Eco RI Endonuclease

Eco RI-DNA Complex

Select:
Protein only.
DNA only.
Whole complex
(including H₂O).

Rotate:
X 90° X -90°
Y 90° Y -90°

Distances:
DNA
(in Å units).
Protein
(in Å units).

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Overall Architecture of the EcoRI dimer complex with DNA.
The starting display shows the DNA as sticks with white backbone and green bases. The 5' and 3' ends are labeled. The subunits of the EcoRI homodimer are labeled at their C-termini. Note the kink in the DNA at the center of the structure. This localized, four base pair distortion widens the major groove, making it fully accessible to the EcoRI recognition regions.

Highlight the regions of the complex involved in specific binding:

The "b-loop-a" motif and N-terminus of a-helix 5 (shown as cartoons with the "extended chain motif" displayed as magenta Sticks.

The GAATTC recognition sequence (Spacefill, colored CPK). The scissile bonds between the G5 and A6 nucleotides are colored red.

Close-up of the active site residues (Ball & Stick, colored CPK). The scissile bond between G5 and A6 is red.

View a schematic diagram of the Eco RI-DNA interactions in a pop-up window. The diagram is a useful complement to the Chime image and vice versa.
Viewing Suggestions:
1. The "Select" buttons restrict portions of the complex in their original display and coloring modes. (Each button also leaves the image with the corresponding portions selected; thus, alternative color or display choices can be chosen for each group from the Chime menu.)
2. The rotate buttons act on the entire structure. Remove the distance monitors with a second click.

The dimer shown here is the "Biological functional unit" derived from the monomer coordinates (1eri.pdb). Described in Kim, Y. et al. (1990) "Refinement of Eco RI endonuclease crystal structure: A revised protein chain tracing"Science 249, 1307.

The boxed area below contains a RasMol script that will produce the starting display on this page; it then highlights the DNA recognition regions and the six base pair recognition sequence. (Select and copy the text in the box for viewing in RasMol.)

#
The script used to display the starting view and highlighted regions: #!rasmol
-script # File: 1eribio2View.spt # Creator: RasMol Version 2.6 # W. McClure
9/25/98 # Load the Eco RI Dimer file (1eribio2.pdb) into RasMol; # Then
call this script. background [0,0,0] set ambient 60 set specular off reset
slab off rotate z -53 rotate x 97 zoom 130 set bonds off set axes off set
boundingbox off set unitcell off set hbond sidechain set bondmode and dots
off # Avoid Colour Problems! select all wireframe off colour bonds none
colour backbone none colour hbonds none colour ssbonds none colour ribbons
none colour white select dna colour green wireframe 60 select dna and backbone
colour white select dna and 13 and *.O3* label "3'" select dna and 1 and
*.O5* label "5'" color labels yellow set fontsize 9 select protein backbone
60 select *:A color redorange select *:A and 277 and *.ca label 'Chain
A' select *:C color cyan select *:C and 277 and *.ca label 'Chain C' select
all echo "Eco RI-DNA Complex" echo " DNA backbone is white; the bases are
green." echo " The 3' and 5' termini are labeled." echo " Protein chain
A is redorange." echo " Protein chain C is cyan." echo " " echo " Press
SPACE to highlight the DNA recognition regions." echo " " pause # color
the a positions, green and spacefill select 103-158 or 198-207 define bla
selected backbone off cartoons select 137-142 define ecm selected wireframe
60 color magenta restrict dna or bla select dna and 5-10 define site selected
select site and *:B and *.P label %m%r select site and not backbone spacefill
color cpk select (atomno=2138) or (atomno==2152) colour bonds red select
(atomno=4516) or (atomno==4530) colour bonds red select dna echo " The
'beta-loop-alpha motif' and helix 5 are cartoons." echo " The 'extended
chain motif' is displayed as magenta sticks." echo " The GAATTC recognition
sequence is spacefill, colored CPK." echo " The scissile bonds between
G5 and A6 are colored red." echo " " echo " Press SPACE to finish." echo
" " pause select all echo " Viewing suggestions:" echo " 1. View the complex
in spacefill and note the buried" echo " character of the (magenta) DNA
recognition regions." echo " 2. Zoom to identify and view specific residues."
echo " 3. Show waters as Ball & Stick to see bridging interactions."
echo " "

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