PDBsum entry 7d0f

Transferase/RNA

PDB id: 7d0f

Contents

Protein chain

447 a.a.

DNA/RNA

PDB id:

7d0f

Name:

Transferase/RNA

Title:

Cryo-em structure of a pre-catalytic group ii intron rnp

Structure:

RNA (738-mer). Chain: a. Engineered: yes. Group ii intron-encoded protein ltra. Chain: c. Engineered: yes

Source:

Lactococcus lactis subsp. Cremoris. Organism_taxid: 1359. Gene: ltrb. Expressed in: lactococcus lactis subsp. Cremoris. Expression_system_taxid: 1359. Gene: ltra, matr.

Authors:

N.Liu,X.L.Dong,C.X.Hu,J.W.Zeng,J.W.Wang,J.Wang,H.W.Wang,M.Belfort

Key ref:

N.Liu et al. (2020). Exon and protein positioning in a pre-catalytic group II intron RNP primed for splicing. Nucleic Acids Res, 48, 11185-11198. PubMed id: 33021674 DOI: 10.1093/nar/gkaa773

Date:

10-Sep-20 Release date: 30-Sep-20

Protein chain

P0A3U0  (LTRA_LACLC) -  Group II intron-encoded protein LtrA from Lactococcus lactis subsp. cremoris

Seq: 599 a.a.

Struc: 447 a.a.

DNA/RNA chain

C-A-C-A-U-C-C-A-U-A-A-C-G-U-G-C-G-C-C-C-A-G-A-U-A-G-G-G-U-G-U-U-A-A-G-U-C-A-A- ... 738 bases

Enzyme reactions

• Enzyme class 2: E.C.2.7.7.49 - RNA-directed Dna polymerase.
• Reaction: DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate
• Enzyme class 3: E.C.3.1.-.-

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1093/nar/gkaa773

Nucleic Acids Res 48:11185-11198 (2020)

PubMed id: 33021674

Exon and protein positioning in a pre-catalytic group II intron RNP primed for splicing.

N.Liu, X.Dong, C.Hu, J.Zeng, J.Wang, J.Wang, H.W.Wang, M.Belfort.

ABSTRACT

Group II introns are the putative progenitors of nuclear spliceosomal introns and use the same two-step splicing pathway. In the cell, the intron RNA forms a ribonucleoprotein (RNP) complex with the intron-encoded protein (IEP), which is essential for splicing. Although structures of spliced group II intron RNAs and RNP complexes have been characterized, structural insights into the splicing process remain enigmatic due to lack of pre-catalytic structural models. Here, we report two cryo-EM structures of endogenously produced group II intron RNPs trapped in their pre-catalytic state. Comparison of the catalytically activated precursor RNP to its previously reported spliced counterpart allowed identification of key structural rearrangements accompanying splicing, including a remodeled active site and engagement of the exons. Importantly, altered RNA-protein interactions were observed upon splicing among the RNP complexes. Furthermore, analysis of the catalytically inert precursor RNP demonstrated the structural impact of the formation of the active site on RNP architecture. Taken together, our results not only fill a gap in understanding the structural basis of IEP-assisted group II intron splicing, but also provide parallels to evolutionarily related spliceosomal splicing.