The hypothetical protein P47 of Clostridium botulinum E1 strain Beluga has a structural topology similar to bactericidal/permeability-increasing protein

Lam, Kwok-ho; Qi, Ruifeng; Liu, Shun; Kroh, Amelie; Yao, Guorui; Perry, Kay; Rummel, Andreas; Jin, Rongsheng

doi:10.1016/j.toxicon.2017.10.012

The hypothetical protein P47 of Clostridium botulinum E1 strain Beluga has a structural topology similar to bactericidal/permeability-increasing protein

Journal Article · Mon Oct 16 00:00:00 EDT 2017 · Toxicon

DOI:https://doi.org/10.1016/j.toxicon.2017.10.012· OSTI ID:1434740

^[1]; Qi, Ruifeng ^[1]; Liu, Shun ^[1]; Kroh, Amelie ^[2]; ^[1]; Perry, Kay ^[3]; ^[2]; ^[1]

Univ. of California, Irvine, CA (United States)
Medizinische Hochschule Hannover (Germany). Inst. für Toxikologie
Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS), Northeastern Collaborative Access Team (NE-CAT) and Department of Chemistry and Chemical Biology; Cornell Univ., Ithaca, NY (United States)

Botulinum neurotoxins (BoNTs) are causative agents of the life-threatening disease botulism. They are naturally produced by species of the bacteria Clostridium botulinum as stable and non-covalent complexes, in which the BoNT molecule is assembled with several auxiliary non-toxic proteins. Some BoNT serotypes, represented by the well-studied BoNT serotype A (BoNT/A), are produced by Clostridium strains that carry the ha gene cluster, which encodes four neurotoxin-associated proteins (NTNHA, HA17, HA33, and HA70) that play an important role to deliver and protect BoNTs in the gastrointestinal tract during oral intoxication. In contrast, BoNT/E- and BoNT/F-producing strains carry a distinct gene cluster that encodes five proteins (NTNHA, P47, OrfX1, OrfX2, and OrfX3, termed the $orfX$ cluster). The structures and functions of these proteins remain largely unknown. In this paper, we report the crystal structure of P47 resolved at 2.8 Å resolution. Surprisingly, P47 displays a structural topology that is similar to bactericidal/permeability-increasing (BPI) like proteins, which were previously identified only in eukaryotes. The similarity of a hydrophobic cleft of P47 with the phospholipid-binding groove of BPI suggests that P47 might be involved in lipid association to exert its function. Consistently, P47 associates and induces aggregation of asolectin-containing liposomes in a protein- and lipid-concentration dependent manner. These findings laid the foundation for future structural and functional studies of the potential roles of P47 and OrfX proteins in facilitating oral intoxication of BoNTs.

View Accepted Manuscript (DOE)

Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States). Advanced Photon Source (APS); SLAC National Accelerator Laboratory, Menlo Park, CA (United States). Stanford Synchrotron Radiation Lightsource (SSRL)

Sponsoring Organization:: National Institute of Allergy and Infectious Diseases (NIAID); National Institute of General Medical Sciences (NIGMS); National Institutes of Health (NIH); Swiss Federal Office for Civil Protection (FOCP); USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22); USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)

Grant/Contract Number:: AC02-06CH11357; AC02-76SF00515

OSTI ID:: 1434740

Alternate ID(s):: OSTI ID: 1549483

Journal Information:: Toxicon, Journal Name: Toxicon Journal Issue: C Vol. 147; ISSN 0041-0101

Country of Publication:: United States

Language:: ENGLISH

References (45)

