Structural and biochemical studies of an iterative ribosomal peptide macrocyclase

Li, Gengnan; Patel, Krishna; Zhang, Yi; Pugmire, Jackson K.; Ding, Yousong; Bruner, Steven D.

doi:10.1002/prot.26264

Title: Structural and biochemical studies of an iterative ribosomal peptide macrocyclase

Journal Article · 01 March 2022 · Proteins

DOI:https://doi.org/10.1002/prot.26264· OSTI ID:1855496

Li, Gengnan; Patel, Krishna; Zhang, Yi; Pugmire, Jackson K.; Ding, Yousong; Bruner, Steven D.

Cite

Export

Save

Research Organization:: Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)

Sponsoring Organization:: DOE - Office Of Science; National Institutes of Health (NIH); UNIVERSITY

OSTI ID:: 1855496

Journal Information:: Proteins, Vol. 90, Issue (3)

Country of Publication:: United States

Language:: ENGLISH

References (33)

Natural products: A continuing source of novel drug leads Cragg, Gordon M.; Newman, David J. Biochimica et Biophysica Acta (BBA) - General Subjects, Vol. 1830, Issue 6 https://doi.org/10.1016/j.bbagen.2013.02.008	journal	June 2013
The re-emergence of natural products for drug discovery in the genomics era Harvey, Alan L.; Edrada-Ebel, RuAngelie; Quinn, Ronald J. Nature Reviews Drug Discovery, Vol. 14, Issue 2 https://doi.org/10.1038/nrd4510	journal	January 2015
Computational approaches to natural product discovery Medema, Marnix H.; Fischbach, Michael A. Nature Chemical Biology, Vol. 11, Issue 9 https://doi.org/10.1038/nchembio.1884	journal	August 2015
Ribosomally synthesized and post-translationally modified peptide natural products: overview and recommendations for a universal nomenclature Arnison, Paul G.; Bibb, Mervyn J.; Bierbaum, Gabriele Nat. Prod. Rep., Vol. 30, Issue 1 https://doi.org/10.1039/C2NP20085F	journal	January 2013
Cyclisation mechanisms in the biosynthesis of ribosomally synthesised and post-translationally modified peptides Truman, Andrew W. Beilstein Journal of Organic Chemistry, Vol. 12 https://doi.org/10.3762/bjoc.12.120	journal	January 2016
Polycyclic Peptide Therapeutics Baeriswyl, Vanessa; Heinis, Christian ChemMedChem, Vol. 8, Issue 3 https://doi.org/10.1002/cmdc.201200513	journal	January 2013
Ribosomal peptide natural products: bridging the ribosomal and nonribosomal worlds McIntosh, John A.; Donia, Mohamed S.; Schmidt, Eric W. Natural Product Reports, Vol. 26, Issue 4 https://doi.org/10.1039/b714132g	journal	January 2009
Phylogenomic Analysis of the Microviridin Biosynthetic Pathway Coupled with Targeted Chemo-Enzymatic Synthesis Yields Potent Protease Inhibitors Ahmed, Muhammad N.; Reyna-González, Emmanuel; Schmid, Bianca ACS Chemical Biology, Vol. 12, Issue 6 https://doi.org/10.1021/acschembio.7b00124	journal	April 2017
Heterologous expression and characterization of a novel serine protease from Daphnia magna: A possible role in susceptibility to toxic cyanobacteria Lange, Jacqueline; Demir, Fatih; Huesgen, Pitter F. Aquatic Toxicology, Vol. 205 https://doi.org/10.1016/j.aquatox.2018.09.013	journal	December 2018
New developments in RiPP discovery, enzymology and engineering Montalbán-López, Manuel; Scott, Thomas A.; Ramesh, Sangeetha Natural Product Reports, Vol. 38, Issue 1 https://doi.org/10.1039/D0NP00027B	journal	January 2021
Harnessing the Evolvability of Tricyclic Microviridins To Dissect Protease-Inhibitor Interactions Weiz, Annika R.; Ishida, Keishi; Quitterer, Felix Angewandte Chemie International Edition, Vol. 53, Issue 14 https://doi.org/10.1002/anie.201309721	journal	March 2014
Targeting eukaryotic proteases for natural products-based drug development Al-Awadhi, Fatma H.; Luesch, Hendrik Natural Product Reports, Vol. 37, Issue 6 https://doi.org/10.1039/C9NP00060G	journal	January 2020
Current Knowledge on Microviridin from Cyanobacteria do Amaral, Samuel Cavalcante; Monteiro, Patrick Romano; Neto, Joaquim da Silva Pinto Marine Drugs, Vol. 19, Issue 1 https://doi.org/10.3390/md19010017	journal	January 2021
Leader Peptide and a Membrane Protein Scaffold Guide the Biosynthesis of the Tricyclic Peptide Microviridin Weiz, Annika R.; Ishida, Keishi; Makower, Katharina Chemistry & Biology, Vol. 18, Issue 11 https://doi.org/10.1016/j.chembiol.2011.09.011	journal	November 2011
The ATP-grasp enzymes Fawaz, Maria V.; Topper, Melissa E.; Firestine, Steven M. Bioorganic Chemistry, Vol. 39, Issue 5-6 https://doi.org/10.1016/j.bioorg.2011.08.004	journal	December 2011
Ribosomal Synthesis of Tricyclic Depsipeptides in Bloom-Forming Cyanobacteria Ziemert, Nadine; Ishida, Keishi; Liaimer, Anton Angewandte Chemie International Edition, Vol. 47, Issue 40 https://doi.org/10.1002/anie.200802730	journal	September 2008
Structure and function of Escherichia coli RimK, an ATP-grasp fold, l -glutamyl ligase enzyme: Structure of E. coli RimK Zhao, Gengxiang; Jin, Zhongmin; Wang, Yanli Proteins: Structure, Function, and Bioinformatics, Vol. 81, Issue 10 https://doi.org/10.1002/prot.24311	journal	July 2013
