7E44

Crystal structure of NudC complexed with dpCoA

Summary for 7E44

• Entry DOI: 10.2210/pdb7e44/pdb
• Descriptor: NADH pyrophosphatase, ZINC ION, DEPHOSPHO COENZYME A, ... (4 entities in total)
• Functional Keywords: nudc, dpcoa., hydrolase
• Biological source: Escherichia coli BL21(DE3)
• Total number of polymer chains: 4
• Total formula weight: 121369.45

Authors

Zhou, W.,Guan, Z.Y.,Yin, P.,Zhang, D.L. (deposition date: 2021-02-10, release date: 2021-07-28, Last modification date: 2023-11-29)

Primary citation

Zhou, W.,Guan, Z.,Zhao, F.,Ye, Y.,Yang, F.,Yin, P.,Zhang, D.
Structural insights into dpCoA-RNA decapping by NudC.
Rna Biol., 18:244-253, 2021

PubMed Abstract: Various kinds of cap structures, such as mG, triphosphate groups, NAD and dpCoA, protect the 5' terminus of RNA. The cap structures bond covalently to RNA and affect its stability, translation, and transport. The removal of the caps is mainly executed by Nudix hydrolase family proteins, including Dcp2, RppH and NudC. Numerous efforts have been made to elucidate the mechanism underlying the removal of mG, triphosphate group, and NAD caps. In contrast, few studies related to the cleavage of the RNA dpCoA cap have been conducted. Here, we report the hydrolytic activity of NudC towards dpCoA and dpCoA-capped RNA . We also determined the crystal structure of dimeric NudC in complex with dpCoA at 2.0 Å resolution. Structural analysis revealed that dpCoA is recognized and hydrolysed in a manner similar to NAD. In addition, NudC may also remove other dinucleotide derivative caps of RNA, which comprise the AMP moieties. NudC homologs in and exhibited similar dpCoA decapping (deCoAping) activity. These results together indicate a conserved mechanism underpinning the hydrolysis of dpCoA-capped RNA in both prokaryotes and eukaryotes.

PubMed: 34074215
DOI: 10.1080/15476286.2021.1936837

Experimental method

X-RAY DIFFRACTION (2 Å)