The structure of the Clostridium thermocellum RsgI9 ectodomain provides insight into the mechanism o

Mahoney, Brendan J.; Takayesu, Allen; Zhou, Anqi; Cascio, Duilio; Clubb, Robert T.

doi:10.1002/prot.26326

The structure of the Clostridium thermocellum RsgI9 ectodomain provides insight into the mechanism o

Journal Article · 01 July 2022 · Proteins

DOI:https://doi.org/10.1002/prot.26326· OSTI ID:1872612

Mahoney, Brendan J.; Takayesu, Allen; Zhou, Anqi; Cascio, Duilio; Clubb, Robert T.

Research Organization:: Advanced Photon Source (APS), Argonne National Laboratory (ANL), Argonne, IL (US)

Sponsoring Organization:: DOE - Office Of Science; DOE - BIOLOGICAL AND ENVIRONMENTAL RESEARCH

OSTI ID:: 1872612

Journal Information:: Proteins, Journal Name: Proteins Journal Issue: (7) Vol. 90

Country of Publication:: United States

Language:: ENGLISH

References (66)

How does cellulosome composition influence deconstruction of lignocellulosic substrates in Clostridium (Ruminiclostridium) thermocellum DSM 1313? Yoav, Shahar; Barak, Yoav; Shamshoum, Melina Biotechnology for Biofuels, Vol. 10, Issue 1 https://doi.org/10.1186/s13068-017-0909-7	journal	September 2017
Features and development of Coot Emsley, P.; Lohkamp, B.; Scott, W. G. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4 https://doi.org/10.1107/S0907444910007493	journal	March 2010
Integration, scaling, space-group assignment and post-refinement Kabsch, Wolfgang Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 133-144 https://doi.org/10.1107/S0907444909047374	journal	January 2010
Recent progress in consolidated bioprocessing Olson, Daniel G.; McBride, John E.; Joe Shaw, A. Current Opinion in Biotechnology, Vol. 23, Issue 3, p. 396-405 https://doi.org/10.1016/j.copbio.2011.11.026	journal	June 2012
Accurate SAXS Profile Computation and its Assessment by Contrast Variation Experiments Schneidman-Duhovny, Dina; Hammel, Michal; Tainer, John A. Biophysical Journal, Vol. 105, Issue 4 https://doi.org/10.1016/j.bpj.2013.07.020	journal	August 2013
Fine-structural variance of family 3 carbohydrate-binding modules as extracellular biomass-sensing components of Clostridium thermocellum anti-σ ^I factors Yaniv, Oren; Fichman, Galit; Borovok, Ilya Acta Crystallographica Section D Biological Crystallography, Vol. 70, Issue 2 https://doi.org/10.1107/S139900471302926X	journal	January 2014
DAMMIF, a program for rapid ab-initio shape determination in small-angle scattering Franke, Daniel; Svergun, Dmitri I. Journal of Applied Crystallography, Vol. 42, Issue 2, p. 342-346 https://doi.org/10.1107/S0021889809000338	journal	January 2009
Small-angle scattering studies of biological macromolecules in solution Svergun, Dmitri I.; Koch, Michel H. J. Reports on Progress in Physics, Vol. 66, Issue 10 https://doi.org/10.1088/0034-4885/66/10/R05	journal	September 2003
Effective rotational correlation times of proteins from NMR relaxation interference Lee, Donghan; Hilty, Christian; Wider, Gerhard Journal of Magnetic Resonance, Vol. 178, Issue 1 https://doi.org/10.1016/j.jmr.2005.08.014	journal	January 2006
A method for efficient isotopic labeling of recombinant proteins Marley, Jonathan; Lu, Min; Bracken, Clay Journal of Biomolecular NMR, Vol. 20, Issue 1, p. 71-75 https://doi.org/10.1023/A:1011254402785	journal	May 2001
Allosteric Activation of DegS, a Stress Sensor PDZ Protease Sohn, Jungsan; Grant, Robert A.; Sauer, Robert T. Cell, Vol. 131, Issue 3 https://doi.org/10.1016/j.cell.2007.08.044	journal	November 2007