X-ray Crystal Structure of Glycinamide Ribonucleotide Synthetase from Escherichia coli ^, Wang, Weiru; Kappock, T. Joseph; Stubbe, JoAnne Biochemistry, Vol. 37, Issue 45 https://doi.org/10.1021/bi981405n	journal	October 1998
Structural Analysis of the Active Site Geometry of N ⁵ -Carboxyaminoimidazole Ribonucleotide Synthetase from Escherichia coli ^† ^, ^‡ Thoden, James B.; Holden, Hazel M.; Firestine, Steven M. Biochemistry, Vol. 47, Issue 50 https://doi.org/10.1021/bi801734z	journal	December 2008
Crystal Structure of a Lysine Biosynthesis Enzyme, LysX, from Thermus thermophilus HB8 Sakai, Hiroaki; Vassylyeva, Marina N.; Matsuura, Takanori Journal of Molecular Biology, Vol. 332, Issue 3 https://doi.org/10.1016/S0022-2836(03)00946-X	journal	September 2003
Structural basis for precursor protein–directed ribosomal peptide macrocyclization Li, Kunhua; Condurso, Heather L.; Li, Gengnan Nature Chemical Biology, Vol. 12, Issue 11 https://doi.org/10.1038/nchembio.2200	journal	September 2016
Structural Basis for a Dual Function ATP Grasp Ligase That Installs Single and Bicyclic ω-Ester Macrocycles in a New Multicore RiPP Natural Product Zhao, Gengxiang; Kosek, Dalibor; Liu, Hong-Bing Journal of the American Chemical Society, Vol. 143, Issue 21 https://doi.org/10.1021/jacs.1c02316	journal	May 2021
A distributive peptide cyclase processes multiple microviridin core peptides within a single polypeptide substrate Zhang, Yi; Li, Kunhua; Yang, Guang Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-018-04154-3	journal	May 2018
Recent advances in the biosynthesis of RiPPs from multicore-containing precursor peptides Rubin, Garret M.; Ding, Yousong Journal of Industrial Microbiology and Biotechnology, Vol. 47, Issue 9-10 https://doi.org/10.1007/s10295-020-02289-1	journal	October 2020
The Cyanobactin Heterocyclase Enzyme: A Processive Adenylase That Operates with a Defined Order of Reaction Koehnke, Jesko; Bent, Andrew F.; Zollman, David Angewandte Chemie International Edition, Vol. 52, Issue 52 https://doi.org/10.1002/anie.201306302	journal	November 2013
Modularity of RiPP Enzymes Enables Designed Synthesis of Decorated Peptides Sardar, Debosmita; Lin, Zhenjian; Schmidt, Eric W. Chemistry & Biology, Vol. 22, Issue 7 https://doi.org/10.1016/j.chembiol.2015.06.014	journal	July 2015
Benchmarking fold detection by DaliLite v.5 Holm, Liisa Bioinformatics, Vol. 35, Issue 24 https://doi.org/10.1093/bioinformatics/btz536	journal	July 2019
Follow the leader: the use of leader peptides to guide natural product biosynthesis Oman, Trent J.; van der Donk, Wilfred A. Nature Chemical Biology, Vol. 6, Issue 1 https://doi.org/10.1038/nchembio.286	journal	December 2009
T-coffee: a novel method for fast and accurate multiple sequence alignment 1 1Edited by J. Thornton Notredame, Cédric; Higgins, Desmond G.; Heringa, Jaap Journal of Molecular Biology, Vol. 302, Issue 1 https://doi.org/10.1006/jmbi.2000.4042	journal	September 2000
Jalview Version 2--a multiple sequence alignment editor and analysis workbench Waterhouse, A. M.; Procter, J. B.; Martin, D. M. A. Bioinformatics, Vol. 25, Issue 9 https://doi.org/10.1093/bioinformatics/btp033	journal	January 2009
XDS Kabsch, Wolfgang Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2 https://doi.org/10.1107/S0907444909047337	journal	January 2010
Coot model-building tools for molecular graphics Emsley, Paul; Cowtan, Kevin Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 12, p. 2126-2132 https://doi.org/10.1107/S0907444904019158	journal	November 2004
Towards automated crystallographic structure refinement with phenix.refine Afonine, Pavel V.; Grosse-Kunstleve, Ralf W.; Echols, Nathaniel Acta Crystallographica Section D Biological Crystallography, Vol. 68, Issue 4 https://doi.org/10.1107/S0907444912001308	journal	March 2012

Similar Records

Structural and biochemical studies of an iterative ribosomal peptide macrocyclase

Journal Article · 2022 · Proteins · OSTI ID:1855496

Li, Gengnan; Patel, Krishna; Zhang, Yi; +3 more

Biochemical and Structural Characterization of Bisubstrate Inhibitors of Base, the Self-Standing Non-Ribosomal Peptide Synthetase Adenylate-Forming Enzyme of Acinetobactin Synthesis

Journal Article · 2012 · Biochem. 49:9292,2010 · OSTI ID:1855496

Drake, E J; Duckworth, B P; Neres, J; +2 more

Structural and Biochemical Studies of the C-Terminal Domain of Mouse Peptide-N-glycanase Identify it as a Mannose-Binding Module

Journal Article · 2006 · Proceedings of the National Academy of Sciences of the USA · OSTI ID:1855496

Zhou, X; Zhao, G; Truglio, J; +4 more

Title: Structural and biochemical studies of an iterative ribosomal peptide macrocyclase

Citation Formats

References (33)

Similar Records

Related Subjects