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

Title: Structural and functional insight into the universal stress protein family

Authors:
; ; ; ; ;  [1]
  1. UV
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:
1123943
Resource Type:
Journal Article
Journal Name:
Evol. Appl.
Additional Journal Information:
Journal Volume: 6; Journal Issue: (3) ; 04, 2013
Country of Publication:
United States
Language:
ENGLISH

Citation Formats

Tkaczuk, Karolina L., Shumilin, Igor A., Chruszcz, Maksymilian, Evdokimova, Elena, Savchenko, Alexei, Minor, Wladek, MCSG), and Toronto). Structural and functional insight into the universal stress protein family. United States: N. p., 2018. Web. doi:10.1111/eva.12057.
Tkaczuk, Karolina L., Shumilin, Igor A., Chruszcz, Maksymilian, Evdokimova, Elena, Savchenko, Alexei, Minor, Wladek, MCSG), & Toronto). Structural and functional insight into the universal stress protein family. United States. doi:10.1111/eva.12057.
Tkaczuk, Karolina L., Shumilin, Igor A., Chruszcz, Maksymilian, Evdokimova, Elena, Savchenko, Alexei, Minor, Wladek, MCSG), and Toronto). Tue . "Structural and functional insight into the universal stress protein family". United States. doi:10.1111/eva.12057.
@article{osti_1123943,
title = {Structural and functional insight into the universal stress protein family},
author = {Tkaczuk, Karolina L. and Shumilin, Igor A. and Chruszcz, Maksymilian and Evdokimova, Elena and Savchenko, Alexei and Minor, Wladek and MCSG) and Toronto)},
abstractNote = {},
doi = {10.1111/eva.12057},
journal = {Evol. Appl.},
number = (3) ; 04, 2013,
volume = 6,
place = {United States},
year = {2018},
month = {11}
}

Works referenced in this record:

Cloning, mapping and nucleotide sequencing of a gene encoding a universal stress protein in Eschericha coli
journal, November 1992


Density modification for macromolecular phase improvement
journal, October 1999


Protein Structure Comparison by Alignment of Distance Matrices
journal, September 1993


ConSurf: Identification of Functional Regions in Proteins by Surface-Mapping of Phylogenetic Information
journal, January 2003


Overview of the CCP 4 suite and current developments
journal, March 2011

  • Winn, Martyn D.; Ballard, Charles C.; Cowtan, Kevin D.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4
  • DOI: 10.1107/S0907444910045749

The Structural Biology Center 19ID undulator beamline: facility specifications and protein crystallographic results
journal, December 2005

  • Rosenbaum, Gerd; Alkire, Randy W.; Evans, Gwyndaf
  • Journal of Synchrotron Radiation, Vol. 13, Issue 1
  • DOI: 10.1107/S0909049505036721

The universal stress protein paralogues of Escherichia coli are co-ordinately regulated and co-operate in the defence against DNA damage
journal, January 2002


Automated and accurate deposition of structures solved by X-ray diffraction to the Protein Data Bank
journal, September 2004

  • Yang, Huanwang; Guranovic, Vladimir; Dutta, Shuchismita
  • Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 10
  • DOI: 10.1107/S0907444904019419

SFCHECK : a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model
journal, January 1999

  • Vaguine, Alexei A.; Richelle, Jean; Wodak, S. J.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 55, Issue 1
  • DOI: 10.1107/S0907444998006684

Monophyly of class I aminoacyl tRNA synthetase, USPA, ETFP, photolyase, and PP-ATPase nucleotide-binding domains: implications for protein evolution in the RNA world
journal, May 2002

  • Aravind, L.; Anantharaman, Vivek; Koonin, Eugene V.
  • Proteins: Structure, Function, and Genetics, Vol. 48, Issue 1
  • DOI: 10.1002/prot.10064

PROCHECK: a program to check the stereochemical quality of protein structures
journal, April 1993

  • Laskowski, R. A.; MacArthur, M. W.; Moss, D. S.
  • Journal of Applied Crystallography, Vol. 26, Issue 2
  • DOI: 10.1107/S0021889892009944