Consensus Bayesian assessment of protein molecular mass from solution X-ray scattering data Hajizadeh, Nelly R.; Franke, Daniel; Jeffries, Cy M. Scientific Reports, Vol. 8, Issue 1 https://doi.org/10.1038/s41598-018-25355-2	journal	May 2018
UCSF ChimeraX : Structure visualization for researchers, educators, and developers Pettersen, Eric F.; Goddard, Thomas D.; Huang, Conrad C. Protein Science, Vol. 30, Issue 1 https://doi.org/10.1002/pro.3943	journal	October 2020
A Procedure for Renaturation and Purification of the Extracellular Serratia marcescens Nuclease from Genetically Engineered Escherichia coli Friedhoff, P.; Gimadutdinow, O.; Ruter, T. Protein Expression and Purification, Vol. 5, Issue 1 https://doi.org/10.1006/prep.1994.1005	journal	February 1994
Biofuels for a sustainable future Liu, Yuzhong; Cruz-Morales, Pablo; Zargar, Amin Cell, Vol. 184, Issue 6 https://doi.org/10.1016/j.cell.2021.01.052	journal	March 2021
Phaser crystallographic software McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D. Journal of Applied Crystallography, Vol. 40, Issue 4 https://doi.org/10.1107/S0021889807021206	journal	July 2007
Distinctive ligand‐binding specificities of tandem PA14 biomass‐sensory elements from Clostridium thermocellum and Clostridium clariflavum Grinberg, Inna Rozman; Yaniv, Oren; Ora, Lizett Ortiz Proteins: Structure, Function, and Bioinformatics, Vol. 87, Issue 11 https://doi.org/10.1002/prot.25753	journal	June 2019
Scaffoldin Conformation and Dynamics Revealed by a Ternary Complex from the Clostridium thermocellum Cellulosome Currie, Mark A.; Adams, Jarrett J.; Faucher, Frédérick Journal of Biological Chemistry, Vol. 287, Issue 32 https://doi.org/10.1074/jbc.M112.343897	journal	August 2012
DISOPRED3: precise disordered region predictions with annotated protein-binding activity Jones, David T.; Cozzetto, Domenico Bioinformatics, Vol. 31, Issue 6 https://doi.org/10.1093/bioinformatics/btu744	journal	November 2014
Glycoside hydrolases as components of putative carbohydrate biosensor proteins in Clostridium thermocellum Bahari, Liat; Gilad, Yuval; Borovok, Ilya Journal of Industrial Microbiology & Biotechnology, Vol. 38, Issue 7 https://doi.org/10.1007/s10295-010-0848-9	journal	September 2010
Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions Krissinel, E.; Henrick, K. Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 12 https://doi.org/10.1107/S0907444904026460	journal	November 2004
The Lancet Countdown on health and climate change: from 25 years of inaction to a global transformation for public health Watts, Nick; Amann, Markus; Ayeb-Karlsson, Sonja The Lancet, Vol. 391, Issue 10120 https://doi.org/10.1016/S0140-6736(17)32464-9	journal	February 2018
The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database Rawlings, Neil D.; Barrett, Alan J.; Thomas, Paul D. Nucleic Acids Research, Vol. 46, Issue D1 https://doi.org/10.1093/nar/gkx1134	journal	November 2017
Crystal structure of DegP (HtrA) reveals a new protease-chaperone machine Krojer, Tobias; Garrido-Franco, Marta; Huber, Robert Nature, Vol. 416, Issue 6879 https://doi.org/10.1038/416455a	journal	March 2002
Carbohydrate-Binding Module and Linker Allow Cold Adaptation and Salt Tolerance of Maltopentaose-Forming Amylase From Marine Bacterium Saccharophagus degradans 2-40T Ding, Ning; Zhao, Boyang; Ban, Xiaofeng Frontiers in Microbiology, Vol. 12 https://doi.org/10.3389/fmicb.2021.708480	journal	July 2021
