PDBsum entry 1zzn

Structural protein/RNA

PDB id: 1zzn

Contents

Protein chain

95 a.a. *

DNA/RNA

Metals

_MG ×5

__K

Waters ×54

* Residue conservation analysis

PDB id:

1zzn

Name:

Structural protein/RNA

Title:

Crystal structure of a group i intron/two exon complex that includes all catalytic metal ion ligands.

Structure:

197-mer. Chain: b. Engineered: yes. Other_details: group i intron. 5'-r( Ap Ap Gp Cp Cp Ap Cp Ap Cp Ap Ap Ap Cp Cp Ap Gp Ap Cp Gp Gp Cp C)-3'. Chain: c. Engineered: yes. Other_details: group i intron, 3'-exon.

Source:

Synthetic: yes. Other_details: RNA was is transcribed by t7 RNA polymerase. Sequence from azoarcus group i intron. Other_details: solid phase sythesis. Sequence from azoarcus intron and exon sequence.. Other_details: solid phase synthesis. Sequence from azoarcus group i intron 5'-exon sequence.. Homo sapiens. Human.

Biol. unit:

Tetramer (from PQS)

Resolution:

3.37Å R-factor: 0.269 R-free: 0.307

Authors:

M.R.Stahley,S.A.Strobel

Key ref:

M.R.Stahley and S.A.Strobel (2005). Structural evidence for a two-metal-ion mechanism of group I intron splicing. Science, 309, 1587-1590. PubMed id: 16141079 DOI: 10.1126/science.1114994

Date:

14-Jun-05 Release date: 30-Aug-05

Protein chain

P09012  (SNRPA_HUMAN) -  U1 small nuclear ribonucleoprotein A from Homo sapiens

Seq: 282 a.a.

Struc: 95 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

DNA/RNA chains

GTP-G-C-C-G-U-G-U-G-C-C-U-U-G-C-G-C-C-G-G-G-A-A-A-C-C-A-C-G-C-A-A-G-G-G-A-U-G- 197 bases

A-A-G-C-C-A-C-A-C-A-A-A-C-C-A-G-A-C-G-G-C-C 22 bases

C-A-5MU 3 bases

DOI no: 10.1126/science.1114994

Science 309:1587-1590 (2005)

PubMed id: 16141079

Structural evidence for a two-metal-ion mechanism of group I intron splicing.

M.R.Stahley, S.A.Strobel.

ABSTRACT

We report the 3.4 angstrom crystal structure of a catalytically active group I intron splicing intermediate containing the complete intron, both exons, the scissile phosphate, and all of the functional groups implicated in catalytic metal ion coordination, including the 2'-OH of the terminal guanosine. This structure suggests that, like protein phosphoryltransferases, an RNA phosphoryltransferase can use a two-metal-ion mechanism. Two Mg2+ ions are positioned 3.9 angstroms apart and are directly coordinated by all six of the biochemically predicted ligands. The evolutionary convergence of RNA and protein active sites on the same inorganic architecture highlights the intrinsic chemical capacity of the two-metal-ion catalytic mechanism for phosphoryl transfer.

Selected figure(s)

Figure 1.
Fig. 1. The group I intron splicing reaction. (A) Secondary structure of the pre-2S crystallization construct. The residues discussed in the text are shown superimposed on the secondary structure. RNA connectivity is depicted with a dashed line with small arrows to show the 5' to 3' orientation. Exons are shown in red. The coloring of other residues corresponds to the structural element in which they are located: P4 to P6 (green), P3 to P9 (blue), and J8/7 (purple). (B) Summary of the biochemically defined ligands for active-site metal coordination. The six oxygens shown in orange have been implicated in metal-ion coordination on the basis of metal specificity switch experiments (10-15), including four in the substrates and two in the intron. Ligands biochemically shown to coordinate the same metal are depicted with double-ended arrows. The exon splicing reaction involving attack of the U-1 O3' on the scissile phosphate with loss of the G O3' is shown with curved arrows. (C) Proposed three-metal-ion mechanism based on differential Mn2+ affinity to sulfur/amino-substituted substrates (21, 22). The four substrate ligands in (B) are coordinated to three metal ions, M[A], M[B], and M[C].

Figure 3.
Fig. 3. A two-metal mechanism for group I intron splicing. (A) F[O]-F[C] omit map (active-site metals were not included in the model) used to assign M[1] and M[2] positions, superimposed on the refined structure. The native density (5 ) for each metal is depicted in blue. The other residues are as labeled. In (A), (B), and (D), the scissile bond, nucleophile, and leaving group are shown in yellow. (B) Active-site coordination to M[1] and M[2]. In this and (D), the active-site Mg2+ ions are shown as large orange spheres, the predicted inner and outer sphere ligands are shown as small orange spheres, and the metal-to-metal distance is labeled. Orange lines indicate inner sphere coordinations. Labels for the individual nucleotides are as in Fig. 2A. All the coordinations depicted in Fig. 1B are satisfied in this structure. (C) Model of the group I intron transition state stabilized by a two-metal mechanism. (D) Two-metal active-site coordination within the T7 DNA polymerase (1). The incoming deoxy-nucleotide triphosphate (dNTP), the primer oligonucleotide, and active-site aspartates are labeled. The nucleophile was not present in the crystal structure but is modeled here for comparison.

The above figures are reprinted by permission from the AAAs: Science (2005, 309, 1587-1590) copyright 2005.

Figures were selected by the author.