JMol Tutorial created with support from Seth Darst (Darst Lab, Rockefeller University) and Tim Herman (Center for Biomolecular Modeling).

Please email tshata@gmail.com if you have any questions or to report problems with this tutorial.  Thank you.

Using this tutorial:
This website runs the Jmol molecule viewer. You will need a Java-enabled browser to view this website. Refresh your browser to resize applet to your screen size.

You can follow the tutorial below while watching short animated scripts by clicking the appropriate buttons.  At anytime, if you want to change the view of the structure, do the following:
Rotate: Click on mouse and drag
Zoom: Scroll wheel on your mouse or +Shift and left click
Move: +Ctrl and right click

If you are familiar with RasMol commands, you can also use them through the JMol console.

Color-code amino acids

Reset color
 

Introduction

There are a variety of types of microcins encoded by bacterial plasmids. Microcins are naturally occurring antibiotics that inhibit the growth of bacteria. When bacteria are under the stress of low nutrients, they express microcin along with membrane binding “pumps” that export the microcin out of the cell. Microcin is toxic not only to surrounding bacteria but also to the bacteria that produce it, so it is important that during the expression of microcin they also produce these proteins that quickly export it out of the cell. The inhibition of surrounding bacteria gives the microcin producing bacteria more opportunity to acquire sufficient nutrients to survive.
 
The microcin J25 (MccJ25) inhibits bacterial RNA polymerase. The 21 residue microcin J25 forms a very unique “lassoed tail” structure. The chain of amino acids binds to itself forming an 8 amino acid ring and a tail, looped and held through the ring. The free terminal amine group condenses to form a peptide bond with the carboxyl group of the Glu 8 (blue),  8 residues from the amine terminus. The tail amino acids (the 13 amino acids not included in the ring structure) loop through the ring and are held in place. The large Phe19 (green) and Tyr20 (red) residues are facing opposite directions on the tail; one is above the ring and one below.  Their size physically hold the tail from sliding either direction through the ring. Other residues (Val6 (orange), Pro7 (yellow), Glu8 (blue)) on the ring are also thought to stabilize the lasso structure by interacting with the Phe19 (green) and Tyr20 (red) on the tail.

It is unknown how microcin J25 is oriented when it inhibits bacterial RNA polymerase, but it is known that it blocks the secondary channel. The secondary channel is where the nucleotides enter the active cite and combine into a strand of RNA. When this channel is blocked, it is impossible to continue synthesis of RNA. The synthesis of RNA by RNA polymerase is crucial for survival because it is a key stage of protein expression. Without transcription, bacteria will no longer be able to produce proteins to support their functions and growth.

 

Color-code amino acids

Reset color

JMol scripts and text by Sam Williams

PDB file: 1Q71. 

Rosengren, K.J., Clark, R., Daly, N.L., Goransson, U., Jones, A., Craik, D.J. Microcin J25 is a threaded sidechain-to-backbone ring structure and not a head-to-tail cyclized backbone J.Am.Chem.Soc. v125 pp.12464-12474 , 2003