duplex recognition and unwinding by DEAD-box helicase DDX3X
journal, July 2019

Direct binding targets of the stringent response alarmone (p)ppGpp
journal, August 2012

HKL -3000: the integration of data reduction and structure solution – from diffraction images to an initial model in minutes
journal, July 2006

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

Structure of the PPX/GPPA Phosphatase from Aquifex aeolicus in Complex with the Alarmone ppGpp
journal, February 2008

Restoring Low Resolution Structure of Biological Macromolecules from Solution Scattering Using Simulated Annealing
journal, June 1999

New developments in the ATSAS program package for small-angle scattering data analysis
journal, March 2012

Living dangerously: how Helicobacter pylori survives in the human stomach
journal, June 2001

Helicobacter pylori Initiates the Stringent Response upon Nutrient and pH Downshift
journal, May 2006

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

The Functional Cycle of Rnt1p: Five Consecutive Steps of Double-Stranded RNA Processing by a Eukaryotic RNase III
journal, February 2017

Automated matching of high- and low-resolution structural models
journal, February 2001

The Structure of the Exopolyphosphatase (PPX) from Escherichia coli O157:H7 Suggests a Binding Mode for Long Polyphosphate Chains
journal, June 2006

An exopolyphosphatase of Escherichia coli. The enzyme and its ppx gene in a polyphosphate operon.
journal, January 1993

Determination of the molecular weight of proteins in solution from a single small-angle X-ray scattering measurement on a relative scale
journal, December 2009

(p)ppGpp: Still Magical?
journal, October 2008

The Protein Data Bank
journal, January 2000

Differential regulation by ppGpp versus pppGpp in Escherichia coli
journal, April 2013

Origin of Exopolyphosphatase Processivity: Fusion of an ASKHA Phosphotransferase and a Cyclic Nucleotide Phosphodiesterase Homolog
journal, August 2006

Jalview Version 2--a multiple sequence alignment editor and analysis workbench
journal, January 2009

The RelA/SpoT Homolog (RSH) Superfamily: Distribution and Functional Evolution of ppGpp Synthetases and Hydrolases across the Tree of Life
journal, August 2011

Phaser crystallographic software
journal, July 2007