Structural Analysis of Binding Determinants of Salmonella typhimurium Trehalose-6-phosphate Phosphatase Using Ground-State Complexes

Harvey, C; O’Toole, K.; Liu, C.; Mariano, P.; Dunaway-Mariano, D.; Allen, K.

doi:10.1021/acs.biochem.0c00317

Structural Analysis of Binding Determinants of Salmonella typhimurium Trehalose-6-phosphate Phosphatase Using Ground-State Complexes

Journal Article · 01 January 2022 · Biochemistry

DOI:https://doi.org/10.1021/acs.biochem.0c00317· OSTI ID:1690200

Harvey, C; O’Toole, K.; Liu, C.; Mariano, P.; Dunaway-Mariano, D.; Allen, K.

Research Organization:: Brookhaven National Laboratory (BNL), Upton, NY (United States)

Sponsoring Organization:: ~OTHER

DOE Contract Number:: SC0012704

OSTI ID:: 1690200

Report Number(s):: BNL-220521-2020-JACI

Journal Information:: Biochemistry, Vol. 59, Issue 35

Country of Publication:: United States

Language:: English

References (44)

Multiple Effects of Trehalose on Protein Folding In Vitro and In Vivo Singer, Mike A.; Lindquist, Susan Molecular Cell, Vol. 1, Issue 5 https://doi.org/10.1016/S1097-2765(00)80064-7	journal	April 1998
Trehalose Is a Key Determinant of the Quiescent Metabolic State That Fuels Cell Cycle Progression upon Return to Growth Shi, Lei; Sutter, Benjamin M.; Ye, Xinyue Molecular Biology of the Cell, Vol. 21, Issue 12 https://doi.org/10.1091/mbc.e10-01-0056	journal	June 2010
The OtsAB Pathway Is Essential for Trehalose Biosynthesis in Mycobacterium tuberculosis Murphy, Helen N.; Stewart, Graham R.; Mischenko, Vladimir V. Journal of Biological Chemistry, Vol. 280, Issue 15 https://doi.org/10.1074/jbc.M414232200	journal	April 2005
Trehalose-6-Phosphate-Mediated Toxicity Determines Essentiality of OtsB2 in Mycobacterium tuberculosis In Vitro and in Mice Korte, Jan; Alber, Marina; Trujillo, Carolina M. PLOS Pathogens, Vol. 12, Issue 12 https://doi.org/10.1371/journal.ppat.1006043	journal	December 2016
The C. elegans lethal gut-obstructed gob-1 gene is trehalose-6-phosphate phosphatase Kormish, Jay D.; McGhee, James D. Developmental Biology, Vol. 287, Issue 1 https://doi.org/10.1016/j.ydbio.2005.08.027	journal	November 2005
Structure of the Trehalose-6-phosphate Phosphatase from Brugia malayi Reveals Key Design Principles for Anthelmintic Drugs Farelli, Jeremiah D.; Galvin, Brendan D.; Li, Zhiru PLoS Pathogens, Vol. 10, Issue 7 https://doi.org/10.1371/journal.ppat.1004245	journal	July 2014
Trehalose-6-phosphate, a new regulator of yeast glycolysis that inhibits hexokinases Blázquez, Miguel A.; Lagunas, Rosario; Gancedo, Carlos FEBS Letters, Vol. 329, Issue 1-2 https://doi.org/10.1016/0014-5793(93)80191-V	journal	August 1993
Salmonella Nomenclature Brenner, F. W.; Villar, R. G.; Angulo, F. J. Journal of Clinical Microbiology, Vol. 38, Issue 7 https://doi.org/10.1128/JCM.38.7.2465-2467.2000	journal	January 2000
Embracing Diversity: Differences in Virulence Mechanisms, Disease Severity, and Host Adaptations Contribute to the Success of Nontyphoidal Salmonella as a Foodborne Pathogen Cheng, Rachel A.; Eade, Colleen R.; Wiedmann, Martin Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.01368	journal	June 2019
World Health Organization Global Estimates and Regional Comparisons of the Burden of Foodborne Disease in 2010 Havelaar, Arie H.; Kirk, Martyn D.; Torgerson, Paul R. PLOS Medicine, Vol. 12, Issue 12 https://doi.org/10.1371/journal.pmed.1001923	journal	December 2015
Genome Variation and Molecular Epidemiology of Salmonella enterica Serovar Typhimurium Pathovariants Branchu, Priscilla; Bawn, Matt; Kingsley, Robert A. Infection and Immunity, Vol. 86, Issue 8 https://doi.org/10.1128/IAI.00079-18	journal	August 2018
Rational design of first generation inhibitors for trehalose 6-phosphate phosphatases Liu, Chunliang; Dunaway-Mariano, Debra; Mariano, Patrick S. Tetrahedron, Vol. 73, Issue 10 https://doi.org/10.1016/j.tet.2017.01.041	journal	March 2017
