Characterisation of a mobile protein-binding epitope in the translocation domain of colicin E9

The 61 kDa colicin E9 protein toxin enters the cytoplasm of susceptible cells by interacting with outer membrane and periplasmic helper proteins, and kills them by hydrolysing their DNA. The membrane translocation function is located in the N-terminal domain of the colicin, with a key signal sequenc...

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Veröffentlicht in:Journal of biomolecular NMR 2004-09, Vol.30 (1), p.81-96
Hauptverfasser: Macdonald, Colin J, Tozawa, Kaeko, Collins, Emily S, Penfold, Christopher N, James, Richard, Kleanthous, Colin, Clayden, Nigel J, Moore, Geoffrey R
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container_end_page 96
container_issue 1
container_start_page 81
container_title Journal of biomolecular NMR
container_volume 30
creator Macdonald, Colin J
Tozawa, Kaeko
Collins, Emily S
Penfold, Christopher N
James, Richard
Kleanthous, Colin
Clayden, Nigel J
Moore, Geoffrey R
description The 61 kDa colicin E9 protein toxin enters the cytoplasm of susceptible cells by interacting with outer membrane and periplasmic helper proteins, and kills them by hydrolysing their DNA. The membrane translocation function is located in the N-terminal domain of the colicin, with a key signal sequence being a pentapeptide region that governs the interaction with the helper protein TolB (the TolB box). Previous NMR studies (Collins et al., 2002 J. Mol. Biol. 318, 787-804) have shown that the N-terminal 83 residues of colicin E9, which includes the TolB box, is largely unstructured and highly flexible. In order to further define the properties of this region we have studied a fusion protein containing residues 1-61 of colicin E9 connected to the N-terminus of the E9 DNase by an eight-residue linking sequence. 53 of the expected 58 backbone NH resonances for the first 61 residues and all of the expected 7 backbone NH resonances of the linking sequence were assigned with 3D (1)H-(13)C-(15)N NMR experiments, and the backbone dynamics of these regions investigated through measurement of (1)H-(15)N relaxation properties. Reduced spectral density mapping, extended Lipari-Szabo modelling, and fitting backbone R(2) relaxation rates to a polymer dynamics model identifies three clusters of interacting residues, each containing a tryptophan. Each of these clusters is perturbed by TolB binding to the intact colicin, showing that the significant region for TolB binding extends beyond the recognized five amino acids of the TolB box and demonstrating that the binding epitope for TolB involves a considerable degree of order within an otherwise disordered and flexible domain. Abbreviations : Im9, the immunity protein for colicin E9; E9 DNase, the endonuclease domain of colicin E9; HSQC, heteronuclear single quantum coherence; ppm, parts per million; DSS, 2,2-(dimethylsilyl)propanesulfonic acid; TSP, sodium 3-trimethylsilypropionate; T(1 - 61)-DNase fusion protein, residues 1-61 of colicin E9 connected to the N-terminus of the E9 DNase by an eight residue thrombin cleavage sequence.
doi_str_mv 10.1023/B:JNMR.0000042963.71790.19
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The membrane translocation function is located in the N-terminal domain of the colicin, with a key signal sequence being a pentapeptide region that governs the interaction with the helper protein TolB (the TolB box). Previous NMR studies (Collins et al., 2002 J. Mol. Biol. 318, 787-804) have shown that the N-terminal 83 residues of colicin E9, which includes the TolB box, is largely unstructured and highly flexible. In order to further define the properties of this region we have studied a fusion protein containing residues 1-61 of colicin E9 connected to the N-terminus of the E9 DNase by an eight-residue linking sequence. 53 of the expected 58 backbone NH resonances for the first 61 residues and all of the expected 7 backbone NH resonances of the linking sequence were assigned with 3D (1)H-(13)C-(15)N NMR experiments, and the backbone dynamics of these regions investigated through measurement of (1)H-(15)N relaxation properties. Reduced spectral density mapping, extended Lipari-Szabo modelling, and fitting backbone R(2) relaxation rates to a polymer dynamics model identifies three clusters of interacting residues, each containing a tryptophan. Each of these clusters is perturbed by TolB binding to the intact colicin, showing that the significant region for TolB binding extends beyond the recognized five amino acids of the TolB box and demonstrating that the binding epitope for TolB involves a considerable degree of order within an otherwise disordered and flexible domain. Abbreviations : Im9, the immunity protein for colicin E9; E9 DNase, the endonuclease domain of colicin E9; HSQC, heteronuclear single quantum coherence; ppm, parts per million; DSS, 2,2-(dimethylsilyl)propanesulfonic acid; TSP, sodium 3-trimethylsilypropionate; T(1 - 61)-DNase fusion protein, residues 1-61 of colicin E9 connected to the N-terminus of the E9 DNase by an eight residue thrombin cleavage sequence.