5Y6B

Crystal structure of ZmASCH Y47F mutant protein from Zymomonas mobilis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.223 

wwPDB Validation 3D Report Full Report



Literature

Crystal structure of an ASCH protein from Zymomonas mobilis and its ribonuclease activity specific for single-stranded RNA.

Kim, B.N.Shin, M.Ha, S.C.Park, S.Y.Seo, P.W.Hofmann, A.Kim, J.S.

(2017) Sci Rep 7: 12303-12303

  • DOI: 10.1038/s41598-017-12186-w
  • Primary Citation of Related Structures:  
    5GUS, 5GUQ, 5Y6C, 5Y6B

  • 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 ran ...

    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.


    Organizational Affiliation

    Department of Chemistry, Chonnam National University, Gwangju, 61186, Republic of Korea. jsunkim@chonnam.ac.kr.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Helix-turn-helix domain-containing proteinABCD149Zymomonas mobilis subsp. mobilis ATCC 10988Mutation(s): 1 
Gene Names: Zmob_0380
Find proteins for A0A0H3G0N3 (Zymomonas mobilis subsp. mobilis (strain ATCC 10988 / DSM 424 / LMG 404 / NCIMB 8938 / NRRL B-806 / ZM1))
Explore A0A0H3G0N3 
Go to UniProtKB:  A0A0H3G0N3
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.223 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.126α = 90
b = 65.963β = 90.18
c = 91.857γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (Korea)Korea, Republic Of2014R1A2A2A01004915
National Research Foundation (Korea)Korea, Republic Of2014R1A4A1003642

Revision History 

  • Version 1.0: 2018-07-18
    Type: Initial release