The BPI/LBP family of proteins: A structural analysis of conserved regions: Analysis of conserved regions of BPI and LBP 907 Beamer, Lesa J.; Carroll, Stephen F.; Eisenberg, David Protein Science, Vol. 7, Issue 4 https://doi.org/10.1002/pro.5560070408	journal	April 1998
Atomic Structures of the Human Immunophilin FKBP-12 Complexes with FK506 and Rapamycin Van Duyne, Gregory D.; Standaert, Robert F.; Karplus, P. Andrew Journal of Molecular Biology, Vol. 229, Issue 1 https://doi.org/10.1006/jmbi.1993.1012	journal	January 1993
The TULIP superfamily of eukaryotic lipid-binding proteins as a mediator of lipid sensing and transport Alva, Vikram; Lupas, Andrei N. Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids, Vol. 1861, Issue 8 https://doi.org/10.1016/j.bbalip.2016.01.016	journal	August 2016
Small-angle X-ray scattering reveals structural dynamics of the botulinum neurotoxin associating protein, nontoxic nonhemagglutinin Sagane, Yoshimasa; Miyashita, Shin-Ichiro; Miyata, Keita Biochemical and Biophysical Research Communications, Vol. 425, Issue 2 https://doi.org/10.1016/j.bbrc.2012.07.077	journal	August 2012
High-resolution crystal structure of HA33 of botulinum neurotoxin type B progenitor toxin complex Lee, Kwangkook; Lam, Kwok-Ho; Kruel, Anna Magdalena Biochemical and Biophysical Research Communications, Vol. 446, Issue 2 https://doi.org/10.1016/j.bbrc.2014.03.008	journal	April 2014
The Crystal Structure of Lipopolysaccharide Binding Protein Reveals the Location of a Frequent Mutation that Impairs Innate Immunity Eckert, Jana K.; Kim, Young J.; Kim, Jung I. Immunity, Vol. 39, Issue 4 https://doi.org/10.1016/j.immuni.2013.09.005	journal	October 2013
Structural Basis of the pH-Dependent Assembly of a Botulinum Neurotoxin Complex Matsui, Tsutomu; Gu, Shenyan; Lam, Kwok-ho Journal of Molecular Biology, Vol. 426, Issue 22 https://doi.org/10.1016/j.jmb.2014.09.009	journal	November 2014
Architecture of the botulinum neurotoxin complex: a molecular machine for protection and delivery Lam, Kwok-Ho; Jin, Rongsheng Current Opinion in Structural Biology, Vol. 31 https://doi.org/10.1016/j.sbi.2015.03.013	journal	April 2015
Inhibiting oral intoxication of botulinum neurotoxin A complex by carbohydrate receptor mimics Lee, Kwangkook; Lam, Kwok-Ho; Kruel, Anna-Magdalena Toxicon, Vol. 107 https://doi.org/10.1016/j.toxicon.2015.08.003	journal	December 2015
Comparative Role of Neurotoxin-Associated Proteins in the Structural Stability and Endopeptidase Activity of Botulinum Neurotoxin Complex Types A and E ^† Kukreja, Roshan V.; Singh, Bal Ram Biochemistry, Vol. 46, Issue 49 https://doi.org/10.1021/bi701564f	journal	December 2007
Free R value: a novel statistical quantity for assessing the accuracy of crystal structures Brünger, Axel T. Nature, Vol. 355, Issue 6359 https://doi.org/10.1038/355472a0	journal	January 1992
The use of differential scanning fluorimetry to detect ligand interactions that promote protein stability Niesen, Frank H.; Berglund, Helena; Vedadi, Masoud Nature Protocols, Vol. 2, Issue 9 https://doi.org/10.1038/nprot.2007.321	journal	September 2007
Botulinum neurotoxins: genetic, structural and mechanistic insights Rossetto, Ornella; Pirazzini, Marco; Montecucco, Cesare Nature Reviews Microbiology, Vol. 12, Issue 8 https://doi.org/10.1038/nrmicro3295	journal	June 2014
Molecular Assembly of Clostridium botulinum progenitor M complex of type E Eswaramoorthy, Subramaniam; Sun, Jingchuan; Li, Huilin Scientific Reports, Vol. 5, Issue 1 https://doi.org/10.1038/srep17795	journal	December 2015
Bioinformatics of the TULIP domain superfamily Kopec, Klaus O.; Alva, Vikram; Lupas, Andrei N. Biochemical Society Transactions, Vol. 39, Issue 4 https://doi.org/10.1042/BST0391033	journal	July 2011
LBP/BPI proteins and their relatives: conservation over evolution and roles in mutualism Krasity, Benjamin C.; Troll, Joshua V.; Weiss, Jerrold P. Biochemical Society Transactions, Vol. 39, Issue 4 https://doi.org/10.1042/BST0391039	journal	July 2011
Bactericidal/permeability-increasing protein (BPI) and lipopolysaccharide-binding protein (LBP): structure, function and regulation in host defence against Gram-negative bacteria Weiss, J. Biochemical Society Transactions, Vol. 31, Issue 4 https://doi.org/10.1042/bst0310785	journal	August 2003
Molecular assembly of botulinum neurotoxin progenitor complexes Benefield, D. A.; Dessain, S. K.; Shine, N. Proceedings of the National Academy of Sciences, Vol. 110, Issue 14 https://doi.org/10.1073/pnas.1222139110	journal	March 2013
Conserved SMP domains of the ERMES complex bind phospholipids and mediate tether assembly AhYoung, Andrew P.; Jiang, Jiansen; Zhang, Jiang Proceedings of the National Academy of Sciences, Vol. 112, Issue 25 https://doi.org/10.1073/pnas.1422363112	journal	June 2015
Electrostatics of nanosystems: Application to microtubules and the ribosome Baker, N. A.; Sept, D.; Joseph, S. Proceedings of the National Academy of Sciences, Vol. 98, Issue 18, p. 10037-10041 https://doi.org/10.1073/pnas.181342398	journal	August 2001
Crystal Structure of Clostridium botulinum Whole Hemagglutinin Reveals a Huge Triskelion-shaped Molecular Complex Amatsu, Sho; Sugawara, Yo; Matsumura, Takuhiro Journal of Biological Chemistry, Vol. 288, Issue 49 https://doi.org/10.1074/jbc.M113.521179	journal	December 2013
