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PDBsum entry 1c5k

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protein metals links
Transport protein PDB id
1c5k
Jmol
Contents
Protein chain
397 a.a. *
Metals
_YB
Waters ×230
* Residue conservation analysis
PDB id:
1c5k
Name: Transport protein
Title: The structure of tolb, an essential component of the tol- dependent translocation system and its interactions with the translocation domain of colicin e9
Structure: Protein (tolb protein). Chain: a. Fragment: entire protein. Engineered: yes. Other_details: in e.Coli tolb forms a heterodimer with pal (peptidoglycan associated lipoprotein)
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
2.00Å     R-factor:   0.234     R-free:   0.271
Authors: S.Carr,C.N.Penfold,V.Bamford,R.James,A.M.Hemmings
Key ref:
S.Carr et al. (2000). The structure of TolB, an essential component of the tol-dependent translocation system, and its protein-protein interaction with the translocation domain of colicin E9. Structure, 8, 57-66. PubMed id: 10673426 DOI: 10.1016/S0969-2126(00)00079-4
Date:
05-Dec-99     Release date:   06-Dec-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P0A855  (TOLB_ECOLI) -  Protein TolB
Seq:
Struc:
430 a.a.
397 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   2 terms 
  Biological process     protein transport   3 terms 

 

 
DOI no: 10.1016/S0969-2126(00)00079-4 Structure 8:57-66 (2000)
PubMed id: 10673426  
 
 
The structure of TolB, an essential component of the tol-dependent translocation system, and its protein-protein interaction with the translocation domain of colicin E9.
S.Carr, C.N.Penfold, V.Bamford, R.James, A.M.Hemmings.
 
  ABSTRACT  
 
BACKGROUND: E colicin proteins have three functional domains, each of which is implicated in one of the stages of killing Escherichia coli cells: receptor binding, translocation and cytotoxicity. The central (R) domain is responsible for receptor-binding activity whereas the N-terminal (T) domain mediates translocation, the process by which the C-terminal cytotoxic domain is transported from the receptor to the site of its cytotoxicity. The translocation of enzymatic E colicins like colicin E9 is dependent upon TolB but the details of the process are not known. RESULTS: We have demonstrated a protein-protein interaction between the T domain of colicin E9 and TolB, an essential component of the tol-dependent translocation system in E. coli, using the yeast two-hybrid system. The crystal structure of TolB, a procaryotic tryptophan-aspartate (WD) repeat protein, reveals an N-terminal alpha + beta domain based on a five-stranded mixed beta sheet and a C-terminal six-bladed beta-propeller domain. CONCLUSIONS: The results suggest that the TolB-box residues of the T domain of colicin E9 interact with the beta-propeller domain of TolB. The protein-protein interactions of other beta-propeller-containing proteins, the yeast yPrp4 protein and G proteins, are mediated by the loops or outer sheets of the propeller blades. The determination of the three-dimensional structure of the T domain-TolB complex and the isolation of mutations in TolB that abolish the interaction with the T domain will reveal fine details of the protein-protein interaction of TolB and the T domain of E colicins.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. Topology and internal structural homology of the b-propeller domain. (a) Closing the circle of b-propeller blades. A view down the central barrel of the b-propeller domain of TolB where each of the six repeated sequence motifs of the amino acid sequence that fold to give the b-propeller structure is shown in a different colour (1, purple; 2, yellow; 3, red; 4, royal blue; 5, gold; and 6, green). This view demonstrates the mechanism of propeller closure in TolB where the C-terminal b strand from the final sequence motif forms the inner b strand of the four-stranded sheet that forms blade 1. (b) An alignment of the six sequence repeats (motifs 1-6) that form the b-propeller domain of the TolB protein. The starting residue number of each motif is indicated. Residues that form b strands are enclosed in boxes. (c) Orthogonal views of a superposition of the six blades of the TolB propeller domain. The colouring of residues in each of the six sequence motifs is the same as in (a) and the nomenclature for the strands follows that in (b).
 
