6ZM2 image
Entry Detail
PDB ID:
6ZM2
Keywords:
Title:
Crystal structure of the DEAH-box ATPase Prp2 in complex with ADP-BeF3 and ssRNA
Biological Source:
PDB Version:
Deposition Date:
2020-07-01
Release Date:
2021-04-21
Method Details:
Experimental Method:
Resolution:
2.10 Å
R-Value Free:
0.23
R-Value Work:
0.18
R-Value Observed:
0.18
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Putative mRNA splicing factor
Chain IDs:A
Chain Length:636
Number of Molecules:1
Biological Source:Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
Polymer Type:polyribonucleotide
Description:RNA (5'-R(P*UP*UP*UP*UP*UP*UP*U)-3')
Chain IDs:B
Chain Length:8
Number of Molecules:1
Biological Source:synthetic construct
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
CSO A CYS modified residue
Primary Citation
The structure of Prp2 bound to RNA and ADP-BeF 3 - reveals structural features important for RNA unwinding by DEAH-box ATPases.
Acta Crystallogr D Struct Biol 77 496 509 (2021)
PMID: 33825710 DOI: 10.1107/S2059798321001194

Abstact

Noncoding intron sequences present in precursor mRNAs need to be removed prior to translation, and they are excised via the spliceosome, a multimegadalton molecular machine composed of numerous protein and RNA components. The DEAH-box ATPase Prp2 plays a crucial role during pre-mRNA splicing as it ensures the catalytic activation of the spliceosome. Despite high structural similarity to other spliceosomal DEAH-box helicases, Prp2 does not seem to function as an RNA helicase, but rather as an RNA-dependent ribonucleoprotein particle-modifying ATPase. Recent crystal structures of the spliceosomal DEAH-box ATPases Prp43 and Prp22, as well as of the related RNA helicase MLE, in complex with RNA have contributed to a better understanding of how RNA binding and processivity might be achieved in this helicase family. In order to shed light onto the divergent manner of function of Prp2, an N-terminally truncated construct of Chaetomium thermophilum Prp2 was crystallized in the presence of ADP-BeF3- and a poly-U12 RNA. The refined structure revealed a virtually identical conformation of the helicase core compared with the ADP-BeF3-- and RNA-bound structure of Prp43, and only a minor shift of the C-terminal domains. However, Prp2 and Prp43 differ in the hook-loop and a loop of the helix-bundle domain, which interacts with the hook-loop and evokes a different RNA conformation immediately after the 3' stack. On replacing these loop residues in Prp43 by the Prp2 sequence, the unwinding activity of Prp43 was abolished. Furthermore, a putative exit tunnel for the γ-phosphate after ATP hydrolysis could be identified in one of the Prp2 structures.

Legend

Protein

Chemical

Disease

Primary Citation of related structures