Structure of the dihydrolipoamide succinyltransferase catalytic domain from Escherichia coli in a novel crystal form: a tale of a common protein crystallization contaminant
Abstract
The crystallization of amidase, the ultimate enzyme in the Trp-dependent auxin-biosynthesis pathway, from Arabidopsis thaliana was attempted using protein samples with at least 95% purity. Cube-shaped crystals that were assumed to be amidase crystals that belonged to space groupI4 (unit-cell parameters a = b = 128.6, c= 249.7 Å) were obtained and diffracted to 3.0 Å resolution. Molecular replacement using structures from the PDB containing the amidase signature fold as search models was unsuccessful in yielding a convincing solution. Using theSequence-Independent Molecular replacement Based on Available Databases(SIMBAD) program, it was discovered that the structure corresponded to dihydrolipoamide succinyltransferase from Escherichia coli(PDB entry 1c4t), which is considered to be a common crystallization contaminant protein. The structure was refined to an Rwork of 23.0% and an Rfree of 27.2% at 3.0 Å resolution. The structure was compared with others of the same protein deposited in the PDB. This is the first report of the structure of dihydrolipoamide succinyltransferase isolated without an expression tag and in this novel crystal form.
- Publication Date:
- Research Org.:
- Brookhaven National Lab. (BNL), Upton, NY (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1561244
- Report Number(s):
- BNL-212052-2019-JAAM
Journal ID: ISSN 2053-230X; ACSFEN
- Grant/Contract Number:
- SC0012704
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Acta Crystallographica. Section F, Structural Biology Communications
- Additional Journal Information:
- Journal Volume: 75; Journal Issue: 9; Journal ID: ISSN 2053-230X
- Publisher:
- International Union of Crystallography
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; Dihydrolipoamide Succinyltransferase; Auxin; Amidase; Contaminant crystallization; Protein Crystallography; Molecular Replacement
Citation Formats
Andi, Babak, Soares, Alexei S., Shi, Wuxian, Fuchs, Martin R., McSweeney, Sean, and Liu, Qun. Structure of the dihydrolipoamide succinyltransferase catalytic domain from Escherichia coli in a novel crystal form: a tale of a common protein crystallization contaminant. United States: N. p., 2019.
Web. doi:10.1107/S2053230X19011488.
Andi, Babak, Soares, Alexei S., Shi, Wuxian, Fuchs, Martin R., McSweeney, Sean, & Liu, Qun. Structure of the dihydrolipoamide succinyltransferase catalytic domain from Escherichia coli in a novel crystal form: a tale of a common protein crystallization contaminant. United States. https://doi.org/10.1107/S2053230X19011488
Andi, Babak, Soares, Alexei S., Shi, Wuxian, Fuchs, Martin R., McSweeney, Sean, and Liu, Qun. Thu .
"Structure of the dihydrolipoamide succinyltransferase catalytic domain from Escherichia coli in a novel crystal form: a tale of a common protein crystallization contaminant". United States. https://doi.org/10.1107/S2053230X19011488. https://www.osti.gov/servlets/purl/1561244.
