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Title: Katanin spiral and ring structures shed light on power stroke for microtubule severing

Abstract

Microtubule-severing enzymes katanin, spastin and fidgetin are AAA ATPases critical for the biogenesis and maintenance of complex microtubule arrays in axons, spindles and cilia. Because of a lack of 3D structures, their mechanism has remained poorly understood. We report the first X-ray structure of the monomeric AAA katanin module and cryo-EM reconstructions of the hexamer in two conformations. These reveal an unexpected asymmetric arrangement of the AAA domains mediated by structural elements unique to severing enzymes and critical for their function. Our reconstructions show that katanin cycles between open spiral and closed ring conformations, depending on the ATP occupancy of a gating protomer that tenses or relaxes inter-protomer interfaces. Cycling of the hexamer between these conformations would provide the power stroke for microtubule severing.

Authors:
 [1];  [1];  [2];  [1];  [3]; ORCiD logo [4]
  1. National Inst. of Neurological Disorders and Stroke, Bethesda, MD (United States). Cell Biology and Biophysics Unit, Porter Neuroscience Research Center
  2. Biophysics Core, National Heart, Lung and Blood Inst., Bethesda, MD (United States)
  3. Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
  4. National Inst. of Neurological Disorders and Stroke, Bethesda, MD (United States). Cell Biology and Biophysics Unit, Porter Neuroscience Research Center; Biophysics Core, National Heart, Lung and Blood Inst., Bethesda, MD (United States)
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22)
OSTI Identifier:
1394618
Grant/Contract Number:  
AC02-06CH11357
Resource Type:
Accepted Manuscript
Journal Name:
Nature Structural & Molecular Biology
Additional Journal Information:
Journal Volume: 24; Journal Issue: 9; Journal ID: ISSN 1545-9993
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES; protein SAXS

Citation Formats

Zehr, Elena, Szyk, Agnieszka, Piszczek, Grzegorz, Szczesna, Ewa, Zuo, Xiaobing, and Roll-Mecak, Antonina. Katanin spiral and ring structures shed light on power stroke for microtubule severing. United States: N. p., 2017. Web. doi:10.1038/nsmb.3448.
Zehr, Elena, Szyk, Agnieszka, Piszczek, Grzegorz, Szczesna, Ewa, Zuo, Xiaobing, & Roll-Mecak, Antonina. Katanin spiral and ring structures shed light on power stroke for microtubule severing. United States. doi:10.1038/nsmb.3448.
Zehr, Elena, Szyk, Agnieszka, Piszczek, Grzegorz, Szczesna, Ewa, Zuo, Xiaobing, and Roll-Mecak, Antonina. Mon . "Katanin spiral and ring structures shed light on power stroke for microtubule severing". United States. doi:10.1038/nsmb.3448. https://www.osti.gov/servlets/purl/1394618.
@article{osti_1394618,
title = {Katanin spiral and ring structures shed light on power stroke for microtubule severing},
author = {Zehr, Elena and Szyk, Agnieszka and Piszczek, Grzegorz and Szczesna, Ewa and Zuo, Xiaobing and Roll-Mecak, Antonina},
abstractNote = {Microtubule-severing enzymes katanin, spastin and fidgetin are AAA ATPases critical for the biogenesis and maintenance of complex microtubule arrays in axons, spindles and cilia. Because of a lack of 3D structures, their mechanism has remained poorly understood. We report the first X-ray structure of the monomeric AAA katanin module and cryo-EM reconstructions of the hexamer in two conformations. These reveal an unexpected asymmetric arrangement of the AAA domains mediated by structural elements unique to severing enzymes and critical for their function. Our reconstructions show that katanin cycles between open spiral and closed ring conformations, depending on the ATP occupancy of a gating protomer that tenses or relaxes inter-protomer interfaces. Cycling of the hexamer between these conformations would provide the power stroke for microtubule severing.},
doi = {10.1038/nsmb.3448},
journal = {Nature Structural & Molecular Biology},
number = 9,
volume = 24,
place = {United States},
year = {2017},
month = {8}
}

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Works referenced in this record:

A Mechanism for Reorientation of Cortical Microtubule Arrays Driven by Microtubule Severing
journal, November 2013


The Cul3/Klhdc5 E3 Ligase Regulates p60/Katanin and Is Required for Normal Mitosis in Mammalian Cells
journal, March 2009

  • Cummings, Cristina M.; Bentley, Cornelia A.; Perdue, Sarah A.
  • Journal of Biological Chemistry, Vol. 284, Issue 17
  • DOI: 10.1074/jbc.M809374200

