PDBsum entry: 1emv

Immune system

PDB id: 1emv

Contents

Protein chains

83 a.a. *

131 a.a. *

Ligands

PO4

Waters ×154

* Residue conservation analysis

PDB id:

1emv

Name:

Immune system

Title:

Crystal structure of colicin e9 dnase domain with its cognate immunity protein im9 (1.7 angstroms)

Structure:

Immunity protein im9. Chain: a. Synonym: imme9, microcin e9 immunity protein. Engineered: yes. Colicin e9. Chain: b. Fragment: c-terminal domain, dnase domain. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

1.70Å R-factor: 0.219 R-free: 0.260

Authors:

U.C.Kuhlmann,A.J.Pommer,G.M.Moore,R.James,C.Kleanthous

Key ref:

U.C.Kühlmann et al. (2000). Specificity in protein-protein interactions: the structural basis for dual recognition in endonuclease colicin-immunity protein complexes. J Mol Biol, 301, 1163-1178. PubMed id: 10966813 DOI: 10.1006/jmbi.2000.3945

Date:

20-Mar-00 Release date: 13-Sep-00

Protein chain

P13479  (IMM9_ECOLX) -  Colicin-E9 immunity protein

Seq: 86 a.a.

Struc: 83 a.a.

Protein chain

P09883  (CEA9_ECOLX) -  Colicin-E9

Seq: 582 a.a.

Struc: 131 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 

• Biological process: cytolysis (4 terms)
• Biochemical function: protein binding (4 terms)

DOI no: 10.1006/jmbi.2000.3945

J Mol Biol 301:1163-1178 (2000)

PubMed id: 10966813

Specificity in protein-protein interactions: the structural basis for dual recognition in endonuclease colicin-immunity protein complexes.

U.C.Kühlmann, A.J.Pommer, G.R.Moore, R.James, C.Kleanthous.

ABSTRACT

Bacteria producing endonuclease colicins are protected against their cytotoxic activity by virtue of a small immunity protein that binds with high affinity and specificity to inactivate the endonuclease. DNase binding by the immunity protein occurs through a "dual recognition" mechanism in which conserved residues from helix III act as the binding-site anchor, while variable residues from helix II define specificity. We now report the 1.7 A crystal structure of the 24.5 kDa complex formed between the endonuclease domain of colicin E9 and its cognate immunity protein Im9, which provides a molecular rationale for this mechanism. Conserved residues of Im9 form a binding-energy hotspot through a combination of backbone hydrogen bonds to the endonuclease, many via buried solvent molecules, and hydrophobic interactions at the core of the interface, while the specificity-determining residues interact with corresponding specificity side-chains on the enzyme. Comparison between the present structure and that reported recently for the colicin E7 endonuclease domain in complex with Im7 highlights how specificity is achieved by very different interactions in the two complexes, predominantly hydrophobic in nature in the E9-Im9 complex but charged in the E7-Im7 complex. A key feature of both complexes is the contact between a conserved tyrosine residue from the immunity proteins (Im9 Tyr54) with a specificity residue on the endonuclease directing it toward the specificity sites of the immunity protein. Remarkably, this tyrosine residue and its neighbour (Im9 Tyr55) are the pivots of a 19 degrees rigid-body rotation that relates the positions of Im7 and Im9 in the two complexes. This rotation does not affect conserved immunity protein interactions with the endonuclease but results in different regions of the specificity helix being presented to the enzyme.

Selected figure(s)

Figure 4.
Figure 4. Hydrogen bonding interactions at the E9 DNase-Im9 interface. (a) and (b) show similar orientations of the interface and are stereo representations in which Im9 is coloured yellow with light side-chains and the DNase red with dark side-chains. Details are given in Table 2 and Table 3. (a) Direct hydrogen bonds between Im9 and the E9 DNase surrounding the core of the interface, made up of a stacking interaction between Tyr54 Im9 with Phe86 E9 DNase. (b) Water-mediated hydrogen bonds.

Figure 10.
Figure 10. Comparison of hydrogen bonding interactions to conserved water molecules in the E7 DNase-Im7 (from [Ko et al 1999]), dark shading, and E9 DNase-Im9 complexes (present work), light shading. With the exception of Asn90 (which is glutamine in the E7 DNase), conserved side-chains and backbone atoms are involved in coordinating the interfacial water molecules. Hydrogen bonds and side-chain numbering are for the E9 DNase-Im9 complex.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2000, 301, 1163-1178) copyright 2000.

Figures were selected by an automated process.