Structural Inhibition of the Colicin D TRNase by the TRNA-mimicking Immunity Protein

Overview

Journal EMBO J

Specialties Biotechnology
Molecular Biology

Date 2004 Mar 12

PMID 15014439

Citations 37

Authors

Marc Graille

Liliana Mora

Richard H Buckingham

Herman Van Tilbeurgh

Miklos de Zamaroczy

Affiliations

Soon will be listed here.

Abstract

Colicins are toxins secreted by Escherichia coli in order to kill their competitors. Colicin D is a 75 kDa protein that consists of a translocation domain, a receptor-binding domain and a cytotoxic domain, which specifically cleaves the anticodon loop of all four tRNA(Arg) isoacceptors, thereby inactivating protein synthesis and leading to cell death. Here we report the 2.0 A resolution crystal structure of the complex between the toxic domain and its immunity protein ImmD. Neither component shows structural homology to known RNases or their inhibitors. In contrast to other characterized colicin nuclease-Imm complexes, the colicin D active site pocket is completely blocked by ImmD, which, by bringing a negatively charged cluster in opposition to a positively charged cluster on the surface of colicin D, appears to mimic the tRNA substrate backbone. Site-directed mutations affecting either the catalytic domain or the ImmD protein have led to the identification of the residues vital for catalytic activity and for the tight colicin D/ImmD interaction that inhibits colicin D toxicity and tRNase catalytic activity.

Citing Articles

The dominant lineage of an emerging pathogen harbours contact-dependent inhibition systems.

Crisan C, Goldberg J Microb Genom. 2025; 11(1).

PMID: 39853206 PMC: 11893273. DOI: 10.1099/mgen.0.001332.

Discovery of antiphage systems in the lactococcal plasmidome.

Grafakou A, Mosterd C, Beck M, Kelleher P, McDonnell B, de Waal P Nucleic Acids Res. 2024; 52(16):9760-9776.

PMID: 39119896 PMC: 11381338. DOI: 10.1093/nar/gkae671.

A Novel Deoxyribonuclease Low-Molecular-Weight Bacteriocin, Carocin S4, from subsp.

Wu H, Derilo R, Hsu S, Hu J, Chuang D Microorganisms. 2023; 11(7).

PMID: 37513026 PMC: 10386115. DOI: 10.3390/microorganisms11071854.

Story of Pore-Forming Proteins from Deadly Disease-Causing Agents to Modern Applications with Evolutionary Significance.

Gupta L, Molla J, Prabhu A Mol Biotechnol. 2023; 66(6):1327-1356.

PMID: 37294530 DOI: 10.1007/s12033-023-00776-1.

Structural basis for the toxic activity of MafB2 from maf genomic island 2 (MGI-2) in N. meningitidis B16B6.

Park S, Jeong S, Ha S Sci Rep. 2023; 13(1):3365.

PMID: 36849501 PMC: 9970974. DOI: 10.1038/s41598-023-30528-9.

References

Kleanthous C, Kuhlmann U, Pommer A, Ferguson N, Radford S, MOORE G . Structural and mechanistic basis of immunity toward endonuclease colicins. Nat Struct Biol. 1999; 6(3):243-52. DOI: 10.1038/6683. View

Terwilliger T, Berendzen J . Automated MAD and MIR structure solution. Acta Crystallogr D Biol Crystallogr. 1999; 55(Pt 4):849-61. PMC: 2746121. DOI: 10.1107/s0907444999000839. View

Ogawa T, Tomita K, Ueda T, Watanabe K, Uozumi T, Masaki H . A cytotoxic ribonuclease targeting specific transfer RNA anticodons. Science. 1999; 283(5410):2097-100. DOI: 10.1126/science.283.5410.2097. View

Kleanthous C, James R, Hemmings A, MOORE G . Protein antibiotics and their inhibitors. Biochem Soc Trans. 1999; 27(2):63-7. DOI: 10.1042/bst0270063. View

Perrakis A, Morris R, Lamzin V . Automated protein model building combined with iterative structure refinement. Nat Struct Biol. 1999; 6(5):458-63. DOI: 10.1038/8263. View