Uniqueness of ab initio shape determination in small-angle scattering
journal, April 2003

  • Volkov, Vladimir V.; Svergun, Dmitri I.
  • Journal of Applied Crystallography, Vol. 36, Issue 3, p. 860-864
  • DOI: 10.1107/S0021889803000268

Vps4 disassembles an ESCRT-III filament by global unfolding and processive translocation
journal, May 2015

  • Yang, Bei; Stjepanovic, Goran; Shen, Qingtao
  • Nature Structural & Molecular Biology, Vol. 22, Issue 6
  • DOI: 10.1038/nsmb.3015

Complete subunit architecture of the proteasome regulatory particle
journal, January 2012

  • Lander, Gabriel C.; Estrin, Eric; Matyskiela, Mary E.
  • Nature, Vol. 482, Issue 7384
  • DOI: 10.1038/nature10774

Mutations in KATNB1 Cause Complex Cerebral Malformations by Disrupting Asymmetrically Dividing Neural Progenitors
journal, December 2014


Mechanochemical basis of protein degradation by a double-ring AAA+ machine
journal, September 2014

  • Olivares, Adrian O.; Nager, Andrew R.; Iosefson, Ohad
  • Nature Structural & Molecular Biology, Vol. 21, Issue 10
  • DOI: 10.1038/nsmb.2885

Katanin p80 Regulates Human Cortical Development by Limiting Centriole and Cilia Number
journal, December 2014


A syndrome of microcephaly, short stature, polysyndactyly, and dental anomalies caused by a homozygous KATNB1 mutation
journal, December 2015

  • Yigit, Gökhan; Wieczorek, Dagmar; Bögershausen, Nina
  • American Journal of Medical Genetics Part A, Vol. 170, Issue 3
  • DOI: 10.1002/ajmg.a.37484

Bsoft: Image and Molecular Processing in Electron Microscopy
journal, February 2001


Molecular mechanisms of substrate-controlled ring dynamics and substepping in a nucleic acid-dependent hexameric motor
journal, November 2016

  • Thomsen, Nathan D.; Lawson, Michael R.; Witkowsky, Lea B.
  • Proceedings of the National Academy of Sciences, Vol. 113, Issue 48
  • DOI: 10.1073/pnas.1616745113

Accuracy of molecular mass determination of proteins in solution by small-angle X-ray scattering
journal, February 2007

  • Mylonas, Efstratios; Svergun, Dmitri I.
  • Journal of Applied Crystallography, Vol. 40, Issue s1
  • DOI: 10.1107/S002188980700252X

Determination of the regularization parameter in indirect-transform methods using perceptual criteria
journal, August 1992


Identification of katanin, an ATPase that severs and disassembles stable microtubules
journal, November 1993


Structural basis of microtubule severing by the hereditary spastic paraplegia protein spastin
journal, January 2008


Microtubule-severing enzymes
journal, February 2010


Structural and mechanistic studies of VPS4 proteins
journal, September 2005

  • Scott, Anna; Chung, Hyo-Young; Gonciarz-Swiatek, Malgorzata
  • The EMBO Journal, Vol. 24, Issue 20
  • DOI: 10.1038/sj.emboj.7600818

Crystal structure of the human spastin AAA domain
journal, August 2012

  • Taylor, Jennifer L.; White, Susan Roehl; Lauring, Brett
  • Journal of Structural Biology, Vol. 179, Issue 2
  • DOI: 10.1016/j.jsb.2012.03.002

Running in Reverse: The Structural Basis for Translocation Polarity in Hexameric Helicases
journal, October 2009


CTFFIND4: Fast and accurate defocus estimation from electron micrographs
journal, November 2015


MolProbity: all-atom contacts and structure validation for proteins and nucleic acids
journal, May 2007

  • Davis, I. W.; Leaver-Fay, A.; Chen, V. B.
  • Nucleic Acids Research, Vol. 35, Issue Web Server
  • DOI: 10.1093/nar/gkm216

Mechanism of DNA translocation in a replicative hexameric helicase
journal, July 2006


Katanin Disrupts the Microtubule Lattice and Increases Polymer Number in C. elegans Meiosis
journal, October 2006


The Drosophila Homologue of the Hereditary Spastic Paraplegia Protein, Spastin, Severs and Disassembles Microtubules
journal, April 2005


The Microtubule-severing Proteins Spastin and Katanin Participate Differently in the Formation of Axonal Branches
journal, April 2008

  • Yu, Wenqian; Qiang, Liang; Solowska, Joanna M.
  • Molecular Biology of the Cell, Vol. 19, Issue 4
  • DOI: 10.1091/mbc.E07-09-0878

