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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 R work of 23.0% and an R free 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:

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