Solvent content of protein crystals Matthews, B. W. Journal of Molecular Biology, Vol. 33, Issue 2 https://doi.org/10.1016/0022-2836(68)90205-2	journal	April 1968
Resonance assignments of the periplasmic domain of a cellulose-sensing trans-membrane anti-sigma factor from Clostridium thermocellum Ding, Xiaoke; Chen, Chao; Cui, Qiu Biomolecular NMR Assignments, Vol. 9, Issue 2 https://doi.org/10.1007/s12104-015-9601-7	journal	February 2015
ATSAS 3.0 : expanded functionality and new tools for small-angle scattering data analysis Manalastas-Cantos, Karen; Konarev, Petr V.; Hajizadeh, Nelly R. Journal of Applied Crystallography, Vol. 54, Issue 1 https://doi.org/10.1107/S1600576720013412	journal	February 2021
Backbone dynamics of calmodulin studied by nitrogen-15 relaxation using inverse detected two-dimensional NMR spectroscopy: the central helix is flexible Barbato, Gaetano; Ikura, Mitsuhiko; Kay, Lewis E. Biochemistry, Vol. 31, Issue 23 https://doi.org/10.1021/bi00138a005	journal	July 1992
Inference of Macromolecular Assemblies from Crystalline State Krissinel, Evgeny; Henrick, Kim Journal of Molecular Biology, Vol. 372, Issue 3 https://doi.org/10.1016/j.jmb.2007.05.022	journal	September 2007
Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix Liebschner, Dorothee; Afonine, Pavel V.; Baker, Matthew L. Acta Crystallographica Section D Structural Biology, Vol. 75, Issue 10 https://doi.org/10.1107/S2059798319011471	journal	October 2019
NADPH oxidase activator p67phox behaves in solution as a multidomain protein with semi-flexible linkers Durand, Dominique; Vivès, Corinne; Cannella, Dominique Journal of Structural Biology, Vol. 169, Issue 1 https://doi.org/10.1016/j.jsb.2009.08.009	journal	January 2010
Clostridium thermocellum cellulosomal genes are regulated by extracytoplasmic polysaccharides via alternative sigma factors Nataf, Y.; Bahari, L.; Kahel-Raifer, H. Proceedings of the National Academy of Sciences, Vol. 107, Issue 43 https://doi.org/10.1073/pnas.1012175107	journal	October 2010
Lignocellulosic ethanol: From science to industry Viikari, L.; Vehmaanperä, J.; Koivula, A. Biomass and Bioenergy, Vol. 46 https://doi.org/10.1016/j.biombioe.2012.05.008	journal	November 2012
FoXS, FoXSDock and MultiFoXS: Single-state and multi-state structural modeling of proteins and their complexes based on SAXS profiles Schneidman-Duhovny, Dina; Hammel, Michal; Tainer, John A. Nucleic Acids Research, Vol. 44, Issue W1 https://doi.org/10.1093/nar/gkw389	journal	May 2016
Enzyme-microbe synergy during cellulose hydrolysis by Clostridium thermocellum Lu, Y.; Zhang, Y. -H. P.; Lynd, L. R. Proceedings of the National Academy of Sciences, Vol. 103, Issue 44 https://doi.org/10.1073/pnas.0605381103	journal	October 2006
HMMER web server: 2018 update Potter, Simon C.; Luciani, Aurélien; Eddy, Sean R. Nucleic Acids Research, Vol. 46, Issue W1 https://doi.org/10.1093/nar/gky448	journal	June 2018
Saccharification of Complex Cellulosic Substrates by the Cellulase System from Clostridium thermocellum Johnson, Eric A.; Sakajoh, Mitsuji; Halliwell, Geoffrey Applied and Environmental Microbiology, Vol. 43, Issue 5 https://doi.org/10.1128/aem.43.5.1125-1132.1982	journal	January 1982
Engineering cellulolytic ability into bioprocessing organisms la Grange, Daniel C.; den Haan, Riaan; van Zyl, Willem H. Applied Microbiology and Biotechnology, Vol. 87, Issue 4 https://doi.org/10.1007/s00253-010-2660-x	journal	May 2010
