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PDBsum entry 1jch

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protein ligands Protein-protein interface(s) links
Ribosome inhibitor, hydrolase PDB id
1jch
Jmol
Contents
Protein chains
468 a.a. *
84 a.a. *
Ligands
CIT ×4
GOL ×4
Waters ×396
* Residue conservation analysis
PDB id:
1jch
Name: Ribosome inhibitor, hydrolase
Title: Crystal structure of colicin e3 in complex with its immunity
Structure: Colicin e3. Chain: a, c. Synonym: ribonuclease, colicin e3 a chain. Engineered: yes. Colicin e3 immunity protein. Chain: b, d. Synonym: imme3. Microcin e3 immunity protein. Colicin e3 ch immunity protein 2. Engineered: yes
Source: Escherichia coli str. K12 substr.. Organism_taxid: 316407. Strain: w3110. Expressed in: escherichia coli str. K12 substr. W3110. Expression_system_taxid: 316407.
Biol. unit: Tetramer (from PQS)
Resolution:
3.02Å     R-factor:   0.237     R-free:   0.283
Authors: S.Soelaiman,K.Jakes,N.Wu,C.Li,M.Shoham
Key ref:
S.Soelaiman et al. (2001). Crystal structure of colicin E3: implications for cell entry and ribosome inactivation. Mol Cell, 8, 1053-1062. PubMed id: 11741540 DOI: 10.1016/S1097-2765(01)00396-3
Date:
09-Jun-01     Release date:   30-Nov-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P00646  (CEA3_ECOLX) -  Colicin-E3
Seq:
Struc:
 
Seq:
Struc:
551 a.a.
468 a.a.*
Protein chains
Pfam   ArchSchema ?
P02984  (IMM3_ECOLX) -  Colicin-E3 immunity protein
Seq:
Struc:
85 a.a.
84 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extrachromosomal circular DNA   1 term 
  Biological process     metabolic process   6 terms 
  Biochemical function     protein binding     8 terms  

 

 
DOI no: 10.1016/S1097-2765(01)00396-3 Mol Cell 8:1053-1062 (2001)
PubMed id: 11741540  
 
 
Crystal structure of colicin E3: implications for cell entry and ribosome inactivation.
S.Soelaiman, K.Jakes, N.Wu, C.Li, M.Shoham.
 
  ABSTRACT  
 
Colicins kill E. coli by a process that involves binding to a surface receptor, entering the cell, and, finally, intoxicating it. The lethal action of colicin E3 is a specific cleavage in the ribosomal decoding A site. The crystal structure of colicin E3, reported here in a binary complex with its immunity protein (IP), reveals a Y-shaped molecule with the receptor binding domain forming a 100 A long stalk and the two globular heads of the translocation domain (T) and the catalytic domain (C) comprising the two arms. Active site residues are D510, H513, E517, and R545. IP is buried between T and C. Rather than blocking the active site, IP prevents access of the active site to the ribosome.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Schematic Representation of the Mechanism of Action of Colicin E3T, translocation domain; R, receptor binding domain; C, catalytic domain; IP, immunity protein to colicin E3.
Figure 2.
Figure 2. Ribbon Diagrams(A) The colicin E3-IP complex is Y shaped with dimensions of 75 × 135 × 45 Å.(B) Close-up of the jellyroll structure of the translocation domain in the same orientation as in (A). The three β sheets are shown in red, blue, and yellow. The β strands are numbered consecutively from the N terminus. The β barrel is flanked by two α-helical stretches. The second and longer α helix ends with P315, which causes a kink in the helix and leads directly into the helical receptor binding domain.(C) Close-up of the catalytic domain and the IP. The C domain is shown in gray and the IP in red. Catalytic residues are shown in ball-and-stick. This orientation shows that the two β sheets are roughly perpendicular to each other.
 
