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PDBsum entry 2jaa
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protein Protein-protein interface(s) links
Cell invasion PDB id
2jaa

 

 

 

 

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Contents
Protein chains
167 a.a. *
182 a.a. *
Waters ×8
* Residue conservation analysis
PDB id:
2jaa
Name: Cell invasion
Title: Semet substituted shigella flexneri ipad
Structure: Invasin ipad. Chain: a, b. Fragment: residues 121-332. Engineered: yes. Other_details: protelysis product. Semet substituted
Source: Shigella flexneri. Organism_taxid: 623. Strain: 301. Variant: serotype 2a. Atcc: 700930. Expressed in: escherichia coli. Expression_system_taxid: 469008.
Resolution:
3.10Å     R-factor:   0.262     R-free:   0.276
Authors: S.Johnson,P.Roversi,M.Espina,A.Olive,J.E.Deane,S.Birket,T.Field, W.D.Picking,A.J.Blocker,E.E.Galyov,W.L.Picking,S.M.Lea
Key ref:
S.Johnson et al. (2007). Self-chaperoning of the type III secretion system needle tip proteins IpaD and BipD. J Biol Chem, 282, 4035-4044. PubMed id: 17077085 DOI: 10.1074/jbc.M607945200
Date:
24-Nov-06     Release date:   30-Nov-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P18013  (IPAD_SHIFL) -  Invasin IpaD from Shigella flexneri
Seq:
Struc: 		332 a.a.
167 a.a.
Protein chain
Pfam   ArchSchema ?
P18013  (IPAD_SHIFL) -  Invasin IpaD from Shigella flexneri
Seq:
Struc: 		332 a.a.
182 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 

 
DOI no: 10.1074/jbc.M607945200 J Biol Chem 282:4035-4044 (2007)
PubMed id: 17077085  
 
 
Self-chaperoning of the type III secretion system needle tip proteins IpaD and BipD.
S.Johnson, P.Roversi, M.Espina, A.Olive, J.E.Deane, S.Birket, T.Field, W.D.Picking, A.J.Blocker, E.E.Galyov, W.L.Picking, S.M.Lea.
 
  ABSTRACT  
 
Bacteria expressing type III secretion systems (T3SS) have been responsible for the deaths of millions worldwide, acting as key virulence elements in diseases ranging from plague to typhoid fever. The T3SS is composed of a basal body, which traverses both bacterial membranes, and an external needle through which effector proteins are secreted. We report multiple crystal structures of two proteins that sit at the tip of the needle and are essential for virulence: IpaD from Shigella flexneri and BipD from Burkholderia pseudomallei. The structures reveal that the N-terminal domains of the molecules are intramolecular chaperones that prevent premature oligomerization, as well as sharing structural homology with proteins involved in eukaryotic actin rearrangement. Crystal packing has allowed us to construct a model for the tip complex that is supported by mutations designed using the structure.
 
  Selected figure(s)  
 
Figure 4.
FIGURE 4. Consequences of removal of the N-terminal domain. a, proteolytic sensitivity of the N-terminal domain of IpaD. IpaD was incubated with trypsin at various ratios (w:w), and the resulting digests were resolved on SDS-PAGE. Band 1 (24 kDa) begins at residue 120 and Band 2 (20 kDa) at residue 138. b, surface representation of IpaD[39-130] (left) and IpaD[131-322] (right) with hydrophobic residues colored green and brown, respectively. IpaD[39-130] is rotated through 180° along the long axis relative to IpaD[131-322] to demonstrate the complementary hydrophobic surfaces. The surface is presented as transparent to allow visualization of the secondary structure. c, analytical gel filtration chromatography (Superdex 200, HR 10/30) of IpaD before and after subtilisin treatment. Elution volume of each species is noted along with the M[r] calculated from SDS-PAGE. d, overlay of five structures of the IpaD coiled-coil demonstrating the flexibility of the helices in the absence of the N-terminal domain. The conformation of the coil in the presence of the N-terminal domain is shown in green. The C-terminal domain has been removed to aid clarity. 		Figure 5.
FIGURE 5. Oligomerization of IpaD. a, ribbon diagram of the non-crystallographic dimer found in crystal form 2 (18). Molecule A is shown in green and molecule B in blue. b, detailed view of the dimer interaction site with side chains displayed, colored as in a. Only structural elements that contribute to the binding site are displayed for clarity. c, pentamer produced using the non-crystallographic symmetry from crystal form 2. At the top are ribbon representations and at the bottom surface views. The panels on the left are related to the panels on the right by a rotation of 90°.
 