  The above figure is reprinted by permission from Cell Press: Structure (2000, 8, 57-66) copyright 2000.  
  Figure was selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19627502 Y.Zhang, C.Li, M.N.Vankemmelbeke, P.Bardelang, M.Paoli, C.N.Penfold, and R.James (2010).
The crystal structure of the TolB box of colicin A in complex with TolB reveals important differences in the recruitment of the common TolB translocation portal used by group A colicins.
  Mol Microbiol, 75, 623-636.
PDB code: 3iax
19696740 D.A.Bonsor, O.Hecht, M.Vankemmelbeke, A.Sharma, A.M.Krachler, N.G.Housden, K.J.Lilly, R.James, G.R.Moore, and C.Kleanthous (2009).
Allosteric beta-propeller signalling in TolB and its manipulation by translocating colicins.
  EMBO J, 28, 2846-2857.
PDB code: 2w8b
18291013 T.den Blaauwen, M.A.de Pedro, M.Nguyen-Distèche, and J.A.Ayala (2008).
Morphogenesis of rod-shaped sacculi.
  FEMS Microbiol Rev, 32, 321-344.  
17671979 C.Wang, O.Schueler-Furman, I.Andre, N.London, S.J.Fleishman, P.Bradley, B.Qian, and D.Baker (2007).
RosettaDock in CAPRI rounds 6-12.
  Proteins, 69, 758-763.  
17347522 E.Cascales, S.K.Buchanan, D.Duché, C.Kleanthous, R.Lloubès, K.Postle, M.Riley, S.Slatin, and D.Cavard (2007).
Colicin biology.
  Microbiol Mol Biol Rev, 71, 158-229.  
17548346 O.Sharma, E.Yamashita, M.V.Zhalnina, S.D.Zakharov, K.A.Datsenko, B.L.Wanner, and W.A.Cramer (2007).
Structure of the complex of the colicin E2 R-domain and its BtuB receptor. The outer membrane colicin translocon.
  J Biol Chem, 282, 23163-23170.
PDB code: 2ysu
17085563 O.Sharma, and W.A.Cramer (2007).
Minimum length requirement of the flexible N-terminal translocation subdomain of colicin E3.
  J Bacteriol, 189, 363-368.  
16934981 P.A.Hoskisson, and M.I.Hutchings (2006).
MtrAB-LpqB: a conserved three-component system in actinobacteria?
  Trends Microbiol, 14, 444-449.  
15808743 L.Aravind, V.Anantharaman, S.Balaji, M.M.Babu, and L.M.Iyer (2005).
The many faces of the helix-turn-helix domain: transcription regulation and beyond.
  FEMS Microbiol Rev, 29, 231-262.  
15774871 N.Rolhion, N.Barnich, L.Claret, and A.Darfeuille-Michaud (2005).
Strong decrease in invasive ability and outer membrane vesicle release in Crohn's disease-associated adherent-invasive Escherichia coli strain LF82 with the yfgL gene deleted.
  J Bacteriol, 187, 2286-2296.  
16166536 S.L.Hands, L.E.Holland, M.Vankemmelbeke, L.Fraser, C.J.Macdonald, G.R.Moore, R.James, and C.N.Penfold (2005).
Interactions of TolB with the translocation domain of colicin E9 require an extended TolB box.
  J Bacteriol, 187, 6733-6741.  
15231784 C.N.Penfold, B.Healy, N.G.Housden, R.Boetzel, M.Vankemmelbeke, G.R.Moore, C.Kleanthous, and R.James (2004).
Flexibility in the receptor-binding domain of the enzymatic colicin E9 is required for toxicity against Escherichia coli cells.
  J Bacteriol, 186, 4520-4527.  
11994151 A.Walburger, C.Lazdunski, and Y.Corda (2002).
The Tol/Pal system function requires an interaction between the C-terminal domain of TolA and the N-terminal domain of TolB.
  Mol Microbiol, 44, 695-708.  
12377130 H.Jing, J.Takagi, J.H.Liu, S.Lindgren, R.G.Zhang, A.Joachimiak, J.H.Wang, and T.A.Springer (2002).
Archaeal surface layer proteins contain beta propeller, PKD, and beta helix domains and are related to metazoan cell surface proteins.
  Structure, 10, 1453-1464.
PDB code: 1l0q
11937049 Z.Jawad, and M.Paoli (2002).
Novel sequences propel familiar folds.
  Structure, 10, 447-454.  
11703658 L.Journet, E.Bouveret, A.Rigal, R.Lloubes, C.Lazdunski, and H.Bénédetti (2001).
Import of colicins across the outer membrane of Escherichia coli involves multiple protein interactions in the periplasm.
  Mol Microbiol, 42, 331-344.  
11069686 C.N.Penfold, C.Garinot-Schneider, A.M.Hemmings, G.R.Moore, C.Kleanthous, and R.James (2000).
A 76-residue polypeptide of colicin E9 confers receptor specificity and inhibits the growth of vitamin B12-dependent Escherichia coli 113/3 cells.
  Mol Microbiol, 38, 639-649.  
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.