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Title: 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.

Authors:
ORCiD logo [1];  [1];  [1]; ORCiD logo [1]; ORCiD logo [1]; ORCiD logo [1]
  1. Brookhaven National Lab. (BNL), Upton, NY (United States)
Publication Date:
Research Org.:
Brookhaven National Lab. (BNL), Upton, NY (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
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. doi: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. doi: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 = {2019},
month = {8}
}

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Works referenced in this record:

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
  • DOI: 10.1016/j.bbagen.2006.03.027

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
  • DOI: 10.1107/S174430910604200X

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
  • DOI: 10.1107/S1744309106039583

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
  • DOI: 10.1107/S0907444910007493

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
  • DOI: 10.1074/jbc.RA118.001996

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
  • DOI: 10.1107/S0021889801017824

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
  • DOI: 10.1107/S1600576716014965

Two enzymes bound to one transfer RNA assume alternative conformations for consecutive reactions
journal, September 2010


XDS
journal, January 2010

  • Kabsch, Wolfgang
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2
  • DOI: 10.1107/S0907444909047337

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
  • DOI: 10.1107/S0907444909047374

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
  • DOI: 10.1110/ps.9.1.37

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
  • DOI: 10.1006/jmbi.1998.1924

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

Atomic structure of the cubic core of the pyruvate dehydrogenase multienzyme complex
journal, March 1992


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

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

AMoRe : an automated package for molecular replacement
journal, March 1994

  • Navaza, J.
  • Acta Crystallographica Section A Foundations of Crystallography, Vol. 50, Issue 2
  • DOI: 10.1107/S0108767393007597

Arabidopsis amidase 1, a member of the amidase signature family: Molecular dissection of AMI1 activity
journal, June 2007


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
  • DOI: 10.1002/pro.2861

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
  • DOI: 10.1107/S2059798318005752

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
  • DOI: 10.1073/pnas.1423314112

Molecular replacement with MOLREP
journal, December 2009

  • Vagin, Alexei; Teplyakov, Alexei
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 1
  • DOI: 10.1107/S0907444909042589

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
  • DOI: 10.1107/S1744309108028248

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

Automated data collection for macromolecular crystallography
journal, September 2011