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:
-
- 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)
- 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}
}
Web of Science
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