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PMID: 19217396 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

Crystal structure of the N-terminal domain of the secretin GspD from ETEC determined with the assistance of a nanobody.

Structure (London, England : 1993) ·Vol. 17 ·No. 2 ·2009-02-13 ·Pages 255-65

Korotkov KV, Pardon E, Steyaert J, Hol WG

Abstract

Secretins are among the largest bacterial outer membrane proteins known. Here we report the crystal structure of the periplasmic N-terminal domain of GspD (peri-GspD) from the type 2 secretion system (T2SS) secretin in complex with a nanobody, the VHH domain of a heavy-chain camelid antibody. Two different crystal forms contained the same compact peri-GspD:nanobody heterotetramer. The nanobody contacts peri-GspD mainly via CDR3 and framework residues. The peri-GspD structure reveals three subdomains, with the second and third subdomains exhibiting the KH fold which also occurs in ring-forming proteins of the type 3 secretion system. The first subdomain of GspD is related to domains in phage tail proteins and outer membrane TonB-dependent receptors. A dodecameric peri-GspD model is proposed in which a solvent-accessible beta strand of the first subdomain interacts with secreted proteins and/or T2SS partner proteins by beta strand complementation.

MeSH Terms
Amino Acid Sequence Crystallography, X-Ray Enterotoxigenic Escherichia coli/chemistry Escherichia coli Proteins/chemistry,metabolism Immunoglobulin Heavy Chains/chemistry,metabolism Models, Biological Models, Molecular Molecular Sequence Data Porins/chemistry,metabolism Protein Binding Protein Multimerization/physiology Protein Structure, Quaternary Protein Structure, Secondary Protein Structure, Tertiary Secretin/chemistry,metabolism Sequence Homology, Amino Acid
Chemicals
Escherichia coli Proteins GspD protein, E coli Immunoglobulin Heavy Chains Porins Secretin
Authors & Affiliations
4 authors, click to expand affiliations / ORCID
Korotkov Konstantin V
Department of Biochemistry, Biomolecular Structure Center, University of Washington, Seattle, WA 98195, USA.
Pardon Els
Steyaert Jan
Hol Wim G J
References (68)
68 references, click to expand
  1. Complementation of deletion mutations in a cloned functional cluster of Erwinia chrysanthemi out genes with Erwinia carotovora out homologues reveals OutC and OutD as candidate gatekeepers of species-specific secretion of proteins via the type II pathway.
    Mol Microbiol. 1996 Apr;20(1):175-90 PMID: 8861215
  2. Single domain camel antibodies: current status.
    J Biotechnol. 2001 Jun;74(4):277-302 PMID: 11526908
  3. The crystal structure of a binary complex of two pseudopilins: EpsI and EpsJ from the type 2 secretion system of Vibrio vulnificus.
    J Mol Biol. 2008 Jan 11;375(2):471-86 PMID: 18022192
  4. Conformation of protein secreted across bacterial outer membranes: a study of enterotoxin translocation from Vibrio cholerae.
    Proc Natl Acad Sci U S A. 1987 Nov;84(21):7418-22 PMID: 3478701
  5. The pre-mRNA binding K protein contains a novel evolutionarily conserved motif.
    Nucleic Acids Res. 1993 Mar 11;21(5):1193-8 PMID: 8464704
  6. Three camelid VHH domains in complex with porcine pancreatic alpha-amylase. Inhibition and versatility of binding topology.
