Crystal structure of the cysteine desulfurase DndA from Streptomyces lividans which is involved in DNA phosphorothioation.

PloS One
Fukun ChenGeng Wu

Abstract

DNA phosphorothioation is widespread among prokaryotes, and might function to restrict gene transfer among different kinds of bacteria. There has been little investigation into the structural mechanism of the DNA phosphorothioation process. DndA is a cysteine desulfurase which is involved in the first step of DNA phosphorothioation. In this study, we determined the crystal structure of Streptomyces lividans DndA in complex with its covalently bound cofactor PLP, to a resolution of 2.4 Å. Our structure reveals the molecular mechanism that DndA employs to recognize its cofactor PLP, and suggests the potential binding site for the substrate L-cysteine on DndA. In contrast to previously determined structures of cysteine desulfurases, the catalytic cysteine of DndA was found to reside on a β strand. This catalytic cysteine is very far away from the presumable location of the substrate, suggesting that a conformational change of DndA is required during the catalysis process to bring the catalytic cysteine close to the substrate cysteine. Moreover, our in vitro enzymatic assay results suggested that this conformational change is unlikely to be a simple result of random thermal motion, since moving the catalytic cysteine two residues f...Continue Reading

References

Apr 1, 1993·Proceedings of the National Academy of Sciences of the United States of America·L ZhengD R Dean
Oct 17, 2002·Applied Microbiology and Biotechnology·H Mihara, N Esaki
Jul 16, 2003·Journal of Molecular Biology·Jill R Cupp-VickeryLarry E Vickery
Sep 1, 1994·Acta Crystallographica. Section D, Biological Crystallography·UNKNOWN Collaborative Computational Project, Number 4
Dec 2, 2004·Acta Crystallographica. Section D, Biological Crystallography·Paul Emsley, Kevin Cowtan
Aug 17, 2005·Molecular Microbiology·Xiufen ZhouZixin Deng
Mar 21, 2006·Nature Chemical Biology·Eugene G Mueller
Feb 3, 2011·Proceedings of the National Academy of Sciences of the United States of America·Lianrong WangPeter C Dedon
Nov 22, 2011·Acta Crystallographica. Section F, Structural Biology and Crystallization Communications·Fukun ChenGeng Wu

❮ Previous
Next ❯

Citations

Mar 9, 2013·Nucleic Acids Research·Kira S MakarovaEugene V Koonin
Apr 13, 2019·Nature Communications·Lei XiongShi Chen
Jun 29, 2017·Annual Review of Microbiology·Eugene V KooninYuri I Wolf
Oct 6, 2018·FEMS Microbiology Reviews·Lianrong WangShi Chen

❮ Previous
Next ❯

Methods Mentioned

BETA
PCR
gel filtration

Software Mentioned

PROCHECK
MOSFLM
PHASER
CCP4
PyMOL
REFMAC

Related Concepts

Related Feeds

Biosynthetic Transformations

Biosyntheic transformtions are multi-step, enzyme-catalyzed processes where substrates are converted into more complex products in living organisms. Simple compounds are modified, converted into other compounds, or joined together to form macromolecules. Discover the latest research on biosynthetic transformations here.