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Immune system PDB id
7cei
Jmol
Contents
Protein chains
87 a.a. *
127 a.a. *
Metals
_ZN
Waters ×162
* Residue conservation analysis
PDB id:
7cei
Name: Immune system
Title: The endonuclease domain of colicin e7 in complex with its in im7 protein
Structure: Protein (colicin e7 immunity protein). Chain: a. Synonym: im7. Engineered: yes. Protein (colicin e7 immunity protein). Chain: b. Fragment: endonuclease domain. Synonym: cole7 dnase domain
Source: Escherichia coli str. K12 substr.. Organism_taxid: 316407. Strain: w3110. Gene: ceie7. Expressed in: escherichia coli. Expression_system_taxid: 562. Plasmid: pcole7
Biol. unit: Octamer (from PQS)
Resolution:
2.30Å     R-factor:   0.203     R-free:   0.270
Authors: T.P.Ko,C.C.Liao,W.Y.Ku,K.F.Chak,H.S.Yuan
Key ref:
T.P.Ko et al. (1999). The crystal structure of the DNase domain of colicin E7 in complex with its inhibitor Im7 protein. Structure, 7, 91. PubMed id: 10368275 DOI: 10.1016/S0969-2126(99)80012-4
Date:
17-Sep-98     Release date:   17-Sep-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q03708  (IMM7_ECOLX) -  Colicin-E7 immunity protein
Seq:
Struc: 		87 a.a.
87 a.a.
Protein chain
Pfam   ArchSchema ?
Q47112  (CEA7_ECOLX) -  Colicin-E7
Seq:
Struc: 		 
Seq:
Struc: 		576 a.a.
127 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     cytolysis   4 terms 
  Biochemical function     protein binding     4 terms  

 

 
DOI no: 10.1016/S0969-2126(99)80012-4 Structure 7:91 (1999)
PubMed id: 10368275  
 
 
The crystal structure of the DNase domain of colicin E7 in complex with its inhibitor Im7 protein.
T.P.Ko, C.C.Liao, W.Y.Ku, K.F.Chak, H.S.Yuan.
 
  ABSTRACT  
 
BACKGROUND: Colicin E7 (ColE7) is one of the bacterial toxins classified as a DNase-type E-group colicin. The cytotoxic activity of a colicin in a colicin-producing cell can be counteracted by binding of the colicin to a highly specific immunity protein. This biological event is a good model system for the investigation of protein recognition. RESULTS: The crystal structure of a one-to-one complex between the DNase domain of colicin E7 and its cognate immunity protein Im7 has been determined at 2.3 A resolution. Im7 in the complex is a varied four-helix bundle that is identical to the structure previously determined for uncomplexed Im7. The structure of the DNase domain of ColE7 displays a novel alpha/beta fold and contains a Zn2+ ion bound to three histidine residues and one water molecule in a distorted tetrahedron geometry. Im7 has a V-shaped structure, extending two arms to clamp the DNase domain of ColE7. One arm (alpha1(*)-loop12-alpha2(*); where * represents helices in Im7) is located in the region that displays the greatest sequence variation among members of the immunity proteins in the same subfamily. This arm mainly uses acidic sidechains to interact with the basic sidechains in the DNase domain of ColE7. The other arm (loop 23-alpha3(*)-loop 34) is more conserved and it interacts not only with the sidechain but also with the mainchain atoms of the DNase domain of ColE7. CONCLUSIONS: The protein interfaces between the DNase domain of ColE7 and Im7 are charge-complementary and charge interactions contribute significantly to the tight and specific binding between the two proteins. The more variable arm in Im7 dominates the binding specificity of the immunity protein to its cognate colicin. Biological and structural data suggest that the DNase active site for ColE7 is probably near the metal-binding site.
 
  Selected figure(s)  
 
Figure 6.
Figure 6. Stereoview of the interactions between the DNase domain of ColE7 and Im7. (a) The sidechains of Im7 in the region of a1^*-loop12-a2^* interact with the sidechains of the residues in the DNase domain. This region of Im7 dominates its specificity. Coloring is as in Figure 3. The green spheres represent water molecules. The detailed hydrogen-bond distances are listed in the top half of Table 1. (b) The sidechains in the region of loop23-a3^*-loop34 in Im7 interact not only with the sidechain, but also with the mainchain atoms of the DNase domain of ColE7. The detailed hydrogen-bond distances are listed in the bottom half of Table 1.
 
  The above figure is reprinted by permission from Cell Press: Structure (1999, 7, 91-0) copyright 1999.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

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11917029 W.Y.Ku, Y.W.Liu, Y.C.Hsu, C.C.Liao, P.H.Liang, H.S.Yuan, and K.F.Chak (2002).
The zinc ion in the HNH motif of the endonuclease domain of colicin E7 is not required for DNA binding but is essential for DNA hydrolysis.
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11292843 N.V.Grishin (2001).
Treble clef finger--a functionally diverse zinc-binding structural motif.
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11567151 R.A.Pauptit, C.A.Dennis, D.J.Derbyshire, A.L.Breeze, S.A.Weston, S.Rowsell, and G.N.Murshudov (2001).
NMR trial models: experiences with the colicin immunity protein Im7 and the p85alpha C-terminal SH2-peptide complex.
  Acta Crystallogr D Biol Crystallogr, 57, 1397-1404.
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Crystal structure of colicin E3: implications for cell entry and ribosome inactivation.
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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.  
  10973051 H.S.Malik, and S.Henikoff (2000).
Dual recognition-incision enzymes might be involved in mismatch repair and meiosis.
  Trends Biochem Sci, 25, 414-418.  
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A novel activation mechanism of caspase-activated DNase from Drosophila melanogaster.
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  11045617 R.Boetzel, M.Czisch, R.Kaptein, A.M.Hemmings, R.James, C.Kleanthous, and G.R.Moore (2000).
NMR investigation of the interaction of the inhibitor protein Im9 with its partner DNase.
  Protein Sci, 9, 1709-1718.
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  10794413 S.B.Whittaker, M.Czisch, R.Wechselberger, R.Kaptein, A.M.Hemmings, R.James, C.Kleanthous, and G.R.Moore (2000).
Slow conformational dynamics of an endonuclease persist in its complex with its natural protein inhibitor.
  Protein Sci, 9, 713-720.  
  10673426 S.Carr, C.N.Penfold, V.Bamford, R.James, and A.M.Hemmings (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.
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  10986462 S.Carr, D.Walker, R.James, C.Kleanthous, and A.M.Hemmings (2000).
Inhibition of a ribosome-inactivating ribonuclease: the crystal structure of the cytotoxic domain of colicin E3 in complex with its immunity protein.
  Structure, 8, 949-960.
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10480931 A.J.Pommer, U.C.Kühlmann, A.Cooper, A.M.Hemmings, G.R.Moore, R.James, and C.Kleanthous (1999).
Homing in on the role of transition metals in the HNH motif of colicin endonucleases.
  J Biol Chem, 274, 27153-27160.  
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.