Crystal structure of colicin E3 immunity protein: an inhibitor of a ribosome-inactivating RNase

Li, Chunmin; Zhao, Dong; Djebli, Abdellah; Shoham, Menachem

doi:10.1016/s0969-2126(00)80026-x

Cited by 16 publications

(15 citation statements)

References 44 publications

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“…In this procedure, 15 biological contacts, which are seven entries that can be monomeric proteins, seven entries with the second or third largest interfaces in the multimeric oligomers, and one entry judged as the dimer protein according to their primary citations, were excluded. The last entry, 3eip (Li et al 1999), contains two subunits of immunity protein Im3 which is a specific inhibitor of colicin E3, in the ASU. The two subunits form the loosely-packed interface, because the zinc and two water molecules mediate the inter-subunit interaction.…”

Section: Methodsmentioning

confidence: 99%

Discrimination between biological interfaces and crystal-packing contacts

Tsuchiya¹

2008

AABC

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A discrimination method between biologically relevant interfaces and artificial crystal-packing contacts in crystal structures was constructed. The method evaluates protein-protein interfaces in terms of complementarities for hydrophobicity, electrostatic potential and shape on the protein surfaces, and chooses the most probable biological interfaces among all possible contacts in the crystal. The method uses a discriminator named as “COMP”, which is a linear combination of the complementarities for the above three surface features and does not correlate with the contact area. The discrimination of homo-dimer interfaces from symmetry-related crystal-packing contacts based on the COMP value achieved the modest success rate. Subsequent detailed review of the discrimination results raised the success rate to about 88.8%. In addition, our discrimination method yielded some clues for understanding the interaction patterns in several examples in the PDB. Thus, the COMP discriminator can also be used as an indicator of the “biological-ness” of protein-protein interfaces.

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Section: Methodsmentioning

confidence: 99%

Discrimination between biological interfaces and crystal-packing contacts

Tsuchiya¹

2008

AABC

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“…The antibiotic-like protein colicin E3 of E. coli acts as an RNase that specifically cleaves 16S rRNA (Li et al 1999a). E. coli is protected from the action of this enzyme by forming a tight complex with an immunity protein, 1m3.…”

Section: Zinc-cys Protein Interface Sitesmentioning

confidence: 99%

Zinc coordination sphere in biochemical zinc sites

Auld

2001

Zinc Biochemistry, Physiology, and Homeostasis

235

290

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Zinc is known to be indispensable to growth and development and transmission of the genetic message. It does this through a remarkable mosaic of zinc binding motifs that orchestrate all aspects of metabolism. There are now nearly 200 three dimensional structures for zinc proteins, representing all six classes of enzymes and covering a wide range of phyla and species. These structures provide standards of reference for the identity and nature of zinc ligands in other proteins for which only the primary structure is known. Three primary types of zinc sites are apparent from examination of these structures: structural, catalytic and cocatalytic. The most common amino acids that supply ligands to these sites are His, Glu, Asp and Cys. In catalytic sites zinc generally forms complexes with water and any three nitrogen, oxygen and sulfur donors with His being the predominant amino acid chosen. Water is always a ligand to such sites. Structural zinc sites have four protein ligands and no bound water molecule. Cys is the preferred ligand in such sites. Cocatalytic sites contain two or three metals in close proximity with two of the metals bridged by a side chain moiety of a single amino acid residue, such as Asp, Glu or His and sometimes a water molecule. Asp and His are the preferred amino acids for these sites. No Cys ligands are found in such sites. The scaffolding of the zinc sites is also important to the function and reactivity of the bound metal. The influence of zinc on quaternary protein structure has led to the identification of a fourth type of zinc binding site, protein interface. In this case zinc sites are formed from ligands supplied from amino acid residues residing in the binding surface of two proteins. The resulting zinc site usually has the coordination properties of a catalytic or structural zinc binding site.Abbreviations: ABC -ATP-binding cassette; AAP -Aeromonas proteolytica aminopeptidase; ADAadenosine deaminase; ADAM -A disintegrin and metalloprotease domain; ADH -alcohol dehydrogenase; ALA-5-aminolevulinic acid; ALAD-5-aminolevulinic acid dehydratase; Apo2L or TRAIL-apoptosis-inducing ligand 2; BIR-baculovirus inhibitor of apoptosis repeat; BLAP-bovine lens leucine aminopeptidase; CA-carbonic anhydrase; CAM-y-carbonic anhydrase; CPD A-carboxypeptidase A; CDA-cytidine deaminase; EDTA -ethylenediaminetetraacetic acid; eNOS or NOS-3-endothelial nitric oxide synthase; FPP-farnesyl diphosphate; FTase -farnesyl transferase; H4B -tetrahydrobiopterin; HIV -human immunodeficiency virus; GGPPgeranylgeranyl diphosphate; GSNO-S-nitrosoglutathione; HLA-DR-class II major histocompatibility molecule; huiFN-human interferon; lAP-inhibitor of apoptosis; iNOS or NOS-2 -inducible nitric oxide synthase; Im3 -E. coli immunity protein; IUB -International Union of Biochemistry; MEROPS -system for classification of peptidase sequences; MetAP-1 -methionine aminopeptidase-); MetAP-2 -methionine aminopeptidase-2; MHC-major histocompatibility complex; MMP-matrix metalloproteinase; MPD-2-methyl-2,4-pentanediol; NAD...

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“…As shown in Figure 2, the electrostatic potentials on the two sides of the interface of the E3 RNase/Im3 complex show high complementarity, suggesting that the two proteins will have strong electrostatic attraction in the transition state for association. The immunity protein was found not to undergo any significant structural change upon binding with colicin E3 (Li et al 1999; Soelaiman et al 2001), likely allowing interprotein relative diffusion to be rate limiting for association. Electrostatic attraction and diffusion control provide optimization of the association rate constant.…”

Section: Disparate Ionic‐strength Dependences Of Ka and Kd For Rnase mentioning

confidence: 99%

Association and dissociation kinetics of colicin E3 and immunity protein 3: Convergence of theory and experiment

Zhou

2003

Protein Science

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The rapid binding of cytotoxic colicin E3 by its cognate immunity protein Im3 is essential in safeguarding the producing cell. The X-ray structure of the E3/Im3 complex shows that the Im3 molecule interfaces with both the C-terminal ribonuclease (RNase) domain and the N-terminal translocation domain of E3. The association and dissociation rates of the RNase domain and Im3 show drastically different sensitivities to ionic strength, as previously rationalized for electrostatically enhanced diffusion-limited protein-protein associations. Relative to binding to the RNase domain, binding to full-length E3 shows a comparable association rate but a significantly lower dissociation rate. This outcome is just what was anticipated by a theory for the binding of two linked domains to a protein. The E3/Im3 system thus provides a powerful paradigm for the interplay of theory and experiment.

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Crystal structure of colicin E3 immunity protein: an inhibitor of a ribosome-inactivating RNase

Cited by 16 publications

References 44 publications

Discrimination between biological interfaces and crystal-packing contacts

Discrimination between biological interfaces and crystal-packing contacts

Zinc coordination sphere in biochemical zinc sites

Association and dissociation kinetics of colicin E3 and immunity protein 3: Convergence of theory and experiment

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