Botulinum hemagglutinin disrupts the intercellular epithelial barrier by directly binding E-cadherin Sugawara, Yo; Matsumura, Takuhiro; Takegahara, Yuki Journal of Cell Biology, Vol. 189, Issue 4 https://doi.org/10.1083/jcb.200910119	journal	May 2010
The Pfam Protein Families Database Bateman, A. Nucleic Acids Research, Vol. 30, Issue 1 https://doi.org/10.1093/nar/30.1.276	journal	January 2002
Flexible Structural Neighborhood--a database of protein structural similarities and alignments Li, Z. Nucleic Acids Research, Vol. 34, Issue 90001 https://doi.org/10.1093/nar/gkj124	journal	January 2006
PROMALS3D: a tool for multiple protein sequence and structure alignments Pei, Jimin; Kim, Bong-Hyun; Grishin, Nick V. Nucleic Acids Research, Vol. 36, Issue 7 https://doi.org/10.1093/nar/gkn072	journal	February 2008
Deciphering key features in protein structures with the new ENDscript server Robert, Xavier; Gouet, Patrice Nucleic Acids Research, Vol. 42, Issue W1 https://doi.org/10.1093/nar/gku316	journal	April 2014
Dali server update Holm, Liisa; Laakso, Laura M. Nucleic Acids Research, Vol. 44, Issue W1 https://doi.org/10.1093/nar/gkw357	journal	April 2016
Expression of botulinum neurotoxins A and E, and associated non-toxin genes, during the transition phase and stability at high temperature: analysis by quantitative reverse transcription-PCR Couesnon, Aurélie; Raffestin, Stéphanie; Popoff, Michel R. Microbiology, Vol. 152, Issue 3 https://doi.org/10.1099/mic.0.28561-0	journal	March 2006
A graphical user interface to the CCP 4 program suite Potterton, Elizabeth; Briggs, Peter; Turkenburg, Maria Acta Crystallographica Section D Biological Crystallography, Vol. 59, Issue 7 https://doi.org/10.1107/S0907444903008126	journal	June 2003
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
MolProbity : all-atom structure validation for macromolecular crystallography Chen, Vincent B.; Arendall, W. Bryan; Headd, Jeffrey J. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 1 https://doi.org/10.1107/S0907444909042073	journal	December 2009
XDS Kabsch, Wolfgang Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2 https://doi.org/10.1107/S0907444909047337	journal	January 2010
PHENIX: a comprehensive Python-based system for macromolecular structure solution Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221 https://doi.org/10.1107/S0907444909052925	journal	January 2010
Gene arrangement in the upstream region of Clostridium botulinum type E and Clostridium butyricum BL6340 progenitor toxin genes is different from that of other types Kubota, Toru; Yonekura, Noriyuki; Hariya, Yasushi FEMS Microbiology Letters, Vol. 158, Issue 2 https://doi.org/10.1111/j.1574-6968.1998.tb12823.x	journal	January 1998
Nucleotide sequence and transcriptional analysis of the type A2 neurotoxin gene cluster in Clostridium botulinum Dineen, Sean S.; Bradshaw, Marite; Karasek, Charles E. FEMS Microbiology Letters, Vol. 235, Issue 1 https://doi.org/10.1111/j.1574-6968.2004.tb09561.x	journal	June 2004
Botulinum Neurotoxin Is Shielded by NTNHA in an Interlocked Complex Gu, S.; Rumpel, S.; Zhou, J. Science, Vol. 335, Issue 6071 https://doi.org/10.1126/science.1214270	journal	February 2012
Molecular basis for disruption of E-cadherin adhesion by botulinum neurotoxin A complex Lee, K.; Zhong, X.; Gu, S. Science, Vol. 344, Issue 6190 https://doi.org/10.1126/science.1253823	journal	June 2014
Crystal Structure of Human BPI and Two Bound Phospholipids at 2.4 Angstrom Resolution Beamer, L. J. Science, Vol. 276, Issue 5320 https://doi.org/10.1126/science.276.5320.1861	journal	June 1997
Expression of the Clostridium botulinum A2 Neurotoxin Gene Cluster Proteins and Characterization of the A2 Complex Lin, Guangyun; Tepp, William H.; Pier, Christina L. Applied and Environmental Microbiology, Vol. 76, Issue 1 https://doi.org/10.1128/AEM.01882-09	journal	November 2009
Analysis of Neurotoxin Cluster Genes in Clostridium botulinum Strains Producing Botulinum Neurotoxin Serotype A Subtypes Jacobson, Mark J.; Lin, Guangyun; Raphael, Brian Applied and Environmental Microbiology, Vol. 74, Issue 9 https://doi.org/10.1128/AEM.02828-07	journal	March 2008
Characterization of Botulinum Progenitor Toxins by Mass Spectrometry Hines, Harry B.; Lebeda, Frank; Hale, Martha Applied and Environmental Microbiology, Vol. 71, Issue 8 https://doi.org/10.1128/AEM.71.8.4478-4486.2005	journal	August 2005
Comparative genomic analyses reveal broad diversity in botulinum-toxin-producing Clostridia Williamson, Charles H. D.; Sahl, Jason W.; Smith, Theresa J. BMC Genomics, Vol. 17, Issue 1 https://doi.org/10.1186/s12864-016-2502-z	journal	March 2016
Structure of a Bimodular Botulinum Neurotoxin Complex Provides Insights into Its Oral Toxicity Lee, Kwangkook; Gu, Shenyan; Jin, Lei PLoS Pathogens, Vol. 9, Issue 10 https://doi.org/10.1371/journal.ppat.1003690	journal	October 2013
Botulinum Neurotoxin A Complex Recognizes Host Carbohydrates through Its Hemagglutinin Component Yao, Guorui; Lee, Kwangkook; Gu, Shenyan Toxins, Vol. 6, Issue 2 https://doi.org/10.3390/toxins6020624	journal	February 2014
Characterization of Hemagglutinin Negative Botulinum Progenitor Toxins Kalb, Suzanne; Baudys, Jakub; Smith, Theresa Toxins, Vol. 9, Issue 6 https://doi.org/10.3390/toxins9060193	journal	June 2017