  The above figures are reprinted by permission from Cell Press: Mol Cell (2001, 8, 1053-1062) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21455261 K.D.Krewulak, and H.J.Vogel (2011).
TonB or not TonB: is that the question?
  Biochem Cell Biol, 89, 87-97.  
20941706 L.Prieto, and T.Lazaridis (2011).
Computational studies of colicin insertion into membranes: the closed state.
  Proteins, 79, 126-141.  
20676430 B.Apostolovic, M.Danial, and H.A.Klok (2010).
Coiled coils: attractive protein folding motifs for the fabrication of self-assembled, responsive and bioactive materials.
  Chem Soc Rev, 39, 3541-3575.  
21060316 C.Kleanthous (2010).
Swimming against the tide: progress and challenges in our understanding of colicin translocation.
  Nat Rev Microbiol, 8, 843-848.  
20852642 C.L.Ng, K.Lang, N.A.Meenan, A.Sharma, A.C.Kelley, C.Kleanthous, and V.Ramakrishnan (2010).
Structural basis for 16S ribosomal RNA cleavage by the cytotoxic domain of colicin E3.
  Nat Struct Mol Biol, 17, 1241-1246.
PDB codes: 2xfz 2xg0 2xg1 2xg2
19919671 K.S.Jakes, and A.Finkelstein (2010).
The colicin Ia receptor, Cir, is also the translocator for colicin Ia.
  Mol Microbiol, 75, 567-578.  
18996848 S.Nithianantham, M.Xu, M.Yamada, A.Ikegami, M.Shoham, and Y.W.Han (2009).
Crystal Structure of FadA Adhesin from Fusobacterium nucleatum Reveals a Novel Oligomerization Motif, the Leucine Chain.
  J Biol Chem, 284, 3865-3872.
PDB codes: 3etw 3etx 3ety 3etz
19056731 T.Arnold, K.Zeth, and D.Linke (2009).
Structure and Function of Colicin S4, a Colicin with a Duplicated Receptor-binding Domain.
  J Biol Chem, 284, 6403-6413.
PDB code: 3few
18636093 E.Yamashita, M.V.Zhalnina, S.D.Zakharov, O.Sharma, and W.A.Cramer (2008).
Crystal structures of the OmpF porin: function in a colicin translocon.
  EMBO J, 27, 2171-2180.
PDB codes: 2zfg 2zld
18554332 J.Hullmann, S.I.Patzer, C.Römer, K.Hantke, and V.Braun (2008).
Periplasmic chaperone FkpA is essential for imported colicin M toxicity.
  Mol Microbiol, 69, 926-937.  
18375563 J.Singh, and N.Banerjee (2008).
Transcriptional analysis and functional characterization of a gene pair encoding iron-regulated xenocin and immunity proteins of Xenorhabdus nematophila.
  J Bacteriol, 190, 3877-3885.  
18640984 K.Zeth, C.Römer, S.I.Patzer, and V.Braun (2008).
Crystal structure of colicin M, a novel phosphatase specifically imported by Escherichia coli.
  J Biol Chem, 283, 25324-25331.
PDB codes: 3da3 3da4
18408035 Y.Zhang, M.N.Vankemmelbeke, L.E.Holland, D.C.Walker, R.James, and C.N.Penfold (2008).
Investigating early events in receptor binding and translocation of colicin E9 using synchronized cell killing and proteolytic cleavage.
  J Bacteriol, 190, 4342-4350.  
17416663 D.Duché (2007).
Colicin E2 is still in contact with its receptor and import machinery when its nuclease domain enters the cytoplasm.
  J Bacteriol, 189, 4217-4222.  
17720814 D.Walker, K.Mosbahi, M.Vankemmelbeke, R.James, and C.Kleanthous (2007).
The role of electrostatics in colicin nuclease domain translocation into bacterial cells.
  J Biol Chem, 282, 31389-31397.  
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.  