  The above figures are reprinted from an Open Access publication published by the ASBMB: J Biol Chem (2007, 282, 4035-4044) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21479247 H.Sato, M.L.Hunt, J.J.Weiner, A.T.Hansen, and D.W.Frank (2011).
Modified needle-tip PcrV proteins reveal distinct phenotypes relevant to the control of type III secretion and intoxication by Pseudomonas aeruginosa.
  PLoS One, 6, e18356.  
21412437 L.Gong, M.Cullinane, P.Treerat, G.Ramm, M.Prescott, B.Adler, J.D.Boyce, and R.J.Devenish (2011).
The Burkholderia pseudomallei type III secretion system and BopA are required for evasion of LC3-associated phagocytosis.
  PLoS One, 6, e17852.  
21112241 L.J.Worrall, E.Lameignere, and N.C.Strynadka (2011).
Structural overview of the bacterial injectisome.
  Curr Opin Microbiol, 14, 3-8.  
21182592 P.J.Matteï, E.Faudry, V.Job, T.Izoré, I.Attree, and A.Dessen (2011).
Membrane targeting and pore formation by the type III secretion system translocon.
  FEBS J, 278, 414-426.  
21031487 S.Chatterjee, D.Zhong, B.A.Nordhues, K.P.Battaile, S.Lovell, and R.N.De Guzman (2011).
The crystal structures of the Salmonella type III secretion system tip protein SipD in complex with deoxycholate and chenodeoxycholate.
  Protein Sci, 20, 75-86.
PDB codes: 3nzz 3o00 3o01 3o02
20086081 A.D.Roehrich, I.Martinez-Argudo, S.Johnson, A.J.Blocker, and A.K.Veenendaal (2010).
The extreme C terminus of Shigella flexneri IpaB is required for regulation of type III secretion, needle tip composition, and binding.
  Infect Immun, 78, 1682-1691.  
20845449 A.P.Markham, B.S.Barrett, R.Esfandiary, W.L.Picking, W.D.Picking, S.B.Joshi, and C.R.Middaugh (2010).
Formulation and immunogenicity of a potential multivalent type III secretion system-based protein vaccine.
  J Pharm Sci, 99, 4497-4509.  
21047256 C.S.Hayes, S.K.Aoki, and D.A.Low (2010).
Bacterial contact-dependent delivery systems.
  Annu Rev Genet, 44, 71-90.  
20528691 E.E.Galyov, P.J.Brett, and D.DeShazer (2010).
Molecular insights into Burkholderia pseudomallei and Burkholderia mallei pathogenesis.
  Annu Rev Microbiol, 64, 495-517.  
21143311 I.Martinez-Argudo, and A.J.Blocker (2010).
The Shigella T3SS needle transmits a signal for MxiC release, which controls secretion of effectors.
  Mol Microbiol, 78, 1365-1378.  
21046319 J.Peng, J.Yang, and Q.Jin (2010).
Research progress in Shigella in the postgenomic era.
  Sci China Life Sci, 53, 1284-1290.  
20141759 T.Rathinavelan, L.Zhang, W.L.Picking, D.D.Weis, R.N.De Guzman, and W.Im (2010).
A repulsive electrostatic mechanism for protein export through the type III secretion apparatus.
  Biophys J, 98, 452-461.  
19396171 J.L.Hodgkinson, A.Horsley, D.Stabat, M.Simon, S.Johnson, P.C.da Fonseca, E.P.Morris, J.S.Wall, S.M.Lea, and A.J.Blocker (2009).
Three-dimensional reconstruction of the Shigella T3SS transmembrane regions reveals 12-fold symmetry and novel features throughout.
  Nat Struct Mol Biol, 16, 477-485.  
19576779 M.C.Chibucos, T.T.Tseng, and J.C.Setubal (2009).
Describing commonalities in microbial effector delivery using the Gene Ontology.
  Trends Microbiol, 17, 312-319.  
18458349 A.J.Blocker, J.E.Deane, A.K.Veenendaal, P.Roversi, J.L.Hodgkinson, S.Johnson, and S.M.Lea (2008).
What's the point of the type III secretion system needle?
  Proc Natl Acad Sci U S A, 105, 6507-6513.  
18175320 A.P.Markham, S.E.Birket, W.D.Picking, W.L.Picking, and C.R.Middaugh (2008).
pH sensitivity of type III secretion system tip proteins.
  Proteins, 71, 1830-1842.  
18430138 C.A.Mueller, P.Broz, and G.R.Cornelis (2008).
The type III secretion system tip complex and translocon.
  Mol Microbiol, 68, 1085-1095.  
18202440 G.N.Schroeder, and H.Hilbi (2008).
Molecular pathogenesis of Shigella spp.: controlling host cell signaling, invasion, and death by type III secretion.
  Clin Microbiol Rev, 21, 134-156.  
18485071 J.E.Deane, S.C.Graham, E.P.Mitchell, D.Flot, S.Johnson, and S.M.Lea (2008).
Crystal structure of Spa40, the specificity switch for the Shigella flexneri type III secretion system.
  Mol Microbiol, 69, 267-276.
PDB code: 2vt1
18450744 K.F.Stensrud, P.R.Adam, C.D.La Mar, A.J.Olive, G.H.Lushington, R.Sudharsan, N.L.Shelton, R.S.Givens, W.L.Picking, and W.D.Picking (2008).
Deoxycholate interacts with IpaD of Shigella flexneri in inducing the recruitment of IpaB to the type III secretion apparatus needle tip.
  J Biol Chem, 283, 18646-18654.  
18250627 K.U.Wendt, M.S.Weiss, P.Cramer, and D.W.Heinz (2008).
Structures and diseases.
  Nat Struct Mol Biol, 15, 117-120.  
18258424 T.F.Moraes, T.Spreter, and N.C.Strynadka (2008).
Piecing together the type III injectisome of bacterial pathogens.
  Curr Opin Struct Biol, 18, 258-266.  
17327391 M.Espina, S.F.Ausar, C.R.Middaugh, M.A.Baxter, W.D.Picking, and W.L.Picking (2007).
Conformational stability and differential structural analysis of LcrV, PcrV, BipD, and SipD from type III secretion systems.
  Protein Sci, 16, 704-714.  
17697254 P.Broz, C.A.Mueller, S.A.Müller, A.Philippsen, I.Sorg, A.Engel, and G.R.Cornelis (2007).
Function and molecular architecture of the Yersinia injectisome tip complex.
  Mol Microbiol, 65, 1311-1320.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.

 

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