Rational design of reversible inhibitors for trehalose 6-phosphate phosphatases Liu, Chunliang; Dunaway-Mariano, Debra; Mariano, Patrick S. European Journal of Medicinal Chemistry, Vol. 128 https://doi.org/10.1016/j.ejmech.2017.02.001	journal	March 2017
An improved method for the large scale preparation of α,α′-trehalose-6-phosphate Liu, Chunliang; Mariano, Patrick S. Tetrahedron Letters, Vol. 56, Issue 23 https://doi.org/10.1016/j.tetlet.2014.10.003	journal	June 2015
Preparation of selenomethionyl proteins for phase determination Doublié, Sylvie Methods in Enzymology https://doi.org/10.1016/S0076-6879(97)76075-0 p. 523-530	book	January 1997
A combined approach to improving large-scale production of tobacco etch virus protease Blommel, Paul G.; Fox, Brian G. Protein Expression and Purification, Vol. 55, Issue 1, p. 53-68 https://doi.org/10.1016/j.pep.2007.04.013	journal	September 2007
XDS Kabsch, Wolfgang Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2 https://doi.org/10.1107/S0907444909047337	journal	January 2010
[20] Processing of X-ray diffraction data collected in oscillation mode Otwinowski, Zbyszek; Minor, Wladek Macromolecular Crystallography Part A, 307-326 https://doi.org/10.1016/S0076-6879(97)76066-X	book	January 1997
PHENIX: a comprehensive Python-based system for macromolecular structure solution Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221 https://doi.org/10.1107/S0907444909052925	journal	January 2010
Coot model-building tools for molecular graphics Emsley, Paul; Cowtan, Kevin Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 12, p. 2126-2132 https://doi.org/10.1107/S0907444904019158	journal	November 2004
Protein structure alignment by incremental combinatorial extension (CE) of the optimal path Shindyalov, I. N.; Bourne, P. E. Protein Engineering Design and Selection, Vol. 11, Issue 9 https://doi.org/10.1093/protein/11.9.739	journal	September 1998
CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures Chovancova, Eva; Pavelka, Antonin; Benes, Petr PLoS Computational Biology, Vol. 8, Issue 10 https://doi.org/10.1371/journal.pcbi.1002708	journal	October 2012
UCSF Chimera?A visualization system for exploratory research and analysis Pettersen, Eric F.; Goddard, Thomas D.; Huang, Conrad C. Journal of Computational Chemistry, Vol. 25, Issue 13 https://doi.org/10.1002/jcc.20084	journal	January 2004
Three-dimensional hydrogen-bond geometry and probability information from a crystal survey Mills, J. E. J.; Dean, P. M. Journal of Computer-Aided Molecular Design, Vol. 10, Issue 6 https://doi.org/10.1007/BF00134183	journal	December 1996
Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega Sievers, Fabian; Wilm, Andreas; Dineen, David Molecular Systems Biology, Vol. 7, Issue 1 https://doi.org/10.1038/msb.2011.75	journal	January 2011
Deciphering key features in protein structures with the new ENDscript server Robert, Xavier; Gouet, Patrice Nucleic Acids Research, Vol. 42, Issue W1 https://doi.org/10.1093/nar/gku316	journal	April 2014
Genetic Variations and Diseases in UniProtKB/Swiss-Prot: The Ins and Outs of Expert Manual Curation Famiglietti, Maria Livia; Estreicher, Anne; Gos, Arnaud Human Mutation, Vol. 35, Issue 8 https://doi.org/10.1002/humu.22594	journal	June 2014
Markers of fitness in a successful enzyme superfamily Allen, Karen N.; Dunaway-Mariano, Debra Current Opinion in Structural Biology, Vol. 19, Issue 6 https://doi.org/10.1016/j.sbi.2009.09.008	journal	December 2009
Analysis of the Structural Determinants Underlying Discrimination between Substrate and Solvent in β-Phosphoglucomutase Catalysis Dai, Jianying; Finci, Lorenzo; Zhang, Chunchun Biochemistry, Vol. 48, Issue 9 https://doi.org/10.1021/bi801653r	journal	January 2009
