nativeproteins.blogspot.com

Return to Gallery index.

Reassembled Triose phosphate isomerase

From Thermotoga maritima(n1_1B9B.pdb)

(Display produced using JSmol and HTML5. If you don't see a structure try a different browser.)

Access a full JSmol function menu by clicking the link, below right, or right-clicking inside the black box.

You can manipulate the structure directly by dragging with the mouse. Mouse drag down with Shift key to zoom. Try gestures on touch screen devices. Click on the links below the black box to see other useful views of the structure. Advanced users can select the Console from the function menu and directly enter JSmol commands.

JSmol Menu

spin on / spin off
View chain A down the alpha-helix barrel
Spacefilling display.
Cut halfway through the protein to show the interior (best in conjunction with spacefilling). Can rotate while viewing.
Restore original view.

As with other enzymes, the catalytic site is enclosed and physically constrained. Constraint is produced by the focussed compressive stress of four barrels. The orientation of the barrels deviates from a regular tetrahedron to provide the optimum spatial distribution of stress for catalysis at the active site.

Note that, as in all enzyme barrels containing helices, these helices are orientated as if the barrel has a right-handed twist. Analysis of the structural elements within an alpha helix suggests that this twist maximises stiffness through the central axis of the barrel. The calculation suggests that maximum stiffness is achieved when the helices are inclined 25° away from the direction of the barrel. Conversely a left-handed twist would maximise longitudinal stiffness at the periphery. A left-handed twist is seen in almost all structural proteins composed of bundles of alpha helices, such as keratin, presumably because stiffness at the periphery provides resistance to bending.

The sulfur atoms of pairs of cys142 can be seen coloured yellow on the y axis. These form intersubunit disulfide links in the native form and in the crystal. In the reassembled pdb file the first entry is the N-terminal amino acid numbered 501 as it is in the original 1B9B.pdb so that it is clear which data have been transformed. Consequently cys142 is numbered cys642.

For further information about this protein, see the post of 7 January 2012 on nativeproteins.blogspot.com Or contact the author, Dr Don Vanselow at dvanselow@hotmail.com

Further details of JSmol available here