5OSY

Human Decapping Scavenger enzyme (hDcpS) in complex with m7G(5'S)ppSp(5'S)G mRNA 5' cap analog


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.181 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

5'-Phosphorothiolate Dinucleotide Cap Analogues: Reagents for Messenger RNA Modification and Potent Small-Molecular Inhibitors of Decapping Enzymes.

Wojtczak, B.A.Sikorski, P.J.Fac-Dabrowska, K.Nowicka, A.Warminski, M.Kubacka, D.Nowak, E.Nowotny, M.Kowalska, J.Jemielity, J.

(2018) J Am Chem Soc 140: 5987-5999

  • DOI: 10.1021/jacs.8b02597
  • Primary Citation of Related Structures:  
    5OSX, 5OSY

  • PubMed Abstract: 
  • The 5' cap consists of 7-methylguanosine (m 7 G) linked by a 5'-5'-triphosphate bridge to messenger RNA (mRNA) and acts as the master regulator of mRNA turnover and translation initiation in eukaryotes. Cap analogues that influence mRNA translation and turnover (either as small molecules or as part of an RNA transcript) are valuable tools for studying gene expression, which is often also of therapeutic relevance ...

    The 5' cap consists of 7-methylguanosine (m 7 G) linked by a 5'-5'-triphosphate bridge to messenger RNA (mRNA) and acts as the master regulator of mRNA turnover and translation initiation in eukaryotes. Cap analogues that influence mRNA translation and turnover (either as small molecules or as part of an RNA transcript) are valuable tools for studying gene expression, which is often also of therapeutic relevance. Here, we synthesized a series of 15 dinucleotide cap (m 7 GpppG) analogues containing a 5'-phosphorothiolate (5'-PSL) moiety (i.e., an O-to-S substitution within the 5'-phosphoester) and studied their biological properties in the context of three major cap-binding proteins: translation initiation factor 4E (eIF4E) and two decapping enzymes, DcpS and Dcp2. While the 5'-PSL moiety was neutral or slightly stabilizing for cap interactions with eIF4E, it significantly influenced susceptibility to decapping. Replacing the γ-phosphoester with the 5'-PSL moiety (γ-PSL) prevented β-γ-pyrophosphate bond cleavage by DcpS and conferred strong inhibitory properties. Combining the γ-PSL moiety with α-PSL and β-phosphorothioate (PS) moiety afforded first cap-derived hDcpS inhibitor with low nanomolar potency. Susceptibility to Dcp2 and translational properties were studied after incorporation of the new analogues into mRNA transcripts by RNA polymerase. Transcripts containing the γ-PSL moiety were resistant to cleavage by Dcp2. Surprisingly, superior translational properties were observed for mRNAs containing the α-PSL moiety, which were Dcp2-susceptible. The overall protein expression measured in HeLa cells for this mRNA was comparable to mRNA capped with the translation augmenting β-PS analogue reported previously. Overall, our study highlights 5'-PSL as a synthetically accessible cap modification, which, depending on the substitution site, can either reduce susceptibility to decapping or confer superior translational properties on the mRNA. The 5'-PSL-analogues may find application as reagents for the preparation of efficiently expressed mRNA or for investigation of the role of decapping enzymes in mRNA processing or neuromuscular disorders associated with decapping.


    Organizational Affiliation

    Centre of New Technologies , University of Warsaw , Banacha 2c Street , 02-097 Warsaw , Poland.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
m7GpppX diphosphataseA, B301Homo sapiensMutation(s): 0 
Gene Names: DCPSDCS1HINT5HSPC015
EC: 3.6.1.59
Find proteins for Q96C86 (Homo sapiens)
Explore Q96C86 
Go to UniProtKB:  Q96C86
NIH Common Fund Data Resources
PHAROS:  Q96C86
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AJQ
Query on AJQ

Download Ideal Coordinates CCD File 
C [auth A], D [auth B][(2~{S},3~{S},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanylidene-1~{H}-purin-7-ium-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylsulfanyl-[[[(2~{S},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylsulfanyl-oxidanyl-phosphoryl]oxy-sulfanyl-phosphoryl]oxy-phosphinic acid
C21 H30 N10 O15 P3 S3
UOUACWJATBZTPY-ACTLBPNMSA-O
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth B], F [auth B], G [auth B], H [auth B], I [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
AJQIC50:  44.70000076293945   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.181 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.904α = 90
b = 84.549β = 90
c = 126.16γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Higher EducationPolandDI2012 024842
Foundation for Polish SciencePolandTEAM/2016-2/13

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-02
    Type: Initial release
  • Version 1.1: 2018-05-09
    Changes: Data collection, Database references
  • Version 1.2: 2018-05-16
    Changes: Data collection, Database references