Conformational Cycling in β-Phosphoglucomutase Catalysis: Reorientation of the β- d -Glucose 1,6-(Bis)phosphate Intermediate Dai, Jianying; Wang, Liangbing; Allen, Karen N. Biochemistry, Vol. 45, Issue 25 https://doi.org/10.1021/bi060136v	journal	June 2006
Catalytic Cycling in β-Phosphoglucomutase: A Kinetic and Structural Analysis ^, Zhang, Guofeng; Dai, Jianying; Wang, Liangbing Biochemistry, Vol. 44, Issue 27 https://doi.org/10.1021/bi050558p	journal	June 2005
Evolutionary Genomics of the HAD Superfamily: Understanding the Structural Adaptations and Catalytic Diversity in a Superfamily of Phosphoesterases and Allied Enzymes Burroughs, A. Maxwell; Allen, Karen N.; Dunaway-Mariano, Debra Journal of Molecular Biology, Vol. 361, Issue 5 https://doi.org/10.1016/j.jmb.2006.06.049	journal	September 2006
Phosphoryl group transfer: evolution of a catalytic scaffold Allen, Karen N.; Dunaway-Mariano, Debra Trends in Biochemical Sciences, Vol. 29, Issue 9 https://doi.org/10.1016/j.tibs.2004.07.008	journal	September 2004
The catalytic scaffold of the haloalkanoic acid dehalogenase enzyme superfamily acts as a mold for the trigonal bipyramidal transition state Lu, Z.; Dunaway-Mariano, D.; Allen, K. N. Proceedings of the National Academy of Sciences, Vol. 105, Issue 15 https://doi.org/10.1073/pnas.0710800105	journal	April 2008
Analysis of the Substrate Specificity Loop of the HAD Superfamily Cap Domain ^, Lahiri, Sushmita D.; Zhang, Guofeng; Dai, Jianying Biochemistry, Vol. 43, Issue 10 https://doi.org/10.1021/bi0356810	journal	February 2004
Structures of trehalose-6-phosphate phosphatase from pathogenic fungi reveal the mechanisms of substrate recognition and catalysis Miao, Yi; Tenor, Jennifer L.; Toffaletti, Dena L. Proceedings of the National Academy of Sciences, Vol. 113, Issue 26 https://doi.org/10.1073/pnas.1601774113	journal	June 2016
Functional and structural analysis of trehalose-6-phosphate phosphatase from Burkholderia pseudomallei: Insights into the catalytic mechanism Suthisawat, Sarocha; Gourlay, Louise Jane; Bolognesi, Martino Biochemical and Biophysical Research Communications, Vol. 523, Issue 4 https://doi.org/10.1016/j.bbrc.2019.12.088	journal	March 2020
Crystal structure of trehalose-6-phosphate phosphatase-related protein: Biochemical and biological implications Rao, Krishnamurthy N.; Kumaran, Desigan; Seetharaman, Jayaraman Protein Science, Vol. 15, Issue 7 https://doi.org/10.1110/ps.062096606	journal	July 2006
Structural insight into dephosphorylation by trehalose 6‐phosphate phosphatase (OtsB2) from Mycobacterium tuberculosis Shan, Shan; Min, Haowei; Liu, Ting The FASEB Journal, Vol. 30, Issue 12 https://doi.org/10.1096/fj.201600463R	journal	August 2016
Trehalose 6‐phosphate phosphatases of Pseudomonas aeruginosa Cross, Megan; Biberacher, Sonja; Park, Suk‐Youl The FASEB Journal, Vol. 32, Issue 10 https://doi.org/10.1096/fj.201800500R	journal	April 2018
Architecture of the sugar binding sites in carbohydrate binding proteins—a computer modeling study Rao, V. S. R.; Lam, King; Qasba, P. K. International Journal of Biological Macromolecules, Vol. 23, Issue 4 https://doi.org/10.1016/S0141-8130(98)00056-7	journal	November 1998
Analysis and prediction of carbohydrate binding sites Taroni, Chiara; Jones, Susan; Thornton, Janet M. Protein Engineering, Design and Selection, Vol. 13, Issue 2 https://doi.org/10.1093/protein/13.2.89	journal	February 2000
Prediction of protein-glucose binding sites using support vector machines Nassif, Houssam; Al-Ali, Hassan; Khuri, Sawsan Proteins: Structure, Function, and Bioinformatics, Vol. 77, Issue 1 https://doi.org/10.1002/prot.22424	journal	October 2009
Identification of common structural features of binding sites in galactose-specific proteins Sujatha, M. S.; Balaji, Petety V. Proteins: Structure, Function, and Bioinformatics, Vol. 55, Issue 1 https://doi.org/10.1002/prot.10612	journal	February 2004

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