Structural dynamics of a methionine γ-lyase for calicheamicin biosynthesis: Rotation of the conserved tyrosine stacking with pyridoxal phosphate
Abstract
CalE6 from Micromonospora echinospora is a (pyridoxal 50 phosphate) PLP-dependent methionine γ-lyase involved in the biosynthesis of calicheamicins. Here, we report the crystal structure of a CalE6 2-(N-morpholino)ethanesulfonic acid complex showing ligand-induced rotation of Tyr100, which stacks with PLP, resembling the corresponding tyrosine rotation of true catalytic intermediates of CalE6 homologs. Elastic network modeling and crystallographic ensemble refinement reveal mobility of the N-terminal loop, which involves both tetrameric assembly and PLP binding. Modeling and comparative structural analysis of PLP-dependent enzymes involved in Cys/Met metabolism shine light on the functional implications of the intrinsic dynamic properties of CalE6 in catalysis and holoenzyme maturation.
- Authors:
-
- Rice Univ., Houston, TX (United States). Biosciences at Rice
- Argonne National Lab. (ANL), Argonne, IL (United States). Biosciences Division and Midwest Center for Structural Genomics
- Rice Univ., Houston, TX (United States). Biosciences at Rice; Jaypee Univ. of Information Technology, Waknaghat (India). Dept. of Biotechnology and Bioinformatics
- Univ. of Wisconsin, Madison, WI (United States). Dept. of Biochemistry
- Univ. of Kentucky, Lexington, KY (United States). Dept. of Pharmaceutical Sciences and College of Pharmacy
- Univ. of Kentucky, Lexington, KY (United States). Dept. of Pharmaceutical Sciences and College of Pharmacy; Univ. of Oklahoma, Norman, OK (United States). Dept. of Chemistry and Biochemistry
- Publication Date:
- Research Org.:
- Argonne National Laboratory (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER); National Institutes of Health (NIH); National Center for Advancing Translational Sciences (NCATS)
- OSTI Identifier:
- 1439871
- Grant/Contract Number:
- AC02-06CH11357; CA84374; U01GM098248; GM094585; UL1TR000117
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Structural Dynamics
- Additional Journal Information:
- Journal Volume: 3; Journal Issue: 3; Journal ID: ISSN 2329-7778
- Publisher:
- American Crystallographic Association/AIP
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; Enzymes; Conformational dynamics; Crystal structure; Normal modes; Elasticity; Catalysis; Data analysis; Acids; Computer modeling
Citation Formats
Cao, Hongnan, Tan, Kemin, Wang, Fengbin, Bigelow, Lance, Yennamalli, Ragothaman M., Jedrzejczak, Robert, Babnigg, Gyorgy, Bingman, Craig A., Joachimiak, Andrzej, Kharel, Madan K., Singh, Shanteri, Thorson, Jon S., and Phillips, George N. Structural dynamics of a methionine γ-lyase for calicheamicin biosynthesis: Rotation of the conserved tyrosine stacking with pyridoxal phosphate. United States: N. p., 2016.
Web. doi:10.1063/1.4948539.
Cao, Hongnan, Tan, Kemin, Wang, Fengbin, Bigelow, Lance, Yennamalli, Ragothaman M., Jedrzejczak, Robert, Babnigg, Gyorgy, Bingman, Craig A., Joachimiak, Andrzej, Kharel, Madan K., Singh, Shanteri, Thorson, Jon S., & Phillips, George N. Structural dynamics of a methionine γ-lyase for calicheamicin biosynthesis: Rotation of the conserved tyrosine stacking with pyridoxal phosphate. United States. https://doi.org/10.1063/1.4948539
Cao, Hongnan, Tan, Kemin, Wang, Fengbin, Bigelow, Lance, Yennamalli, Ragothaman M., Jedrzejczak, Robert, Babnigg, Gyorgy, Bingman, Craig A., Joachimiak, Andrzej, Kharel, Madan K., Singh, Shanteri, Thorson, Jon S., and Phillips, George N. Fri .
"Structural dynamics of a methionine γ-lyase for calicheamicin biosynthesis: Rotation of the conserved tyrosine stacking with pyridoxal phosphate". United States. https://doi.org/10.1063/1.4948539. https://www.osti.gov/servlets/purl/1439871.
@article{osti_1439871,
title = {Structural dynamics of a methionine γ-lyase for calicheamicin biosynthesis: Rotation of the conserved tyrosine stacking with pyridoxal phosphate},
author = {Cao, Hongnan and Tan, Kemin and Wang, Fengbin and Bigelow, Lance and Yennamalli, Ragothaman M. and Jedrzejczak, Robert and Babnigg, Gyorgy and Bingman, Craig A. and Joachimiak, Andrzej and Kharel, Madan K. and Singh, Shanteri and Thorson, Jon S. and Phillips, George N.},
abstractNote = {CalE6 from Micromonospora echinospora is a (pyridoxal 50 phosphate) PLP-dependent methionine γ-lyase involved in the biosynthesis of calicheamicins. Here, we report the crystal structure of a CalE6 2-(N-morpholino)ethanesulfonic acid complex showing ligand-induced rotation of Tyr100, which stacks with PLP, resembling the corresponding tyrosine rotation of true catalytic intermediates of CalE6 homologs. Elastic network modeling and crystallographic ensemble refinement reveal mobility of the N-terminal loop, which involves both tetrameric assembly and PLP binding. Modeling and comparative structural analysis of PLP-dependent enzymes involved in Cys/Met metabolism shine light on the functional implications of the intrinsic dynamic properties of CalE6 in catalysis and holoenzyme maturation.},
doi = {10.1063/1.4948539},
journal = {Structural Dynamics},
number = 3,
volume = 3,
place = {United States},
year = {Fri Apr 29 00:00:00 EDT 2016},
month = {Fri Apr 29 00:00:00 EDT 2016}
}
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