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
journal, September 1997

  • Altschul, Stephen F.; Madden, Thomas L.; Schäffer, Alejandro A.
  • Nucleic Acids Research, Vol. 25, Issue 17, p. 3389-3402
  • DOI: 10.1093/nar/25.17.3389

Improved methods for building protein models in electron density maps and the location of errors in these models
journal, March 1991

  • Jones, T. A.; Zou, J. Y.; Cowan, S. W.
  • Acta Crystallographica Section A Foundations of Crystallography, Vol. 47, Issue 2, p. 110-119
  • DOI: 10.1107/S0108767390010224

A ?FRankenstein's monster? approach to comparative modeling: Merging the finest fragments of Fold-Recognition models and iterative model refinement aided by 3D structure evaluation
journal, January 2003

  • Kosinski, Jan; Cymerman, Iwona A.; Feder, Marcin
  • Proteins: Structure, Function, and Genetics, Vol. 53, Issue S6
  • DOI: 10.1002/prot.10545

Crystal structure of the tandem-type universal stress protein TTHA0350 from Thermus thermophilus HB8
journal, May 2011

  • Iino, Hitoshi; Shimizu, Nobutaka; Goto, Masaru
  • The Journal of Biochemistry, Vol. 150, Issue 3
  • DOI: 10.1093/jb/mvr057

The Pfam protein families database
journal, January 2004

  • Bateman, Alex; Coin, Lachlan; Durbin, Richard
  • Nucleic Acids Research, Vol. 32, Issue S1, p. D138-D141
  • DOI: 10.1093/nar/gkh121

CLANS: a Java application for visualizing protein families based on pairwise similarity
journal, July 2004


Assessment of protein models with three-dimensional profiles
journal, March 1992

  • Lüthy, Roland; Bowie, James U.; Eisenberg, David
  • Nature, Vol. 356, Issue 6364
  • DOI: 10.1038/356083a0

Structure-based assignment of the biochemical function of a hypothetical protein: A test case of structural genomics
journal, December 1998

  • Zarembinski, T. I.; Hung, L. -W.; Mueller-Dieckmann, H. -J.
  • Proceedings of the National Academy of Sciences, Vol. 95, Issue 26
  • DOI: 10.1073/pnas.95.26.15189

Universal stress proteins and Mycobacterium tuberculosis
journal, July 2003


Improvement of macromolecular electron-density maps by the simultaneous application of real and reciprocal space constraints
journal, January 1993

  • Cowtan, K. D.; Main, P.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 49, Issue 1
  • DOI: 10.1107/S0907444992007698

CD-Search: protein domain annotations on the fly
journal, July 2004

  • Marchler-Bauer, A.; Bryant, S. H.
  • Nucleic Acids Research, Vol. 32, Issue Web Server
  • DOI: 10.1093/nar/gkh454

SWISS-MODEL: an automated protein homology-modeling server
journal, July 2003


Structure of Thermotoga maritima Stationary Phase Survival Protein SurE
journal, November 2001


Confidence Limits on Phylogenies: An Approach Using the Bootstrap
journal, July 1985

  • Felsenstein, Joseph
  • Evolution, Vol. 39, Issue 4, p. 783-791
  • DOI: 10.2307/2408678

A short history of SHELX
journal, December 2007

  • Sheldrick, George M.
  • Acta Crystallographica Section A Foundations of Crystallography, Vol. 64, Issue 1, p. 112-122
  • DOI: 10.1107/S0108767307043930

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

  • Minor, Wladek; Cymborowski, Marcin; Otwinowski, Zbyszek
  • Acta Crystallographica Section D Biological Crystallography, Vol. 62, Issue 8
  • DOI: 10.1107/S0907444906019949

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

Role of the universal stress protein UspA of Salmonella in growth arrest, stress and virulence
journal, January 2007


ConSurf: an algorithmic tool for the identification of functional regions in proteins by surface mapping of phylogenetic information
journal, March 2001