Ko T, Liao C, Ku W, Chak K, Yuan H . The crystal structure of the DNase domain of colicin E7 in complex with its inhibitor Im7 protein. Structure. 1999; 7(1):91-102. DOI: 10.1016/s0969-2126(99)80012-4. View

Lu F, Yuan H, Hsu Y, Chang S, Chak K . Hierarchical order of critical residues on the immunity-determining region of the Im7 protein which confer specific immunity to its cognate colicin. Biochem Biophys Res Commun. 1999; 264(1):69-75. DOI: 10.1006/bbrc.1999.1424. View

Terwilliger T . Reciprocal-space solvent flattening. Acta Crystallogr D Biol Crystallogr. 1999; 55(Pt 11):1863-71. PMC: 2745881. DOI: 10.1107/s0907444999010033. View

Kaufmann G . Anticodon nucleases. Trends Biochem Sci. 2000; 25(2):70-4. DOI: 10.1016/s0968-0004(99)01525-x. View

10.

Tomita K, Ogawa T, Uozumi T, Watanabe K, Masaki H . A cytotoxic ribonuclease which specifically cleaves four isoaccepting arginine tRNAs at their anticodon loops. Proc Natl Acad Sci U S A. 2000; 97(15):8278-83. PMC: 26938. DOI: 10.1073/pnas.140213797. View

11.

Kuhlmann U, Pommer A, MOORE G, James R, Kleanthous C . Specificity in protein-protein interactions: the structural basis for dual recognition in endonuclease colicin-immunity protein complexes. J Mol Biol. 2000; 301(5):1163-78. DOI: 10.1006/jmbi.2000.3945. View

12.

Carr S, Walker D, James R, Kleanthous C, Hemmings A . Inhibition of a ribosome-inactivating ribonuclease: the crystal structure of the cytotoxic domain of colicin E3 in complex with its immunity protein. Structure. 2000; 8(9):949-60. DOI: 10.1016/s0969-2126(00)00186-6. View

13.

Delagoutte B, Moras D, Cavarelli J . tRNA aminoacylation by arginyl-tRNA synthetase: induced conformations during substrates binding. EMBO J. 2000; 19(21):5599-610. PMC: 305789. DOI: 10.1093/emboj/19.21.5599. View

14.

Lazdunski C, Bouveret E, Rigal A, Journet L, Lloubes R, Benedetti H . Colicin import into Escherichia coli cells requires the proximity of the inner and outer membranes and other factors. Int J Med Microbiol. 2000; 290(4-5):337-44. DOI: 10.1016/S1438-4221(00)80037-5. View

15.

de Zamaroczy M, Mora L, Lecuyer A, Geli V, Buckingham R . Cleavage of colicin D is necessary for cell killing and requires the inner membrane peptidase LepB. Mol Cell. 2001; 8(1):159-68. DOI: 10.1016/s1097-2765(01)00276-3. View

16.

Ahmed S, Byrne M, Jensen M, Hines H, Brueggemann E, Smith L . Enzymatic autocatalysis of botulinum A neurotoxin light chain. J Protein Chem. 2001; 20(3):221-31. DOI: 10.1023/a:1010952025677. View

17.

Soelaiman S, Jakes K, Wu N, Li C, Shoham M . Crystal structure of colicin E3: implications for cell entry and ribosome inactivation. Mol Cell. 2001; 8(5):1053-62. DOI: 10.1016/s1097-2765(01)00396-3. View

18.

Roth M, Carpentier P, Kaikati O, Joly J, Charrault P, Pirocchi M . FIP: a highly automated beamline for multiwavelength anomalous diffraction experiments. Acta Crystallogr D Biol Crystallogr. 2002; 58(Pt 5):805-14. DOI: 10.1107/s0907444902003943. View

19.

Ferguson A, Deisenhofer J . TonB-dependent receptors-structural perspectives. Biochim Biophys Acta. 2002; 1565(2):318-32. DOI: 10.1016/s0005-2736(02)00578-3. View

20.

Zakharov S, Cramer W . Colicin crystal structures: pathways and mechanisms for colicin insertion into membranes. Biochim Biophys Acta. 2002; 1565(2):333-46. DOI: 10.1016/s0005-2736(02)00579-5. View