Mechanistic insights into the recycling machine of the SNARE complex
journal, January 2015

  • Zhao, Minglei; Wu, Shenping; Zhou, Qiangjun
  • Nature, Vol. 518, Issue 7537
  • DOI: 10.1038/nature14148

N-Terminal Phosphorylation of p60 Katanin Directly Regulates Microtubule Severing
journal, January 2013

  • Whitehead, Evan; Heald, Rebecca; Wilbur, Jeremy D.
  • Journal of Molecular Biology, Vol. 425, Issue 2
  • DOI: 10.1016/j.jmb.2012.11.022

Katanin regulates dynamics of microtubules and biogenesis of motile cilia
journal, September 2007

  • Sharma, Neeraj; Bryant, Jessica; Wloga, Dorota
  • The Journal of Cell Biology, Vol. 178, Issue 6
  • DOI: 10.1083/jcb.200704021

Microtubule Disassembly by ATP-Dependent Oligomerization of the AAA Enzyme Katanin
journal, October 1999


Microtubule Severing at Crossover Sites by Katanin Generates Ordered Cortical Microtubule Arrays in Arabidopsis
journal, November 2013


Flexural rigidity of microtubules and actin filaments measured from thermal fluctuations in shape
journal, February 1993


Structure of a AAA+ unfoldase in the process of unfolding substrate
journal, April 2017


UCSF Chimera?A visualization system for exploratory research and analysis
journal, January 2004

  • Pettersen, Eric F.; Goddard, Thomas D.; Huang, Conrad C.
  • Journal of Computational Chemistry, Vol. 25, Issue 13
  • DOI: 10.1002/jcc.20084

Flexible Fitting of Atomic Structures into Electron Microscopy Maps Using Molecular Dynamics
journal, May 2008


3.9 Å structure of the nucleosome core particle determined by phase-plate cryo-EM
journal, August 2016

  • Chua, Eugene Y. D.; Vogirala, Vinod K.; Inian, Oviya
  • Nucleic Acids Research, Vol. 44, Issue 17
  • DOI: 10.1093/nar/gkw708

Structures of Asymmetric ClpX Hexamers Reveal Nucleotide-Dependent Motions in a AAA+ Protein-Unfolding Machine
journal, November 2009


Operational Plasticity Enables Hsp104 to Disaggregate Diverse Amyloid and Nonamyloid Clients
journal, November 2012


FREALIGN: High-resolution refinement of single particle structures
journal, January 2007


A Common Substrate Recognition Mode Conserved between Katanin p60 and VPS4 Governs Microtubule Severing and Membrane Skeleton Reorganization
journal, March 2010

  • Iwaya, Naoko; Kuwahara, Yohta; Fujiwara, Yoshie
  • Journal of Biological Chemistry, Vol. 285, Issue 22
  • DOI: 10.1074/jbc.M110.108365

Structural insights into the functional cycle of the ATPase module of the 26S proteasome
journal, January 2017

  • Wehmer, Marc; Rudack, Till; Beck, Florian
  • Proceedings of the National Academy of Sciences, Vol. 114, Issue 6
  • DOI: 10.1073/pnas.1621129114

Mechanism of Vps4 hexamer function revealed by cryo-EM
journal, April 2017


Spiral architecture of the Hsp104 disaggregase reveals the basis for polypeptide translocation
journal, August 2016

  • Yokom, Adam L.; Gates, Stephanie N.; Jackrel, Meredith E.
  • Nature Structural & Molecular Biology, Vol. 23, Issue 9
  • DOI: 10.1038/nsmb.3277

Spectrum of SPG4 mutations in autosomal dominant spastic paraplegia
journal, March 2000


Coot model-building tools for molecular graphics
journal, November 2004

  • Emsley, Paul; Cowtan, Kevin
  • Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 12, p. 2126-2132
  • DOI: 10.1107/S0907444904019158

Katanin maintains meiotic metaphase chromosome alignment and spindle structure in vivo and has multiple effects on microtubules in vitro
journal, April 2014

  • McNally, Karen; Berg, Evan; Cortes, Daniel B.
  • Molecular Biology of the Cell, Vol. 25, Issue 7
  • DOI: 10.1091/mbc.E13-12-0764

RELION: Implementation of a Bayesian approach to cryo-EM structure determination
journal, December 2012


Microtubule-severing activity of the AAA+ ATPase Katanin is essential for female meiotic spindle assembly
journal, August 2016

  • Joly, Nicolas; Martino, Lisa; Gigant, Emmanuelle
  • Development, Vol. 143, Issue 19
  • DOI: 10.1242/dev.140830

