PDBsum entry 1jch

Ribosome inhibitor, hydrolase

PDB id: 1jch

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 protein

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 chain b, 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

Protein chains

P00646  (CEA3_ECOLX) -  Colicin E3 from Escherichia coli

Seq: 551 a.a.

Struc: 468 a.a.*

Protein chains

P02984  (IMM3_ECOLX) -  Colicin E3 immunity protein from Escherichia coli

Seq: 85 a.a.

Struc: 84 a.a.

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: Chains A, C: E.C.4.6.1.- - ?????

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.