17277071 M.Masi, P.Vuong, M.Humbard, K.Malone, and R.Misra (2007).
Initial steps of colicin E1 import across the outer membrane of Escherichia coli.
  J Bacteriol, 189, 2667-2676.  
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.  
17180733 X.Wang, M.Li, J.Zhang, Y.Zhang, G.Zhang, and J.Wang (2007).
Identification of a key functional region in harpins from Xanthomonas that suppresses protein aggregation and mediates harpin expression in E. coli.
  Mol Biol Rep, 34, 189-198.  
16603632 C.Zhu, E.Lau, R.Schwarzenbacher, E.Bossy-Wetzel, and W.Jiang (2006).
Spatiotemporal control of spindle midzone formation by PRC1 in human cells.
  Proc Natl Acad Sci U S A, 103, 6196-6201.  
17012383 D.Duché, A.Frenkian, V.Prima, and R.Lloubès (2006).
Release of immunity protein requires functional endonuclease colicin import machinery.
  J Bacteriol, 188, 8593-8600.  
16894158 S.R.Loftus, D.Walker, M.J.Maté, D.A.Bonsor, R.James, G.R.Moore, and C.Kleanthous (2006).
Competitive recruitment of the periplasmic translocation portal TolB by a natively disordered domain of colicin E9.
  Proc Natl Acad Sci U S A, 103, 12353-12358.
PDB code: 2ivz
17099236 S.Yajima, S.Inoue, T.Ogawa, T.Nonaka, K.Ohsawa, and H.Masaki (2006).
Structural basis for sequence-dependent recognition of colicin E5 tRNase by mimicking the mRNA-tRNA interaction.
  Nucleic Acids Res, 34, 6074-6082.
PDB codes: 2dfx 2djh
15739204 J.Ko, L.F.Murga, P.André, H.Yang, M.J.Ondrechen, R.J.Williams, A.Agunwamba, and D.E.Budil (2005).
Statistical criteria for the identification of protein active sites using Theoretical Microscopic Titration Curves.
  Proteins, 59, 183-195.  
15995205 M.Vankemmelbeke, B.Healy, G.R.Moore, C.Kleanthous, C.N.Penfold, and R.James (2005).
Rapid detection of colicin E9-induced DNA damage using Escherichia coli cells carrying SOS promoter-lux fusions.
  J Bacteriol, 187, 4900-4907.  
16166265 N.G.Housden, S.R.Loftus, G.R.Moore, R.James, and C.Kleanthous (2005).
Cell entry mechanism of enzymatic bacterial colicins: porin recruitment and the thermodynamics of receptor binding.
  Proc Natl Acad Sci U S A, 102, 13849-13854.  
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.  
15857830 Z.Shi, K.F.Chak, and H.S.Yuan (2005).
Identification of an essential cleavage site in ColE7 required for import and killing of cells.
  J Biol Chem, 280, 24663-24668.  
15333634 A.Martins, and S.Shuman (2004).
An RNA ligase from Deinococcus radiodurans.
  J Biol Chem, 279, 50654-50661.  
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.  
15133158 D.Walker, L.Lancaster, R.James, and C.Kleanthous (2004).
Identification of the catalytic motif of the microbial ribosome inactivating cytotoxin colicin E3.
  Protein Sci, 13, 1603-1611.  
15004032 G.Anderluh, I.Gökçe, and J.H.Lakey (2004).
A natively unfolded toxin domain uses its receptor as a folding template.
  J Biol Chem, 279, 22002-22009.  
14731273 J.L.Hilsenbeck, H.Park, G.Chen, B.Youn, K.Postle, and C.Kang (2004).
Crystal structure of the cytotoxic bacterial protein colicin B at 2.5 A resolution.
  Mol Microbiol, 51, 711-720.
PDB code: 1rh1
15014439 M.Graille, L.Mora, R.H.Buckingham, H.van Tilbeurgh, and M.de Zamaroczy (2004).
