Biochem 503, Fall 2000

Structure and Mechanism: Ribonuclease A


Further Reading

Mathews and van Holde, Biochemistry(text book), pp. 186
Borah et al (1985) Biochemistry 24 2058-2064.

The 3-D structure of ribonuclease A has been determined crystallographically. It has three a-helical regions and a long twisted saddle-shaped b-sheet segments consisting of 3 strands. You can apply RasMol program to view the 3-D molecular image of ribonulease A by clicking the PDB file 3RN3. In this molecular structure, a [SO42-] group is present in the active site. Specifically, the ribbon-representation of the 3-D image can be generated as follows: After you open up the PDB file 3RN3, you need first to select Ribbons under Display menu, and then select Structure under Colours menu. Now you get the 3-D image of this enzyme without the ligand of [SO42-], and you can view it "your way" with RasMol. If you are interested in finding out the locations of the four S-S linkages (1: 26 - 84; 2: 40 - 95; 3: 58 - 110; 4: 65 - 72) in this enzyme, you can locate them by typing the following command lines:

background white
ssbonds 50
set ssbonds backbone
color ssbonds cyan

You can press the mouse's pointer at one end of the S-S bond, and the command-line window will report back to you the name and number of the residue (Cys26, for instance) that you just picked. Keep the display window open. And you can continue to explore the spatial relationships of the five residues (His12, Lys41, Thr45, His119, Asp121) that are present in the active site of the enzyme by typing the following script:

define act (his12,lys41,thr45,his119,asp121)
select (act and sidechain),,,,,,[SO4]
save act.pdb
wireframe 60
color cpk
select [SO4]
cpk 250

With the pointer, you can easily identify that the Ne2 of His12, Nd1 of His119, and Nz of Lys41 are all oriented towards the negatively charged ligand, [SO42-]. In addition, one carboxyl oxygen of Asp121 and the Ne2 atom of His119 are in close proximity with a separation distance of 2.6 ; hence, a H-bond between them can be inferred. Interestingly, the spatial arrangement of Asp121 and His119 residues seen here resembles that of His57 and Asp102 residues in the catalytic triad of all serine proteases. It should be mentioned that the side chain and the backbone of Thr45 could form H-bonds with the pyrimidine ring of the substrate; however, these H-bonds are not seen here. At this point, if you are not sure about the nomenclature designated to different atoms in the side chain of various amino acids, you should go back to the web page dated 9/4/00 in which the nomenclatures are given in the GIF images. Next, you can focus at the active site of ribonuclease A by using the following command lines:

load act.pdb
background white
wireframe 80
select his12.ne2
label H12
label K41
select thr45.cg2
label T45
select his119.nd1
label H119
label D121
color label black
set fontsize 10
select [so4]
cpk 300

With the 6rsa, you can examine the complex of ribonuclease A and vanadate. This complex closely mimics the pentacovalent transition state of ribonuclease as it catalyzes the formation of cyclic intermediate in the presence of substrate.

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