    J Biol Chem. 2002 Jun 28;277(26):23645-50 PMID: 11960990
  7. Beta-lactamase inhibitors derived from single-domain antibody fragments elicited in the camelidae.
    Antimicrob Agents Chemother. 2001 Oct;45(10):2807-12 PMID: 11557473
  8. Structural characterization of the molecular platform for type III secretion system assembly.
    Nature. 2005 Jun 2;435(7042):702-7 PMID: 15931226
  9. Structural and functional studies of EpsC, a crucial component of the type 2 secretion system from Vibrio cholerae.
    J Mol Biol. 2006 Oct 20;363(2):311-21 PMID: 16978643
  10. Optimal description of a protein structure in terms of multiple groups undergoing TLS motion.
    Acta Crystallogr D Biol Crystallogr. 2006 Apr;62(Pt 4):439-50 PMID: 16552146
  11. Type II secretion: from structure to function.
    FEMS Microbiol Lett. 2006 Feb;255(2):175-86 PMID: 16448494
  12. The C-terminal domain of the Pseudomonas secretin XcpQ forms oligomeric rings with pore activity.
    J Mol Biol. 1999 Dec 17;294(5):1169-79 PMID: 10600375
  13. A beta strand lock exchange for signal transduction in TonB-dependent transducers on the basis of a common structural motif.
    Structure. 2007 Nov;15(11):1383-91 PMID: 17997964
  14. Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions.
    Acta Crystallogr D Biol Crystallogr. 2004 Dec;60(Pt 12 Pt 1):2256-68 PMID: 15572779
  15. General secretion pathway (eps) genes required for toxin secretion and outer membrane biogenesis in Vibrio cholerae.
    J Bacteriol. 1997 Nov;179(22):6994-7003 PMID: 9371445
  16. Secretin PulD: association with pilot PulS, structure, and ion-conducting channel formation.
    Proc Natl Acad Sci U S A. 1999 Jul 6;96(14):8173-7 PMID: 10393967
  17. Translocation of a folded protein across the outer membrane in Escherichia coli.
    Proc Natl Acad Sci U S A. 1992 Dec 15;89(24):12058-62 PMID: 1465440
  18. Enterotoxigenic Escherichia coli in developing countries: epidemiology, microbiology, clinical features, treatment, and prevention.
    Clin Microbiol Rev. 2005 Jul;18(3):465-83 PMID: 16020685
  19. Atomic structures of the human immunophilin FKBP-12 complexes with FK506 and rapamycin.
    J Mol Biol. 1993 Jan 5;229(1):105-24 PMID: 7678431
  20. Crystal structure of a cholera toxin-related heat-labile enterotoxin from E. coli.
    Nature. 1991 May 30;351(6325):371-7 PMID: 2034287
  21. Intermolecular interactions between the A and B subunits of heat-labile enterotoxin from Escherichia coli promote holotoxin assembly and stability in vivo.
    Proc Natl Acad Sci U S A. 1992 Dec 15;89(24):12140-4 PMID: 1465452
  22. Nuclear magnetic resonance solution structure of the periplasmic signalling domain of the TonB-dependent outer membrane transporter FecA from Escherichia coli.
    Mol Microbiol. 2005 Dec;58(5):1226-37 PMID: 16313612
  23. Mechanism of toxin secretion by Vibrio cholerae investigated in strains harboring plasmids that encode heat-labile enterotoxins of Escherichia coli.
    Proc Natl Acad Sci U S A. 1984 Dec;81(24):7752-6 PMID: 6393126
  24. Vibrio spp. secrete proaerolysin as a folded dimer without the need for disulphide bond formation.
    Mol Microbiol. 1995 Sep;17(6):1035-44 PMID: 8594324
  25. Essential role of a sodium dodecyl sulfate-resistant protein IV multimer in assembly-export of filamentous phage.
    J Bacteriol. 1996 Apr;178(7):1962-70 PMID: 8606171
  26. Structure of the minor pseudopilin EpsH from the Type 2 secretion system of Vibrio cholerae.
    J Mol Biol. 2008 Mar 14;377(1):91-103 PMID: 18241884
  27. Weapons of mass destruction: virulence factors of the global killer enterotoxigenic Escherichia coli.
    FEMS Microbiol Lett. 2006 Oct;263(1):10-20 PMID: 16958845
  28. Type II secretion: a protein secretion system for all seasons.
    Trends Microbiol. 2005 Dec;13(12):581-8 PMID: 16216510
  29. The outer membrane component, YscC, of the Yop secretion machinery of Yersinia enterocolitica forms a ring-shaped multimeric complex.
