BIOINORGANIC CHEMISTRY A Short Course Second Edition

246 GROUP I AND II METALS IN BIOLOGICAL SYSTEMS: GROUP II

are defi ned as joining regions. The catalytic core is located at the junction of
the P4 – P6 and P3 – P9 domains. The 5 ′ exon splice site is located in the P1 – P2
(substrate) domain. The internal guide sequence (IGS) guides the substrate to
form an open complex with the enzyme to form the so - called P1 duplex that
subsequently docks via tertiary interactions to form the active, closed ribo-
zyme - substrate complex. Note that the fi nal G of the IGS forms a mismatch
base pair with a uracil, U ; this is called the G – U wobble base. Wobble bases
are a common motif in RNA secondary structure, and they have important
and specifi c functions in all types of RNA. All group I introns contain a G – U
wobble base pair at the cleavage site that is almost universally conserved.^25

Figure 6.4 Secondary structure of a group I intron ribozyme. (From Figure 1 of refer-
ence 13. Reprinted with permission of AAAS.) (See color plate)

C–G U A

G–C

GU

U G

C–G

C–G

C–G

G–C

U–A

C–G

A–U

G–C

U AGA

AA

U

A–U

C–G

C–G•180

UAU

G

G

G

AG

U G

A A

A A

G U

G U

C–G

AAGG

P4–P6 P1–P2.1 P3–P9

UJ3/4

C A

U J6/7

3 ′

5 ′

• (^110260)
C–G
C–G
C–C
G–C
C–G
C–G
C–G
GU
U–A
C–G
A–U
A–U
C–G
A–U
G–C
AU
UUC
U A
AA
A–U
U–A
U
•250
•240
A
AG
GU
U–A
C–G
U–A
P5bC–G
Tetraloop
(L5b) Tetraloopreceptor
(J6a/6b)
220 •
P6a
P6b
230 •
L6b
A–U
G–C
G A
AA
G U
G U
AAA
L5c P4
P6
C A
AA
C
G
C
CCUUG
A-rich
bulge
P5
200 •
•120
P5a

• 190

130 •

J5/5a

GACA

ACA

J4/5

210•A

P5a

P5c

170

• 160

140 •

150 •

U G–U

3 ′

5 ′