Pfam: The protein families database in 2021 Mistry, Jaina; Chuguransky, Sara; Williams, Lowri Nucleic Acids Research, Vol. 49, Issue D1 https://doi.org/10.1093/nar/gkaa913	journal	October 2020
Ten years of probabilistic estimates of biocrystal solvent content: new insights via nonparametric kernel density estimate Weichenberger, Christian X.; Rupp, Bernhard Acta Crystallographica Section D Biological Crystallography, Vol. 70, Issue 6 https://doi.org/10.1107/S1399004714005550	journal	May 2014
Characterization and subcellular localization of the Clostridium thermocellum scaffoldin dockerin binding protein SdbA. Leibovitz, E.; Ohayon, H.; Gounon, P. Journal of bacteriology, Vol. 179, Issue 8 https://doi.org/10.1128/jb.179.8.2519-2523.1997	journal	January 1997
Filling out the structural map of the NTF2-like superfamily Eberhardt, Ruth Y.; Chang, Yuanyuan; Bateman, Alex BMC Bioinformatics, Vol. 14, Issue 1 https://doi.org/10.1186/1471-2105-14-327	journal	November 2013
BioXTAS RAW : improvements to a free open-source program for small-angle X-ray scattering data reduction and analysis Hopkins, Jesse Bennett; Gillilan, Richard E.; Skou, Soren Journal of Applied Crystallography, Vol. 50, Issue 5 https://doi.org/10.1107/S1600576717011438	journal	September 2017
Research progress and the biotechnological applications of multienzyme complex Jiang, Yi; Zhang, Xinyi; Yuan, Haibo Applied Microbiology and Biotechnology, Vol. 105, Issue 5 https://doi.org/10.1007/s00253-021-11121-4	journal	February 2021
Matthews coefficient probabilities: Improved estimates for unit cell contents of proteins, DNA, and protein-nucleic acid complex crystals Kantardjieff, Katherine A.; Rupp, Bernhard Protein Science, Vol. 12, Issue 9 https://doi.org/10.1110/ps.0350503	journal	September 2003
Optimal description of a protein structure in terms of multiple groups undergoing TLS motion Painter, Jay; Merritt, Ethan A. Acta Crystallographica Section D Biological Crystallography, Vol. 62, Issue 4 https://doi.org/10.1107/S0907444906005270	journal	March 2006
Structural and mechanistic classification of uronic acid-containing polysaccharide lyases Garron, M. -L.; Cygler, M. Glycobiology, Vol. 20, Issue 12 https://doi.org/10.1093/glycob/cwq122	journal	August 2010
DegS and YaeL participate sequentially in the cleavage of RseA to activate the sigma E-dependent extracytoplasmic stress response Alba, B. M. Genes & Development, Vol. 16, Issue 16 https://doi.org/10.1101/gad.1008902	journal	August 2002
The unique set of putative membrane-associated anti-σ factors in Clostridium thermocellum suggests a novel extracellular carbohydrate-sensing mechanism involved in gene regulation: Biomass-sensing anti-σ factors in C. thermocellum Kahel-Raifer, Hamutal; Jindou, Sadanari; Bahari, Liat FEMS Microbiology Letters, Vol. 308, Issue 1 https://doi.org/10.1111/j.1574-6968.2010.01997.x	journal	April 2010
Carbohydrate–Aromatic Interactions in Proteins Hudson, Kieran L.; Bartlett, Gail J.; Diehl, Roger C. Journal of the American Chemical Society, Vol. 137, Issue 48 https://doi.org/10.1021/jacs.5b08424	journal	November 2015
Implementation and performance of SIBYLS: a dual endstation small-angle X-ray scattering and macromolecular crystallography beamline at the Advanced Light Source Classen, Scott; Hura, Greg L.; Holton, James M. Journal of Applied Crystallography, Vol. 46, Issue 1 https://doi.org/10.1107/S0021889812048698	journal	January 2013