    Mol Microbiol. 1997 Nov;26(4):789-97 PMID: 9427408
  30. SOLVE and RESOLVE: automated structure solution, density modification and model building.
    J Synchrotron Radiat. 2004 Jan 1;11(Pt 1):49-52 PMID: 14646132
  31. The PDZ domain of OutC and the N-terminal region of OutD determine the secretion specificity of the type II out pathway of Erwinia chrysanthemi.
    J Mol Biol. 2001 Apr 27;308(2):205-19 PMID: 11327762
  32. Analysis of the PilQ secretin from Neisseria meningitidis by transmission electron microscopy reveals a dodecameric quaternary structure.
    J Bacteriol. 2001 Jul;183(13):3825-32 PMID: 11395444
  33. Signal transduction pathway of TonB-dependent transporters.
    Proc Natl Acad Sci U S A. 2007 Jan 9;104(2):513-8 PMID: 17197416
  34. Refinement of macromolecular structures by the maximum-likelihood method.
    Acta Crystallogr D Biol Crystallogr. 1997 May 1;53(Pt 3):240-55 PMID: 15299926
  35. MolProbity: all-atom contacts and structure validation for proteins and nucleic acids.
    Nucleic Acids Res. 2007 Jul;35(Web Server issue):W375-83 PMID: 17452350
  36. [20] Processing of X-ray diffraction data collected in oscillation mode.
    Methods Enzymol. 1997;276:307-326 PMID: 27799103
  37. The complete general secretory pathway in gram-negative bacteria.
    Microbiol Rev. 1993 Mar;57(1):50-108 PMID: 8096622
  38. Crystal structure of cholera toxin B-pentamer bound to receptor GM1 pentasaccharide.
    Protein Sci. 1994 Feb;3(2):166-75 PMID: 8003954
  39. Structure of the filamentous phage pIV multimer by cryo-electron microscopy.
    J Mol Biol. 2003 Jan 17;325(3):461-70 PMID: 12498796
  40. Insertion of an outer membrane protein in Escherichia coli requires a chaperone-like protein.
    EMBO J. 1996 Mar 1;15(5):978-88 PMID: 8605893
  41. Characterization of pilQ, a new gene required for the biogenesis of type 4 fimbriae in Pseudomonas aeruginosa.
    Mol Microbiol. 1993 Aug;9(4):857-68 PMID: 7901733
  42. AB5 toxins.
    Curr Opin Struct Biol. 1995 Apr;5(2):165-71 PMID: 7648317
  43. Structure and function of KH domains.
    FEBS J. 2008 Jun;275(11):2712-26 PMID: 18422648
  44. A superfamily of proteins involved in different secretion pathways in gram-negative bacteria: modular structure and specificity of the N-terminal domain.
    Mol Gen Genet. 1994 Apr;243(1):112-8 PMID: 8190064
  45. Mapping the protein universe.
    Science. 1996 Aug 2;273(5275):595-603 PMID: 8662544
  46. Specific interaction between OutD, an Erwinia chrysanthemi outer membrane protein of the general secretory pathway, and secreted proteins.
    EMBO J. 1997 Jun 2;16(11):3007-16 PMID: 9214618
  47. Genetic dissection of the outer membrane secretin PulD: are there distinct domains for multimerization and secretion specificity?
    J Bacteriol. 1999 Dec;181(23):7212-20 PMID: 10572123
  48. Periplasmic disulphide bond formation is essential for cellulase secretion by the plant pathogen Erwinia chrysanthemi.