  • Armon, Aharon; Graur, Dan; Ben-Tal, Nir
  • Journal of Molecular Biology, Vol. 307, Issue 1
  • DOI: 10.1006/jmbi.2000.4474

REFMAC 5 for the refinement of macromolecular crystal structures
journal, March 2011

  • Murshudov, Garib N.; Skubák, Pavol; Lebedev, Andrey A.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4
  • DOI: 10.1107/S0907444911001314

The Universal Stress Protein UspC Scaffolds the KdpD/KdpE Signaling Cascade of Escherichia coli under Salt Stress
journal, February 2009

  • Heermann, Ralf; Weber, Arnim; Mayer, Bettina
  • Journal of Molecular Biology, Vol. 386, Issue 1
  • DOI: 10.1016/j.jmb.2008.12.007

Structure validation by Cα geometry: ϕ,ψ and Cβ deviation
journal, January 2003

  • Lovell, Simon C.; Davis, Ian W.; Arendall, W. Bryan
  • Proteins: Structure, Function, and Bioinformatics, Vol. 50, Issue 3
  • DOI: 10.1002/prot.10286

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods
journal, May 2011

  • Tamura, K.; Peterson, D.; Peterson, N.
  • Molecular Biology and Evolution, Vol. 28, Issue 10
  • DOI: 10.1093/molbev/msr121

SWISS-MODEL and the Swiss-Pdb Viewer: An environment for comparative protein modeling
journal, January 1997


Biochemical Properties of UspG, a Universal Stress Protein of Escherichia coli
journal, February 2006


CDD: specific functional annotation with the Conserved Domain Database
journal, January 2009

  • Marchler-Bauer, A.; Anderson, J. B.; Chitsaz, F.
  • Nucleic Acids Research, Vol. 37, Issue Database
  • DOI: 10.1093/nar/gkn845

Structure and Function of the Universal Stress Protein TeaD and Its Role in Regulating the Ectoine Transporter TeaABC of Halomonas elongata DSM 2581 T
journal, March 2010

  • Schweikhard, Eva S.; Kuhlmann, Sonja I.; Kunte, Hans-Jörg
  • Biochemistry, Vol. 49, Issue 10
  • DOI: 10.1021/bi9017522

Crystal contacts as nature's docking solutions
journal, January 2010

  • Krissinel, Evgeny
  • Journal of Computational Chemistry, Vol. 31, Issue 1
  • DOI: 10.1002/jcc.21303

The COG database: an updated version includes eukaryotes
journal, January 2003

  • Tatusov, Roman L.; Fedorova, Natalie D.; Jackson, John D.
  • BMC Bioinformatics, Vol. 4, Article No. 41
  • DOI: 10.1186/1471-2105-4-41

Automated structure solution, density modification and model building
journal, October 2002

  • Terwilliger, Thomas C.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 58, Issue 11
  • DOI: 10.1107/S0907444902016438

Individual Mycobacterium tuberculosis universal stress protein homologues are dispensable in vitro
journal, July 2010


meta-PPISP: a meta web server for protein-protein interaction site prediction
journal, September 2007


Differential Roles of the Universal Stress Proteins of Escherichia coli in Oxidative Stress Resistance, Adhesion, and Motility
journal, September 2005


Structure of the Universal Stress Protein of Haemophilus influenzae
journal, December 2001


Automated MAD and MIR structure solution
journal, April 1999

  • Terwilliger, Thomas C.; Berendzen, Joel
  • Acta Crystallographica Section D Biological Crystallography, Vol. 55, Issue 4
  • DOI: 10.1107/S0907444999000839

Heterodimer Formation within Universal Stress Protein Classes Revealed By an In Silico and Experimental Approach
journal, July 2008

  • Nachin, Laurence; Brive, Lars; Persson, Karin-Cecilia
  • Journal of Molecular Biology, Vol. 380, Issue 2
  • DOI: 10.1016/j.jmb.2008.04.074

The bacterial universal stress protein: function and regulation
journal, April 2003