Cited By (5)

Remote homology searches identify bacterial homologues of eukaryotic lipid transfer proteins, including Chorein-N domains in TamB and AsmA and Mdm31p Levine, Timothy P. BMC Molecular and Cell Biology, Vol. 20, Issue 1 https://doi.org/10.1186/s12860-019-0226-z	journal	October 2019
Botulinum Neurotoxin Diversity from a Gene-Centered View Benoit, Roger Toxins, Vol. 10, Issue 8 https://doi.org/10.3390/toxins10080310	journal	August 2018
A neurotoxin that specifically targets Anopheles mosquitoes Contreras, Estefania; Masuyer, Geoffrey; Qureshi, Nadia Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-10732-w	journal	June 2019
Revisiting the Evolution and Taxonomy of Clostridia, a Phylogenomic Update Cruz-Morales, Pablo; Orellana, Camila A.; Moutafis, George Genome Biology and Evolution, Vol. 11, Issue 7 https://doi.org/10.1093/gbe/evz096	journal	May 2019
Type E Botulinum Neurotoxin-Producing Clostridium butyricum Strains Are Aerotolerant during Vegetative Growth Camerini, Serena; Marcocci, Lucia; Picarazzi, Lara mSystems, Vol. 4, Issue 2 https://doi.org/10.1128/msystems.00299-18	journal	April 2019

Similar Records

Crystal structures of OrfX1, OrfX2 and the OrfX1–OrfX3 complex from the orfX gene cluster of botulinum neurotoxin E1

Journal Article · Tue Jan 17 19:00:00 EST 2023 · FEBS Letters · OSTI ID:2423355

Botulinum Neurotoxin Is Shielded by NTNHA in an Interlocked Complex

Journal Article · Wed Mar 28 00:00:00 EDT 2012 · Science · OSTI ID:1035706

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
Bactericidal/permeability-increasing protein
Botulinum neurotoxin
Crystal structure
Lipid binding
P47
Toxin complex
orfX gene cluster

The hypothetical protein P47 of Clostridium botulinum E1 strain Beluga has a structural topology similar to bactericidal/permeability-increasing protein

Citation Formats

References (45)

Cited By (5)

Similar Records

Related Subjects