Mechanism of Filamentation-Induced Allosteric Activation of the SgrAI Endonuclease

Published on Oct 1, 2019in Structure4.576
路 DOI :10.1016/j.str.2019.08.001
Smarajit Polley6
Estimated H-index: 6
(Bose Institute),
Dmitry Lyumkis18
Estimated H-index: 18
(Salk Institute for Biological Studies),
Nancy C. Horton19
Estimated H-index: 19
(UA: University of Arizona)
Summary Filament formation by enzymes is increasingly recognized as an important phenomenon with potentially unique regulatory properties and biological roles. SgrAI is an allosterically regulated type II restriction endonuclease that forms filaments with enhanced DNA cleavage activity and altered sequence specificity. Here, we present the cryoelectron microscopy (cryo-EM) structure of the filament of SgrAI in its activated configuration. The structural data illuminate the mechanistic origin of hyperaccelerated DNA cleavage activity and suggests how indirect DNA sequence readout within filamentous SgrAI may enable recognition of substantially more nucleotide sequences than its low-activity form, thereby altering and partially relaxing its DNA sequence specificity. Together, substrate DNA binding, indirect readout, and filamentation simultaneously enhance SgrAI's catalytic activity and modulate substrate preference. This unusual enzyme mechanism may have evolved to perform the specialized functions of bacterial innate immunity in rapid defense against invading phage DNA without causing damage to the host DNA.
  • References (58)
  • Citations (2)
馃摉 Papers frequently viewed together
20 Citations
98 Citations
78% of Scinapse members use related papers. After signing in, all features are FREE.
#1Claudia Barahona (UA: University of Arizona)H-Index: 3
#2L. Emilia Basantes (UA: University of Arizona)H-Index: 3
Last. Nancy C. HortonH-Index: 19
view all 10 authors...
3 CitationsSource
#1Chad K. Park (UA: University of Arizona)H-Index: 14
#2Jonathan L. Sanchez (UA: University of Arizona)H-Index: 4
Last. Nancy C. Horton (UA: University of Arizona)H-Index: 19
view all 7 authors...
5 CitationsSource
#1Chad K. Park (UA: University of Arizona)H-Index: 14
#2Jonathan L. Sanchez (UA: University of Arizona)H-Index: 4
Last. Nancy C. Horton (UA: University of Arizona)H-Index: 19
view all 7 authors...
5 CitationsSource
#1Pavel V. Afonine (SHU: Shanghai University)H-Index: 33
#2Bruno P. Klaholz (French Institute of Health and Medical Research)H-Index: 21
Last. Alexandre Urzhumtsev (University of Lorraine)H-Index: 14
view all 8 authors...
Recent advances in the field of electron cryomicroscopy (cryo-EM) have resulted in a rapidly increasing number of atomic models of biomacromolecules that have been solved using this technique and deposited in the Protein Data Bank and the Electron Microscopy Data Bank. Similar to macromolecular crystallography, validation tools for these models and maps are required. While some of these validation tools may be borrowed from crystallography, new methods specifically designed for cryo-EM validatio...
58 CitationsSource
#1M. Hunkeler (University of Basel)H-Index: 3
#2A. Hagmann (University of Basel)H-Index: 2
Last. Timm Maier (University of Basel)H-Index: 25
view all 7 authors...
Acetyl-CoA carboxylase catalyses the ATP-dependent carboxylation of acetyl-CoA, a rate-limiting step in fatty acid biosynthesis1,2. Eukaryotic acetyl-CoA carboxylases are large, homodimeric multienzymes. Human acetyl-CoA carboxylase occurs in two isoforms: the metabolic, cytosolic ACC1, and ACC2, which is anchored to the outer mitochondrial membrane and controls fatty acid 尾-oxidation1,3. ACC1 is regulated by a complex interplay of phosphorylation, binding of allosteric regulators and protein鈥損r...
6 CitationsSource
#1Pavel V. Afonine (SHU: Shanghai University)H-Index: 33
#2Billy K. Poon (LBNL: Lawrence Berkeley National Laboratory)H-Index: 12
Last. Paul D. Adams (University of California, Berkeley)H-Index: 84
view all 7 authors...
This article describes the implementation of real-space refinement in the phenix.real_space_refine program from the PHENIX suite. The use of a simplified refinement target function enables very fast calculation, which in turn makes it possible to identify optimal data-restraint weights as part of routine refinements with little runtime cost. Refinement of atomic models against low-resolution data benefits from the inclusion of as much additional information as is available. In addition to standa...
169 CitationsSource
#1Yong Zi TanH-Index: 9
#2Philip R BaldwinH-Index: 3
Last. Dmitry LyumkisH-Index: 18
view all 7 authors...
The preferred specimen orientation problem limits accuracy and resolution in structure determination by cryo-EM. Collecting data at defined sample tilts yielded near-atomic-resolution structures for the influenza hemagglutinin trimer and ribosomal biogenesis intermediates.
97 CitationsSource
#1Eric M. Lynch (UW: University of Washington)H-Index: 2
#2Derrick R. Hicks (UW: University of Washington)H-Index: 1
Last. Justin M. Kollman (UW: University of Washington)H-Index: 19
view all 10 authors...
漏 2017 Nature America, Inc., part of Springer Nature. All rights reserved. The universally conserved enzyme CTP synthase (CTPS) forms filaments in bacteria and eukaryotes. In bacteria, polymerization inhibits CTPS activity and is required for nucleotide homeostasis. Here we show that for human CTPS, polymerization increases catalytic activity. The cryo-EM structures of bacterial and human CTPS filaments differ considerably in overall architecture and in the conformation of the CTPS protomer, exp...
42 CitationsSource
#1Shawn Q. ZhengH-Index: 12
#2Eugene PalovcakH-Index: 5
Last. David A. AgardH-Index: 84
view all 6 authors...
MotionCor2 software corrects for beam-induced sample motion, improving the resolution of cryo-EM reconstructions.
1,065 CitationsSource
#1Dari Kimanius (Science for Life Laboratory)H-Index: 7
#2Bj枚rn O. Forsberg (Science for Life Laboratory)H-Index: 6
Last. Erik Lindahl (KTH: Royal Institute of Technology)H-Index: 44
view all 4 authors...
By reaching near-atomic resolution for a wide range of specimens, single-particle cryo-EM structure determination is transforming structural biology. However, the necessary calculations come at lar ...
547 CitationsSource
Cited By2
#1Chad K. Park (UA: University of Arizona)H-Index: 14
#2Nancy C. Horton (UA: University of Arizona)H-Index: 19
Enzyme filaments are defined as reversible, functional, linear self-assemblies of a single type of enzyme. Filamentation has recently emerged as a new mode of enzymatic regulation. In this Comment, we briefly introduce the diversity and functional consequences of enzyme filamentation. Filamentation is a relatively unknown mode of enzyme regulation, which increases functional diversity.
#1Chad K. Park (UA: University of Arizona)H-Index: 14
#2Nancy C. Horton (UA: University of Arizona)H-Index: 19
Filament formation by non-cytoskeletal enzymes has been known for decades, yet only relatively recently has its wide-spread role in enzyme regulation and biology come to be appreciated. This comprehensive review summarizes what is known for each enzyme confirmed to form filamentous structures in vitro, and for the many that are known only to form large self-assemblies within cells. For some enzymes, studies describing both the in vitro filamentous structures and cellular self-assembly formation ...
4 CitationsSource