</description><identifier>ISSN: 0925-2738</identifier><identifier>EISSN: 1573-5001</identifier><identifier>DOI: 10.1023/B:JNMR.0000042963.71790.19</identifier><identifier>PMID: 15452437</identifier><language>eng</language><publisher>Netherlands: Springer Nature B.V</publisher><subject>Amino Acid Sequence ; Amino acids ; Binding Sites ; Biological Transport, Active ; Carbon Isotopes ; Colicins - chemistry ; Colicins - genetics ; Colicins - metabolism ; Deoxyribonucleases - metabolism ; Epitopes - metabolism ; Escherichia coli - genetics ; Escherichia coli - metabolism ; Escherichia coli Proteins - chemistry ; Escherichia coli Proteins - genetics ; Escherichia coli Proteins - metabolism ; Molecular Weight ; Nitrogen Isotopes ; Nuclear Magnetic Resonance, Biomolecular ; Polymers ; Protein Binding ; Protein Conformation ; Protein Structure, Tertiary ; Proteins ; Quantum Theory ; Residues ; Toxins ; Translocation</subject><ispartof>Journal of biomolecular NMR, 2004-09, Vol.30 (1), p.81-96</ispartof><rights>Kluwer Academic Publishers 2004</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c373t-6217ee5a857d109c99e7f434c91d38cf4ccf333222d3feab1a13c6fe3cd4fd233</citedby></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,780,784,27924,27925</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/15452437$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Macdonald, Colin J</creatorcontrib><creatorcontrib>Tozawa, Kaeko</creatorcontrib><creatorcontrib>Collins, Emily S</creatorcontrib><creatorcontrib>Penfold, Christopher N</creatorcontrib><creatorcontrib>James, Richard</creatorcontrib><creatorcontrib>Kleanthous, Colin</creatorcontrib><creatorcontrib>Clayden, Nigel J</creatorcontrib><creatorcontrib>Moore, Geoffrey R</creatorcontrib><title>Characterisation of a mobile protein-binding epitope in the translocation domain of colicin E9</title><title>Journal of biomolecular NMR</title><addtitle>J Biomol NMR</addtitle><description>The 61 kDa colicin E9 protein toxin enters the cytoplasm of susceptible cells by interacting with outer membrane and periplasmic helper proteins, and kills them by hydrolysing their DNA. 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Reduced spectral density mapping, extended Lipari-Szabo modelling, and fitting backbone R(2) relaxation rates to a polymer dynamics model identifies three clusters of interacting residues, each containing a tryptophan. Each of these clusters is perturbed by TolB binding to the intact colicin, showing that the significant region for TolB binding extends beyond the recognized five amino acids of the TolB box and demonstrating that the binding epitope for TolB involves a considerable degree of order within an otherwise disordered and flexible domain. 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The membrane translocation function is located in the N-terminal domain of the colicin, with a key signal sequence being a pentapeptide region that governs the interaction with the helper protein TolB (the TolB box). Previous NMR studies (Collins et al., 2002 J. Mol. Biol. 318, 787-804) have shown that the N-terminal 83 residues of colicin E9, which includes the TolB box, is largely unstructured and highly flexible. In order to further define the properties of this region we have studied a fusion protein containing residues 1-61 of colicin E9 connected to the N-terminus of the E9 DNase by an eight-residue linking sequence. 53 of the expected 58 backbone NH resonances for the first 61 residues and all of the expected 7 backbone NH resonances of the linking sequence were assigned with 3D (1)H-(13)C-(15)N NMR experiments, and the backbone dynamics of these regions investigated through measurement of (1)H-(15)N relaxation properties. Reduced spectral density mapping, extended Lipari-Szabo modelling, and fitting backbone R(2) relaxation rates to a polymer dynamics model identifies three clusters of interacting residues, each containing a tryptophan. Each of these clusters is perturbed by TolB binding to the intact colicin, showing that the significant region for TolB binding extends beyond the recognized five amino acids of the TolB box and demonstrating that the binding epitope for TolB involves a considerable degree of order within an otherwise disordered and flexible domain. Abbreviations : Im9, the immunity protein for colicin E9; E9 DNase, the endonuclease domain of colicin E9; HSQC, heteronuclear single quantum coherence; ppm, parts per million; DSS, 2,2-(dimethylsilyl)propanesulfonic acid; TSP, sodium 3-trimethylsilypropionate; T(1 - 61)-DNase fusion protein, residues 1-61 of colicin E9 connected to the N-terminus of the E9 DNase by an eight residue thrombin cleavage sequence.</abstract><cop>Netherlands</cop><pub>Springer Nature B.V</pub><pmid>15452437</pmid><doi>10.1023/B:JNMR.0000042963.71790.19</doi><tpages>16</tpages></addata></record>
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subjects Amino Acid Sequence
Amino acids
Binding Sites
Biological Transport, Active
Carbon Isotopes
Colicins - chemistry
Colicins - genetics
Colicins - metabolism
Deoxyribonucleases - metabolism
Epitopes - metabolism
Escherichia coli - genetics
Escherichia coli - metabolism
Escherichia coli Proteins - chemistry
Escherichia coli Proteins - genetics
Escherichia coli Proteins - metabolism
Molecular Weight
Nitrogen Isotopes
Nuclear Magnetic Resonance, Biomolecular
Polymers
Protein Binding
Protein Conformation
Protein Structure, Tertiary
Proteins
Quantum Theory
Residues
Toxins
Translocation
title Characterisation of a mobile protein-binding epitope in the translocation domain of colicin E9
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