BIOINORGANIC CHEMISTRY A Short Course Second Edition

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

metal ion mechanism proposed for PDB: 1ZZN is similar to that seen for a
wide variety of protein enzymes and for promotion of phosphoryltransfer
reactions (many of these having a metal - metal distance around 3.9 Å ); and (3)
a marked similarity exists between the proposed PDB: 1ZZN active site and
the active sites of RNA and DNA polymerases that feature two metal ions
and very similar coordination spheres.
In early 2005, before publication of the PDB: 1ZZN structure just discussed,
the research group of Barbara Golden published the structure of a third group
I intron [PDB: 1Y0Q; please note that the third character in the PDB accession
number is a zero (0), and not a capitol “ oh ” (O)].^32 This structure visualizes
the second group I intron in theorf 142 gene of Staphylococcus aureus bacte-
riophage Twort. The 242 nucleotide (nt) ribozyme from the intron was co -
crystallized with a 4 - nt product analog RNA, and the structure was determined
by X - ray crystallography at a resolution of 3.6 Å. The Twort ribozyme - product
complex contained an active enzyme, including both 2 ′ - OH groups — on ω G
and U − 1 — at the splice site; however, it lacks the scissile phosphate - containing
nucleotide — A +1.
The tertiary structure of this ribozyme was found to be very similar to that
ofAzoarcus sp. (PDB: 1U6B and 1ZZN). Many of the tertiary interactions
found in the PDB: 1Y0Q structure are similar or identical to those seen as

Figure 6.8 A group I intron transition state stabilized by two magnesium ions (PDB:
1ZZN). Visualized using CambridgeSoft Chem3D Ultra 10.0 with notations in Chem-
Draw Ultra 10.0. (Printed with permission of CambridgeSoft Corporation.) (See color
plate)

C88

A172

A+1

P Mg 2

Mg 1

O1P, C88

G170

O1P, G170

O1P, A172

O2P, A172

exon-exon

bond

formationnucleophile

O3’, U-1

leaving group

O3’,ωG, G206

P, Phosphorus of

scissile

phosphate, A1

Distance = 3.2 A,

Bond angle for O3’,

U-1 (nucleophile) - P,

A+1 - O3’, ωG (G206,

leaving group) = 175o

5MU, U-1

ωG, G206

G128

O2’,ωG

O1P,

G128

pro-Rp O,A+1

1ZZN catalytic site