5Y6C

Crystal structure of ZmASCH S128A mutant protein from Zymomonas mobilis

Summary for 5Y6C

• Entry DOI: 10.2210/pdb5y6c/pdb
• Descriptor: Helix-turn-helix domain-containing protein, CHLORIDE ION (3 entities in total)
• Functional Keywords: rna cleavage activity, rna binding protein
• Biological source: Zymomonas mobilis subsp. mobilis (strain ATCC 10988 / DSM 424 / LMG 404 / NCIMB 8938 / NRRL B-806 / ZM1)
• Total number of polymer chains: 2
• Total formula weight: 34745.50

Authors

Park, S.-Y.,Kim, J.-S. (deposition date: 2017-08-11, release date: 2018-07-18, Last modification date: 2023-11-22)

Primary citation

Kim, B.N.,Shin, M.,Ha, S.C.,Park, S.Y.,Seo, P.W.,Hofmann, A.,Kim, J.S.
Crystal structure of an ASCH protein from Zymomonas mobilis and its ribonuclease activity specific for single-stranded RNA.
Sci Rep, 7:12303-12303, 2017

PubMed Abstract: Activating signal cointegrator-1 homology (ASCH) domains were initially reported in human as a part of the ASC-1 transcriptional regulator, a component of a putative RNA-interacting protein complex; their presence has now been confirmed in a wide range of organisms. Here, we have determined the trigonal and monoclinic crystal structures of an ASCH domain-containing protein from Zymomonas mobilis (ZmASCH), and analyzed the structural determinants of its nucleic acid processing activity. The protein has a central β-barrel structure with several nearby α-helices. Positively charged surface patches form a cleft that runs through the pocket formed between the β-barrel and the surrounding α-helices. We further demonstrate by means of in vitro assays that ZmASCH binds nucleic acids, and degrades single-stranded RNAs in a magnesium ion-dependent manner with a cleavage preference for the phosphodiester bond between the pyrimidine and adenine nucleotides. ZmASCH also removes a nucleotide at the 5'-end. Mutagenesis studies, guided by molecular dynamics simulations, confirmed that three residues (Tyr47, Lys53, and Ser128) situated in the cleft contribute to nucleic acid-binding and RNA cleavage activities. These structural and biochemical studies imply that prokaryotic ASCH may function to control the cellular RNA amount.

PubMed: 28951575
DOI: 10.1038/s41598-017-12186-w

Experimental method

X-RAY DIFFRACTION (2.398 Å)