5MKI

Crystal structure of SmAP (LSm) protein from Methanococcus vannielii

Summary for 5MKI

• Entry DOI: 10.2210/pdb5mki/pdb
• Descriptor: Like-Sm ribonucleoprotein core, CALCIUM ION, 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, ... (4 entities in total)
• Functional Keywords: lsm, smap, rna binding protein
• Biological source: Methanococcus vannielii SB
• Total number of polymer chains: 14
• Total formula weight: 114745.38

Authors

Nikulin, A.D.,Lekontseva, N.V.,Tishchenko, S.V. (deposition date: 2016-12-05, release date: 2017-12-20, Last modification date: 2024-01-17)

Primary citation

Lekontseva, N.,Mikhailina, A.,Fando, M.,Kravchenko, O.,Balobanov, V.,Tishchenko, S.,Nikulin, A.
Crystal structures and RNA-binding properties of Lsm proteins from archaea Sulfolobus acidocaldarius and Methanococcus vannielii: Similarity and difference of the U-binding mode.
Biochimie, 175:1-12, 2020

PubMed Abstract: Sm and Sm-like (Lsm) proteins are considered as an evolutionary conserved family involved in RNA metabolism in organisms from bacteria and archaea to human. Currently, the function of Sm-like archaeal proteins (SmAP) is not well understood. Here, we report the crystal structures of SmAP proteins from Sulfolobus acidocaldarius and Methanococcus vannielii and a comparative analysis of their RNA-binding sites. Our data show that these SmAPs have only a uridine-specific RNA-binding site, unlike their bacterial homolog Hfq, which has three different RNA-binding sites. Moreover, variations in the amino acid composition of the U-binding sites of the two SmAPs lead to a difference in protein affinity for oligo(U) RNA. Surface plasmon resonance data and nucleotide-binding analysis confirm the high affinity of SmAPs for uridine nucleotides and oligo(U) RNA and the reduced affinity for adenines, guanines, cytidines and corresponding oligo-RNAs. In addition, we demonstrate that MvaSmAP1 and SacSmAP2 are capable of melting an RNA hairpin and, apparently, promote its interaction with complementary RNA.

PubMed: 32422160
DOI: 10.1016/j.biochi.2020.05.001

Experimental method

X-RAY DIFFRACTION (2.048 Å)