Structural inhibition of the colicin D tRNase by the tRNA-mimicking immunity protein.
  EMBO J, 23, 1474-1482.
PDB code: 1v74
15084581 M.J.Dubin, P.H.Stokes, E.Y.Sum, R.S.Williams, V.A.Valova, P.J.Robinson, G.J.Lindeman, J.N.Glover, J.E.Visvader, and J.M.Matthews (2004).
Dimerization of CtIP, a BRCA1- and CtBP-interacting protein, is mediated by an N-terminal coiled-coil motif.
  J Biol Chem, 279, 26932-26938.  
15465872 S.D.Zakharov, V.Y.Eroukova, T.I.Rokitskaya, M.V.Zhalnina, O.Sharma, P.J.Loll, H.I.Zgurskaya, Y.N.Antonenko, and W.A.Cramer (2004).
Colicin occlusion of OmpF and TolC channels: outer membrane translocons for colicin import.
  Biophys J, 87, 3901-3911.  
12902336 A.K.Mohanty, C.M.Bishop, T.C.Bishop, W.C.Wimley, and M.C.Wiener (2003).
Enzymatic E-colicins bind to their target receptor BtuB by presentation of a small binding epitope on a coiled-coil scaffold.
  J Biol Chem, 278, 40953-40958.  
12679333 G.Anderluh, Q.Hong, R.Boetzel, C.MacDonald, G.R.Moore, R.Virden, and J.H.Lakey (2003).
Concerted folding and binding of a flexible colicin domain to its periplasmic receptor TolA.
  J Biol Chem, 278, 21860-21868.  
13679579 G.E.Fanucci, N.Cadieux, R.J.Kadner, and D.S.Cafiso (2003).
Competing ligands stabilize alternate conformations of the energy coupling motif of a TonB-dependent outer membrane transporter.
  Proc Natl Acad Sci U S A, 100, 11382-11387.  
14528295 G.Kurisu, S.D.Zakharov, M.V.Zhalnina, S.Bano, V.Y.Eroukova, T.I.Rokitskaya, Y.N.Antonenko, M.C.Wiener, and W.A.Cramer (2003).
The structure of BtuB with bound colicin E3 R-domain implies a translocon.
  Nat Struct Biol, 10, 948-954.
PDB code: 1ujw
14500897 H.X.Zhou (2003).
Association and dissociation kinetics of colicin E3 and immunity protein 3: convergence of theory and experiment.
  Protein Sci, 12, 2379-2382.  
12526800 K.Pedersen, A.V.Zavialov, M.Y.Pavlov, J.Elf, K.Gerdes, and M.Ehrenberg (2003).
The bacterial toxin RelE displays codon-specific cleavage of mRNAs in the ribosomal A site.
  Cell, 112, 131-140.  
12598892 M.Aittaleb, R.Rashid, Q.Chen, J.R.Palmer, C.J.Daniels, and H.Li (2003).
Structure and function of archaeal box C/D sRNP core proteins.
  Nat Struct Biol, 10, 256-263.
PDB code: 1nt2
12629217 Z.Fu, E.Aronoff-Spencer, J.M.Backer, and G.J.Gerfen (2003).
The structure of the inter-SH2 domain of class IA phosphoinositide 3-kinase determined by site-directed spin labeling EPR and homology modeling.
  Proc Natl Acad Sci U S A, 100, 3275-3280.  
11864811 A.H.Parret, and R.De Mot (2002).
Bacteria killing their own kind: novel bacteriocins of Pseudomonas and other gamma-proteobacteria.
  Trends Microbiol, 10, 107-112.  
12136104 D.C.Walker, T.Georgiou, A.J.Pommer, D.Walker, G.R.Moore, C.Kleanthous, and R.James (2002).
Mutagenic scan of the H-N-H motif of colicin E9: implications for the mechanistic enzymology of colicins, homing enzymes and apoptotic endonucleases.
  Nucleic Acids Res, 30, 3225-3234.  
12021774 K.Mosbahi, C.Lemaître, A.H.Keeble, H.Mobasheri, B.Morel, R.James, G.R.Moore, E.J.Lea, and C.Kleanthous (2002).
The cytotoxic domain of colicin E9 is a channel-forming endonuclease.
  Nat Struct Biol, 9, 476-484.  
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.