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PDBsum entry 1yf5

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protein links
Transport protein PDB id
1yf5
Jmol
Contents
Protein chain
238 a.a. *
Waters ×9
* Residue conservation analysis
PDB id:
1yf5
Name: Transport protein
Title: Cyto-epsl: the cytoplasmic domain of epsl, an inner membrane of the type ii secretion system of vibrio cholerae
Structure: General secretion pathway protein l. Chain: l. Synonym: cholera toxin secretion protein epsl. Engineered: yes
Source: Vibrio cholerae. Organism_taxid: 666. Gene: epsl. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.75Å     R-factor:   0.216     R-free:   0.269
Authors: J.Abendroth,P.Murphy,A.Mushtaq,M.Sandkvist,M.Bagdasarian,W.G
Key ref:
J.Abendroth et al. (2005). The X-ray structure of the type II secretion system complex formed by the N-terminal domain of EpsE and the cytoplasmic domain of EpsL of Vibrio cholerae. J Mol Biol, 348, 845-855. PubMed id: 15843017 DOI: 10.1016/j.jmb.2005.02.061
Date:
30-Dec-04     Release date:   03-May-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P45782  (GSPL_VIBCH) -  Type II secretion system protein L
Seq:
Struc:
407 a.a.
238 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     Gram-negative-bacterium-type cell wall   2 terms 
  Biological process     protein transport   1 term 
  Biochemical function     protein transporter activity     1 term  

 

 
DOI no: 10.1016/j.jmb.2005.02.061 J Mol Biol 348:845-855 (2005)
PubMed id: 15843017  
 
 
The X-ray structure of the type II secretion system complex formed by the N-terminal domain of EpsE and the cytoplasmic domain of EpsL of Vibrio cholerae.
J.Abendroth, P.Murphy, M.Sandkvist, M.Bagdasarian, W.G.Hol.
 