The 1.6 Å Resolution Crystal Structure of Nuclear Transport Factor 2 (NTF2) Bullock, Timothy L.; Clarkson, David W.; Kent, Helen M. Journal of Molecular Biology, Vol. 260, Issue 3 https://doi.org/10.1006/jmbi.1996.0411	journal	July 1996
Ab initio electron density determination directly from solution scattering data Grant, Thomas D. Nature Methods, Vol. 15, Issue 3 https://doi.org/10.1038/nmeth.4581	journal	January 2018
Alternative σI/anti-σI factors represent a unique form of bacterial σ/anti-σ complex Wei, Zhen; Chen, Chao; Liu, Ya-Jun Nucleic Acids Research, Vol. 47, Issue 11 https://doi.org/10.1093/nar/gkz355	journal	May 2019
Crystal structure of a bacterial family-III cellulose-binding domain: a general mechanism for attachment to cellulose. Tormo, J.; Lamed, R.; Chirino, A. J. The EMBO Journal, Vol. 15, Issue 21, p. 5739-5751 https://doi.org/10.1002/j.1460-2075.1996.tb00960.x	journal	November 1996
Evolutionary Divergence of Substrate Specificity within the Chymotrypsin-like Serine Protease Fold Perona, John J.; Craik, Charles S. Journal of Biological Chemistry, Vol. 272, Issue 48 https://doi.org/10.1074/jbc.272.48.29987	journal	November 1997
Restoring Low Resolution Structure of Biological Macromolecules from Solution Scattering Using Simulated Annealing Svergun, D. I. Biophysical Journal, Vol. 76, Issue 6, p. 2879-2886 https://doi.org/10.1016/S0006-3495(99)77443-6	journal	June 1999
Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard Terwilliger, Thomas C.; Grosse-Kunstleve, Ralf W.; Afonine, Pavel V. Acta Crystallographica Section D Biological Crystallography, Vol. 64, Issue 1 https://doi.org/10.1107/S090744490705024X	journal	December 2007
Crystal structure of the zinc-bound HhoA protease from Synechocystis sp. PCC 6803 Dong, Wei; Wang, Jia; Niu, Guoqi FEBS Letters, Vol. 590, Issue 19 https://doi.org/10.1002/1873-3468.12416	journal	September 2016
Reconstitution of cellulosome: Research progress and its application in biorefinery Hu, Bin‐Bin; Zhu, Ming‐Jun Biotechnology and Applied Biochemistry, Vol. 66, Issue 5 https://doi.org/10.1002/bab.1804	journal	June 2019
Comparative Protein Structure Modeling Using MODELLER Webb, Benjamin; Sali, Andrej Current Protocols in Bioinformatics, Vol. 54, Issue 1 https://doi.org/10.1002/cpbi.3	journal	June 2016
The emergence of Clostridium thermocellum as a high utility candidate for consolidated bioprocessing applications Akinosho, Hannah; Yee, Kelsey; Close, Dan Frontiers in Chemistry, Vol. 2 https://doi.org/10.3389/fchem.2014.00066	journal	August 2014
Bioconversion of Renewable Plant Biomass. Second-Generation Biofuels: Raw Materials, Biomass Pretreatment, Enzymes, Processes, and Cost Analysis Sinitsyn, Arkadij P.; Sinitsyna, Olga A. Biochemistry (Moscow), Vol. 86, Issue S1 https://doi.org/10.1134/S0006297921140121	journal	January 2021
TRACT revisited: an algebraic solution for determining overall rotational correlation times from cross-correlated relaxation rates Robson, Scott A.; Dağ, Çağdaş; Wu, Hongwei Journal of Biomolecular NMR, Vol. 75, Issue 8-9 https://doi.org/10.1007/s10858-021-00379-5	journal	September 2021
Exploiting structure similarity in refinement: automated NCS and target-structure restraints in BUSTER Smart, Oliver S.; Womack, Thomas O.; Flensburg, Claus Acta Crystallographica Section D Biological Crystallography, Vol. 68, Issue 4 https://doi.org/10.1107/S0907444911056058	journal	March 2012

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