    Mol Microbiol. 1994 Feb;11(3):545-53 PMID: 8152378
  49. Pfam: clans, web tools and services.
    Nucleic Acids Res. 2006 Jan 1;34(Database issue):D247-51 PMID: 16381856
  50. The underlying mechanisms of type II protein secretion.
    Biochim Biophys Acta. 2004 Nov 11;1694(1-3):163-79 PMID: 15546665
  51. Structure of the Neisseria meningitidis outer membrane PilQ secretin complex at 12 A resolution.
    J Biol Chem. 2004 Sep 17;279(38):39750-6 PMID: 15254043
  52. Coot: model-building tools for molecular graphics.
    Acta Crystallogr D Biol Crystallogr. 2004 Dec;60(Pt 12 Pt 1):2126-32 PMID: 15572765
  53. An atomic-level investigation of the disease-causing A629P mutant of the Menkes protein, ATP7A.
    J Mol Biol. 2005 Sep 16;352(2):409-17 PMID: 16083905
  54. Structure and assembly of the pseudopilin PulG.
    Mol Microbiol. 2004 Nov;54(3):647-64 PMID: 15491357
  55. Three-dimensional structure of the Neisseria meningitidis secretin PilQ determined from negative-stain transmission electron microscopy.
    J Bacteriol. 2003 Apr;185(8):2611-7 PMID: 12670986
  56. Principles of protein-protein interactions.
    Proc Natl Acad Sci U S A. 1996 Jan 9;93(1):13-20 PMID: 8552589
  57. Comparison of llama VH sequences from conventional and heavy chain antibodies.
    Mol Immunol. 1997 Nov-Dec;34(16-17):1121-31 PMID: 9566760
  58. Isolation of llama antibody fragments for prevention of dandruff by phage display in shampoo.
    Appl Environ Microbiol. 2005 Jan;71(1):442-50 PMID: 15640220
  59. Crystal structures of Nova-1 and Nova-2 K-homology RNA-binding domains.
    Structure. 1999 Feb 15;7(2):191-203 PMID: 10368286
  60. Structure and function of cholera toxin and the related Escherichia coli heat-labile enterotoxin.
    Microbiol Rev. 1992 Dec;56(4):622-47 PMID: 1480112
  61. Phaser crystallographic software.
    J Appl Crystallogr. 2007 Aug 1;40(Pt 4):658-674 PMID: 19461840
  62. Rapid protein-folding assay using green fluorescent protein.
    Nat Biotechnol. 1999 Jul;17(7):691-5 PMID: 10404163
  63. Identification of a protein secretory pathway for the secretion of heat-labile enterotoxin by an enterotoxigenic strain of Escherichia coli.
    Proc Natl Acad Sci U S A. 2002 May 14;99(10):7066-71 PMID: 12011463
  64. A short history of SHELX.
    Acta Crystallogr A. 2008 Jan;64(Pt 1):112-22 PMID: 18156677
  65. Systematic analysis, by the yeast two-hybrid, of protein interaction between components of the type II secretory machinery of Erwinia chrysanthemi.
    Res Microbiol. 2004 Mar;155(2):71-5 PMID: 14990257
  66. Structure of the cell-puncturing device of bacteriophage T4.
    Nature. 2002 Jan 31;415(6871):553-7 PMID: 11823865
  67. PatchDock and SymmDock: servers for rigid and symmetric docking.
    Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W363-7 PMID: 15980490
  68. Structural insights into the secretin PulD and its trypsin-resistant core.
    J Biol Chem. 2005 Nov 11;280(45):37732-41 PMID: 16129681
Article Info
Journal
Structure (London, England : 1993)
Abbr.
Structure
ISSN
0969-2126
DOI
10.1016/j.str.2008.11.011
Published
2009-02-13
Pages
255-65
Language
English
Region
United States
NLM ID
101087697
PMCID
PMC2662362
Subset
IM
Grants
NIAID NIH HHS · R01 AI034501 · United States
NIAID NIH HHS · R01 AI034501-15 · United States
NIAID NIH HHS · R56 AI034501 · United States
NIAID NIH HHS · AI34501 · United States
External Links
PubMed source DOI: 10.1016/j.str.2008.11.011 PMC Full Text View journal details
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