@article{osti_1561244,
title = {Structure of the dihydrolipoamide succinyltransferase catalytic domain from Escherichia coli in a novel crystal form: a tale of a common protein crystallization contaminant},
author = {Andi, Babak and Soares, Alexei S. and Shi, Wuxian and Fuchs, Martin R. and McSweeney, Sean and Liu, Qun},
abstractNote = {The crystallization of amidase, the ultimate enzyme in the Trp-dependent auxin-biosynthesis pathway, from Arabidopsis thaliana was attempted using protein samples with at least 95% purity. Cube-shaped crystals that were assumed to be amidase crystals that belonged to space groupI4 (unit-cell parameters a = b = 128.6, c= 249.7 Å) were obtained and diffracted to 3.0 Å resolution. Molecular replacement using structures from the PDB containing the amidase signature fold as search models was unsuccessful in yielding a convincing solution. Using theSequence-Independent Molecular replacement Based on Available Databases(SIMBAD) program, it was discovered that the structure corresponded to dihydrolipoamide succinyltransferase from Escherichia coli(PDB entry 1c4t), which is considered to be a common crystallization contaminant protein. The structure was refined to an Rwork of 23.0% and an Rfree of 27.2% at 3.0 Å resolution. The structure was compared with others of the same protein deposited in the PDB. This is the first report of the structure of dihydrolipoamide succinyltransferase isolated without an expression tag and in this novel crystal form.},
doi = {10.1107/S2053230X19011488},
journal = {Acta Crystallographica. Section F, Structural Biology Communications},
number = 9,
volume = 75,
place = {United States},
year = {Thu Aug 29 00:00:00 EDT 2019},
month = {Thu Aug 29 00:00:00 EDT 2019}
}
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Works referenced in this record:
Three-dimensional Structure of the Lipoyl Domain from the Dihydrolipoyl Succinyltransferase Component of the 2-Oxoglutarate Dehydrogenase Multienzyme Complex ofEscherichia coli
journal, November 1996
- Ricaud, Paul M.; Howard, Mark J.; Roberts, Emma L.
- Journal of Molecular Biology, Vol. 264, Issue 1
Three-dimensional solution structure of the E3-binding domain of the dihydrolipoamide succinyltransferase core from the 2-oxoglutarate dehydrogenase multienzyme complex of Escherichia coli
journal, April 1992
- Robien, Mark A.; Clore, G. Marius; Omichinski, James G.
- Biochemistry, Vol. 31, Issue 13
An unexpected vestigial protein complex reveals the evolutionary origins of an s -triazine catabolic enzyme
journal, March 2018
- Esquirol, Lygie; Peat, Thomas S.; Wilding, Matthew
- Journal of Biological Chemistry, Vol. 293, Issue 20
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
ContaMiner and ContaBase: a webserver and database for early identification of unwantedly crystallized protein contaminants
journal, November 2016
- Hungler, Arnaud; Momin, Afaque; Diederichs, Kay
- Journal of Applied Crystallography, Vol. 49, Issue 6
Domains, motifs, and linkers in 2-oxo acid dehydrogenase multienzyme complexes: a paradigm in the design of a multifunctional protein
journal, September 1991
- Perham, Richard N.
- Biochemistry, Vol. 30, Issue 35
SIMBAD : a sequence-independent molecular-replacement pipeline
journal, June 2018
- Simpkin, Adam J.; Simkovic, Felix; Thomas, Jens M. H.
- Acta Crystallographica Section D Structural Biology, Vol. 74, Issue 7
Structure of the Pseudomonas aeruginosa transamidosome reveals unique aspects of bacterial tRNA-dependent asparagine biosynthesis
journal, December 2014
- Suzuki, Tateki; Nakamura, Akiyoshi; Kato, Koji
- Proceedings of the National Academy of Sciences, Vol. 112, Issue 2
Automated data collection for macromolecular crystallography
journal, September 2011
- Winter, Graeme; McAuley, Katherine E.
- Methods, Vol. 55, Issue 1
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
Atomic structure of the cubic core of the pyruvate dehydrogenase multienzyme complex
journal, March 1992
- Mattevi, A.; Obmolova, G.; Schulze, E.
- Science, Vol. 255, Issue 5051
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
AMoRe : an automated package for molecular replacement
journal, March 1994
- Navaza, J.
- Acta Crystallographica Section A Foundations of Crystallography, Vol. 50, Issue 2
Two enzymes bound to one transfer RNA assume alternative conformations for consecutive reactions
journal, September 2010
- Ito, Takuhiro; Yokoyama, Shigeyuki
- Nature, Vol. 467, Issue 7315
There is a baby in the bath water: AcrB contamination is a major problem in membrane-protein crystallization
journal, September 2008
- Veesler, David; Blangy, Stéphanie; Cambillau, Christian
- Acta Crystallographica Section F Structural Biology and Crystallization Communications, Vol. 64, Issue 10
Protein purification and crystallization artifacts: The tale usually not told: Protein Purification and Crystallization Artifacts
journal, January 2016
- Niedzialkowska, Ewa; Gasiorowska, Olga; Handing, Katarzyna B.
