PDBsum entry 2ab5

Protein binding

PDB id: 2ab5

Contents

Protein chains

261 a.a. *

Ligands

SO4 ×8

Waters ×248

* Residue conservation analysis

PDB id:

2ab5

Name:

Protein binding

Title:

Bi3 laglidadg maturase

Structure:

mRNA maturase. Chain: a, b. Fragment: n-terminal insertion of mghhhhh. Engineered: yes

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: cytochrome b intron bi3. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

2.20Å R-factor: 0.208 R-free: 0.265

Authors:

A.Longo,C.W.Leonard,G.S.Bassi,D.Berndt,J.M.Krahn,T.M.Hall,K.M.Weeks

Key ref:

A.Longo et al. (2005). Evolution from DNA to RNA recognition by the bI3 LAGLIDADG maturase. Nat Struct Mol Biol, 12, 779-787. PubMed id: 16116439 DOI: 10.1038/nsmb976

Date:

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

Protein chains

Q9ZZW7  (MBI3_YEAST) -  Cytochrome b mRNA maturase bI3 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 517 a.a.

Struc: 261 a.a.*

* PDB and UniProt seqs differ at 13 residue positions (black crosses)

DOI no: 10.1038/nsmb976

Nat Struct Mol Biol 12:779-787 (2005)

PubMed id: 16116439

Evolution from DNA to RNA recognition by the bI3 LAGLIDADG maturase.

A.Longo, C.W.Leonard, G.S.Bassi, D.Berndt, J.M.Krahn, T.M.Hall, K.M.Weeks.

ABSTRACT

LAGLIDADG endonucleases bind across adjacent major grooves via a saddle-shaped surface and catalyze DNA cleavage. Some LAGLIDADG proteins, called maturases, facilitate splicing by group I introns, raising the issue of how a DNA-binding protein and an RNA have evolved to function together. In this report, crystallographic analysis shows that the global architecture of the bI3 maturase is unchanged from its DNA-binding homologs; in contrast, the endonuclease active site, dispensable for splicing facilitation, is efficiently compromised by a lysine residue replacing essential catalytic groups. Biochemical experiments show that the maturase binds a peripheral RNA domain 50 A from the splicing active site, exemplifying long-distance structural communication in a ribonucleoprotein complex. The bI3 maturase nucleic acid recognition saddle interacts at the RNA minor groove; thus, evolution from DNA to RNA function has been mediated by a switch from major to minor groove interaction.

Selected figure(s)

Figure 7.
Figure 7. Maturase-RNA interactions. (a) Site-directed cleavage patterns superimposed on a three-dimensional model for the bI3 maturase and P5-P4-P6 domain complex. Spheres, sites of derivatization; colored RNA backbones, cleavage sites; green, -strands of the bI3 maturase. (b) Summary of 2'-O-methyl interference in the P5b and P5c helices. Maturase is shown slightly transparent for clarity. Red spheres, sites of 2'-O-methyl interference (Supplementary Fig. 1); blue backbone, solvent-based hydroxyl radical cleavage sites (Fig. 5c,d).

Figure 8.
Figure 8. Maturase-facilitated folding of the bI3 intron RNA via action at a distance. The bI3 maturase recognizes a distal structure in a peripheral domain and lies at least 50 Å from the group I intron active site (orange). Green, the maturase -strands; dark gray, the remainder of the protein; light blue, regions protected from solvent-based hydroxyl radical cleavage upon maturase binding; yellow spheres, sulfate groups visualized crystallographically; brown asterisk, a potential auxiliary RNA-protein interaction site.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Mol Biol (2005, 12, 779-787) copyright 2005.

Figures were selected by the author.