  ABSTRACT  
 
Gram-negative bacteria use type II secretion systems for the transport of virulence factors and hydrolytic enzymes through the outer membrane. These sophisticated multi-protein complexes reach from the pore in the outer membrane via the pseudopilins in the periplasm and a multi-protein inner-membrane sub-complex, to an ATPase in the cytoplasm. The human pathogen Vibrio cholerae uses such a secretion machinery, called the Eps-system, for the export of its major virulence factor cholera toxin into the intestinal tract of the human host. Here, we describe the 2.4 A structure of the hetero-tetrameric complex of the N-terminal domain of the ATPase EpsE and the cytoplasmic domain of the inner membrane protein EpsL, which constitute the major cytoplasmic components of the Eps-system. A stable fragment of EpsE in complex with the cytoplasmic domain of EpsL was identified via limited proteolysis and facilitated the crystallization of the complex. This first structure of a complex between two different proteins of the type II secretion system reveals that the N-terminal domain of EpsE and the cytoplasmic domain of EpsL form a hetero-tetramer, in which EpsL is the central dimer and EpsE binds on the periphery. The dimer of EpsL in this complex is very similar to the dimer seen in the crystal structure of the native cytoplasmic domain of EpsL, suggesting a possible physiological relevance despite a relatively small 675 A2 buried solvent accessible surface. The N-terminal domain of EpsE, which forms a compact domain with an alpha+beta-fold, places its helix alpha2 in a mostly hydrophobic cleft between domains II and III of EpsL burying 1700 A2 solvent accessible surface. This extensive interface involves several residues whose hydrophobic or charged nature is well conserved and is therefore likely to be of general importance in type II secretion systems.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. The structure of the hetero-tetramer of N1E:cytoL and the topology of N1-EpsE. (a) In the representation of the hetero-tetramer of N1E:cytoL, N1-EpsE is colored in purple both in the ribbon representation and in the surface representation. The two protomers of cyto-EpsL are colored according to the domains in blue (domain I), yellow (domain II) and red (domain III) or in yellow, respectively. Cyto-EpsL forms a homo-dimer. N1-EpsE is bound at the periphery of the complex and interacts with domains II and III of the adjacent cyto-EpsL protomer. (b) N1-EpsE forms a compact domain and consists of a central three-stranded mixed b-sheet, which is lined on one side by three helices. The sequence of secondary structure elements in N1-EpsE is a1-bA-bB-a2-bC-a3. (c) The sequence conservation as determined by Consurf16 plotted on the surface of N1-EpsE, which is shown in the same orientation as in (b). Red indicates high, blue indicates low sequence conservation. The surface of the a-helical side, involved in EpsE:EpsL interactions, is much higher conserved than the b-sheet side. The positions of six totally conserved surface residues are indicated. Almost all of them are involved in contacts with cyto-EpsL.
Figure 4.
Figure 4. Interactions between N1-EpsE and cyto-EpsL. (a) Stereo Figure of the location of the binding interface and the interactions between N1-EpsE and cyto-EpsL. N1-EpsE is colored in magenta and green, the three domains of cyto-EpsL are colored in blue, yellow and red, respectively. Residues involved in N1E:cytoL interactions are indicated with spheres on the respective C^a-positions. N1-EpsE protrudes with its helix a2 into the cleft formed by domains II (yellow) and III (red) of cyto-EpsL. The majority of interacting residues of N1-EpsE are located on helix a2, other contributions are made by residues from helix a1 and strand bC. Residues of cyto-EpsL involved in interactions are mostly part of a loop C-terminal of helix aII1 (domain II), further contributions come from residues on strands bE (domain II) and bK, and helix a3 (domain III). (b) "Butterfly" representation of the interface. The N1E:cytoL complex has been taken apart and N1-EpsE rotated by 180°. The original orientation of N1-EpsE is indicated with a translucent gray surface. Residues involved in interactions are colored on the surfaces of N1-EpsE (magenta) and cyto-EpsL (yellow) according to the nature of the contacts. Most of the N1E:cytoL interactions are hydrophobic contacts (green); only a few interactions are polar (blue), all of which involve residues from domain II of cyto-EpsL.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2005, 348, 845-855) copyright 2005.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22466878 K.V.Korotkov, M.Sandkvist, and W.G.Hol (2012).
The type II secretion system: biogenesis, molecular architecture and mechanism.
  Nat Rev Microbiol, 10, 336-351.  
21234771 B.Zolghadr, A.Klingl, R.Rachel, A.J.Driessen, and S.V.Albers (2011).
The bindosome is a structural component of the Sulfolobus solfataricus cell envelope.
  Extremophiles, 15, 235-244.  
21210168 I.Rose, G.Biuković, P.Aderhold, V.Müller, G.Grüber, and B.Averhoff (2011).
Identification and characterization of a unique, zinc-containing transport ATPase essential for natural transformation in Thermus thermophilus HB27.
  Extremophiles, 15, 191-202.  
21255118 M.D.Gray, M.Bagdasarian, W.G.Hol, and M.Sandkvist (2011).
In vivo cross-linking of EpsG to EpsL suggests a role for EpsL as an ATPase-pseudopilin coupling protein in the Type II secretion system of Vibrio cholerae.
  Mol Microbiol, 79, 786-798.  
  20671907 A.F.Ellen, B.Zolghadr, A.M.Driessen, and S.V.Albers (2010).
Shaping the archaeal cell envelope.
  Archaea, 2010, 608243.  
20722599 M.Ayers, P.L.Howell, and L.L.Burrows (2010).
Architecture of the type II secretion and type IV pilus machineries.
  Future Microbiol, 5, 1203-1218.  
19646531 J.Abendroth, A.C.Kreger, and W.G.Hol (2009).
The dimer formed by the periplasmic domain of EpsL from the Type 2 Secretion System of Vibrio parahaemolyticus.
  J Struct Biol, 168, 313-322.
PDB code: 2w7v
19324092 J.Abendroth, D.D.Mitchell, K.V.Korotkov, T.L.Johnson, A.Kreger, M.Sandkvist, and W.G.Hol (2009).
The three-dimensional structure of the cytoplasmic domains of EpsF from the type 2 secretion system of Vibrio cholerae.
  J Struct Biol, 166, 303-315.
PDB codes: 2vma 2vmb 3c1q
18438417 K.V.Korotkov, and W.G.Hol (2008).
Structure of the GspK-GspI-GspJ complex from the enterotoxigenic Escherichia coli type 2 secretion system.
  Nat Struct Mol Biol, 15, 462-468.
PDB code: 3ci0
18249533 L.Craig, and J.Li (2008).
Type IV pili: paradoxes in form and function.
  Curr Opin Struct Biol, 18, 267-277.  
18022192 M.E.Yanez, K.V.Korotkov, J.Abendroth, and W.G.Hol (2008).
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, 375, 471-486.
PDB code: 2ret
18241884 M.E.Yanez, K.V.Korotkov, J.Abendroth, and W.G.Hol (2008).
Structure of the minor pseudopilin EpsH from the Type 2 secretion system of Vibrio cholerae.
  J Mol Biol, 377, 91.
PDB code: 2qv8
17255937 A.Yamagata, and J.A.Tainer (2007).
Hexameric structures of the archaeal secretion ATPase GspE and implications for a universal secretion mechanism.
  EMBO J, 26, 878-890.
PDB codes: 2oap 2oaq
17462024 B.Zolghadr, S.Weber, Z.Szabó, A.J.Driessen, and S.V.Albers (2007).
Identification of a system required for the functional surface localization of sugar binding proteins with class III signal peptides in Sulfolobus solfataricus.
  Mol Microbiol, 64, 795-806.  
17159897 J.L.Camberg, T.L.Johnson, M.Patrick, J.Abendroth, W.G.Hol, and M.Sandkvist (2007).
Synergistic stimulation of EpsE ATP hydrolysis by EpsL and acidic phospholipids.
  EMBO J, 26, 19-27.  
17434972 S.A.Tripathi, and R.K.Taylor (2007).
Membrane association and multimerization of TcpT, the cognate ATPase ortholog of the Vibrio cholerae toxin-coregulated-pilus biogenesis apparatus.
  J Bacteriol, 189, 4401-4409.  
17630971 S.J.Shiue, I.L.Chien, N.L.Chan, W.M.Leu, and N.T.Hu (2007).
Mutation of a key residue in the type II secretion system ATPase uncouples ATP hydrolysis from protein translocation.
  Mol Microbiol, 65, 401-412.  
17921296 T.L.Johnson, M.E.Scott, and M.Sandkvist (2007).
Mapping critical interactive sites within the periplasmic domain of the Vibrio cholerae type II secretion protein EpsM.
  J Bacteriol, 189, 9082-9089.  
16448494 T.L.Johnson, J.Abendroth, W.G.Hol, and M.Sandkvist (2006).
Type II secretion: from structure to function.
  FEMS Microbiol Lett, 255, 175-186.  
16162504 Y.Chen, S.J.Shiue, C.W.Huang, J.L.Chang, Y.L.Chien, N.T.Hu, and N.L.Chan (2005).
Structure and function of the XpsE N-terminal domain, an essential component of the Xanthomonas campestris type II secretion system.
  J Biol Chem, 280, 42356-42363.
PDB codes: 2d27 2d28
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 code is shown on the right.