- Protein Science, Vol. 25, Issue 3
Crystal structure of the truncated cubic core component of the Escherichia coli 2-oxoglutarate dehydrogenase multienzyme complex
journal, July 1998
- Knapp, James E.; Mitchell, David T.; Yazdi, Mohammad A.
- Journal of Molecular Biology, Vol. 280, Issue 4
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
Structural analysis and classification of native proteins from E. coli commonly co-purified by immobilised metal affinity chromatography
journal, September 2006
- Bolanos-Garcia, Victor Martin; Davies, Owen Richard
- Biochimica et Biophysica Acta (BBA) - General Subjects, Vol. 1760, Issue 9
Fortuitous structure determination of `as-isolated' Escherichia coli bacterioferritin in a novel crystal form
journal, October 2006
- van Eerde, André; Wolterink-van Loo, Suzanne; van der Oost, John
- Acta Crystallographica Section F Structural Biology and Crystallization Communications, Vol. 62, Issue 11
Arabidopsis amidase 1, a member of the amidase signature family: Molecular dissection of AMI1 activity
journal, June 2007
- Neu, Daniel; Lehmann, Thomas; Elleuche, Skander
- FEBS Journal, Vol. 274, Issue 13
Molecular cloning and characterization of an amidase from Arabidopsis thaliana capable of converting indole-3-acetamide into the plant growth hormone, indole-3-acetic acid
journal, February 2003
- Pollmann, Stephan; Neu, Daniel; Weiler, Elmar W.
- Phytochemistry, Vol. 62, Issue 3
The Computational Crystallography Toolbox : crystallographic algorithms in a reusable software framework
journal, January 2002
- Grosse-Kunstleve, Ralf W.; Sauter, Nicholas K.; Moriarty, Nigel W.
- Journal of Applied Crystallography, Vol. 35, Issue 1
The 1.1 Å resolution structure of a periplasmic phosphate-binding protein from Stenotrophomonas maltophilia : a crystallization contaminant identified by molecular replacement using the entire Protein Data Bank
journal, July 2016
- Keegan, Ronan; Waterman, David G.; Hopper, David J.
- Acta Crystallographica Section D Structural Biology, Vol. 72, Issue 8
Molecular replacement with MOLREP
journal, December 2009
- Vagin, Alexei; Teplyakov, Alexei
- Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 1
Crystallization and structural analysis of GADPH from Spinacia oleracea in a new form
journal, October 2006
- Cámara-Artigas, Ana; Hirasawa, Masakazu; Knaff, David B.
- Acta Crystallographica Section F Structural Biology and Crystallization Communications, Vol. 62, Issue 11
Integration, scaling, space-group assignment and post-refinement
journal, January 2010
- Kabsch, Wolfgang
- Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 133-144
XDS
journal, January 2010
- Kabsch, Wolfgang
- Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2
Expression, purification, and structural analysis of the trimeric form of the catalytic domain of the Escherichia coli dihydrolipoamide succinyltransferase
journal, January 2000
- Knapp, James E.; Carroll, Donald; Lawson, Janet E.
- Protein Science, Vol. 9, Issue 1
Phaser crystallographic software
journal, July 2007
- McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D.
- Journal of Applied Crystallography, Vol. 40, Issue 4
Structure-function relationships in dihydrolipoamide acyltransferases.
journal, June 1990
- Reed, L. J.; Hackert, M. L.
- Journal of Biological Chemistry, Vol. 265, Issue 16
PARP1 exhibits enhanced association and catalytic efficiency with γH2A.X-nucleosome
journal, December 2019
- Sharma, Deepti; De Falco, Louis; Padavattan, Sivaraman
- Nature Communications, Vol. 10, Issue 1
Overview of the CCP4 suite and current developments.
text, January 2011
- Winn, Martyn D.; Ballard, Charles C.; Cowtan, Kevin D.
- Apollo - University of Cambridge Repository