The Structural and Functional Uniqueness of the glmS Ribozyme - Progress in Molecular Biology and Translational Science - page 173

5. glmS RIBOZYME STRUCTURE AND FUNCTION —
BIOCHEMICAL ANALYSES

The glmS ribozyme contains four paired regions (P1-P4) that fold to
form a catalytic core ( Fig. 5.1 ). 2 Double-nested pseudoknots are a defining
feature of the three-dimensional structure of the glmS ribozyme, with the
P2.1 and P2.2 pseudoknots comprising the catalytic core. P1 and P2 contain

A B

P1

U UA G

50

P4.1

UA C

A G

C G

C

G

C

30

P2.2

P2.1

C A

G

P4

5´- A G

G U

1

A

U

P2

P3

P3.1

- 3´

Figure 5.1 Structure of the glmS ribozyme. (A) Secondary structure. The core
sequence of the Bacillus cereus glmS ribozymeisshownwithhighlyconservednucle-
otides in red (P2.1 and P2.2), while requisite structural elements (P1 and P2) and
peripheral structural elements (P3 - P4) are schematically shown in dark gray and light
gray, respectively. The arrowhead denotes the site of self-cleavage. (B) Tertiary struc-
ture. The ribbon model depicts the structure of the Bacillus anthracis glmS ribozyme
determined by X-ray crystallography in complex with U1A protein (not shown) bound
to a site inserted into the loop of P1 (PDB ID: 2NZ4 rendered using Chimera). 13,22 - 24
The trans-cleaving glmS ribozyme used for crystallography includes a substrate strand
(turquoise) and a catalytic strand (magenta). The coenzyme GlcN6P and nucleotides in
the immediate vicinity of the cleavage site are shown in ball-and-stick format. Nucle-
otide identity and numbering within the catalytic core are identical to that of the
B. cereus ribozyme.