2.3 A resolution cryo-EM structure of human p97 and mechanism of allosteric inhibition
journal, January 2016


An Essential Role for Katanin in Severing Microtubules in the Neuron
journal, April 1999

  • Ahmad, Fridoon J.; Yu, Wenqian; McNally, Francis J.
  • The Journal of Cell Biology, Vol. 145, Issue 2
  • DOI: 10.1083/jcb.145.2.305

Katanin Severing and Binding Microtubules Are Inhibited by Tubulin Carboxy Tails
journal, December 2015

  • Bailey, Megan E.; Sackett, Dan L.; Ross, Jennifer L.
  • Biophysical Journal, Vol. 109, Issue 12
  • DOI: 10.1016/j.bpj.2015.11.011

Microtubule Severing by Katanin p60 AAA+ ATPase Requires the C-terminal Acidic Tails of Both α- and β-Tubulins and Basic Amino Acid Residues in the AAA+ Ring Pore
journal, March 2015

  • Johjima, Ai; Noi, Kentaro; Nishikori, Shingo
  • Journal of Biological Chemistry, Vol. 290, Issue 18
  • DOI: 10.1074/jbc.M114.614768

PHENIX: a comprehensive Python-based system for macromolecular structure solution
journal, January 2010

  • Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221
  • DOI: 10.1107/S0907444909052925

Katanin Contributes to Interspecies Spindle Length Scaling in Xenopus
journal, December 2011


AAA+ proteins: have engine, will work
journal, July 2005

  • Hanson, Phyllis I.; Whiteheart, Sidney W.
  • Nature Reviews Molecular Cell Biology, Vol. 6, Issue 7
  • DOI: 10.1038/nrm1684

Crystal Structure of the Hexamerization Domain of N-ethylmaleimide–Sensitive Fusion Protein
journal, August 1998


Three microtubule severing enzymes contribute to the “Pacman-flux” machinery that moves chromosomes
journal, April 2007

  • Zhang, Dong; Rogers, Gregory C.; Buster, Daniel W.
  • The Journal of Cell Biology, Vol. 177, Issue 2
  • DOI: 10.1083/jcb.200612011

Recognition of C-terminal amino acids in tubulin by pore loops in Spastin is important for microtubule severing
journal, March 2007

  • White, Susan Roehl; Evans, Katia J.; Lary, Jeffrey
  • The Journal of Cell Biology, Vol. 176, Issue 7
  • DOI: 10.1083/jcb.200610072

Graded Control of Microtubule Severing by Tubulin Glutamylation
journal, February 2016


Situs: A Package for Docking Crystal Structures into Low-Resolution Maps from Electron Microscopy
journal, April 1999

  • Wriggers, Willy; Milligan, Ronald A.; McCammon, J. Andrew
  • Journal of Structural Biology, Vol. 125, Issue 2-3
  • DOI: 10.1006/jsbi.1998.4080

Automated electron microscope tomography using robust prediction of specimen movements
journal, October 2005


Structural basis of protein translocation by the Vps4-Vta1 AAA ATPase
journal, April 2017


Accurate assessment of mass, models and resolution by small-angle scattering
journal, April 2013


Phaser crystallographic software
journal, July 2007

  • McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D.
  • Journal of Applied Crystallography, Vol. 40, Issue 4
  • DOI: 10.1107/S0021889807021206

Katanin controls mitotic and meiotic spindle length
journal, December 2006

  • McNally, Karen; Audhya, Anjon; Oegema, Karen
  • The Journal of Cell Biology, Vol. 175, Issue 6
  • DOI: 10.1083/jcb.200608117

Structure and function of the AAA+ nucleotide binding pocket
journal, January 2012

  • Wendler, Petra; Ciniawsky, Susanne; Kock, Malte
  • Biochimica et Biophysica Acta (BBA) - Molecular Cell Research, Vol. 1823, Issue 1
  • DOI: 10.1016/j.bbamcr.2011.06.014

EMAN: Semiautomated Software for High-Resolution Single-Particle Reconstructions
journal, December 1999

  • Ludtke, Steven J.; Baldwin, Philip R.; Chiu, Wah
  • Journal of Structural Biology, Vol. 128, Issue 1
  • DOI: 10.1006/jsbi.1999.4174

Asymmetric ring structure of Vps4 required for ESCRT-III disassembly
journal, December 2015

  • Caillat, Christophe; Macheboeuf, Pauline; Wu, Yuanfei
  • Nature Communications, Vol. 6, Issue 1
  • DOI: 10.1038/ncomms9781