5EEG

Crystal structure of carminomycin-4-O-methyltransferase DnrK in complex with tetrazole-SAH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.255 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Functional AdoMet Isosteres Resistant to Classical AdoMet Degradation Pathways.

Huber, T.D.Wang, F.Singh, S.Johnson, B.R.Zhang, J.Sunkara, M.Van Lanen, S.G.Morris, A.J.Phillips, G.N.Thorson, J.S.

(2016) Acs Chem.Biol. 11: 2484-2491

  • DOI: 10.1021/acschembio.6b00348
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • S-adenosyl-l-methionine (AdoMet) is an essential enzyme cosubstrate in fundamental biology with an expanding range of biocatalytic and therapeutic applications. We report the design, synthesis, and evaluation of stable, functional AdoMet isosteres th ...

    S-adenosyl-l-methionine (AdoMet) is an essential enzyme cosubstrate in fundamental biology with an expanding range of biocatalytic and therapeutic applications. We report the design, synthesis, and evaluation of stable, functional AdoMet isosteres that are resistant to the primary contributors to AdoMet degradation (depurination, intramolecular cyclization, and sulfonium epimerization). Corresponding biochemical and structural studies demonstrate the AdoMet surrogates to serve as competent enzyme cosubstrates and to bind a prototypical class I model methyltransferase (DnrK) in a manner nearly identical to AdoMet. Given this conservation in function and molecular recognition, the isosteres presented are anticipated to serve as useful surrogates in other AdoMet-dependent processes and may also be resistant to, and/or potentially even inhibit, other therapeutically relevant AdoMet-dependent metabolic transformations (such as the validated drug target AdoMet decarboxylase). This work also highlights the ability of the prototypical class I model methyltransferase DnrK to accept non-native surrogate acceptors as an enabling feature of a new high-throughput methyltransferase assay.


    Organizational Affiliation

    Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky , 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Carminomycin 4-O-methyltransferase DnrK
A, B
376Streptomyces peucetiusMutation(s): 0 
Gene Names: dnrK
EC: 2.1.1.292
Find proteins for Q06528 (Streptomyces peucetius)
Go to UniProtKB:  Q06528
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
S8M
Query on S8M

Download SDF File 
Download CCD File 
A, B
(2~{R},3~{R},4~{S},5~{S})-2-(6-aminopurin-9-yl)-5-[[(3~{S})-3-azanyl-3-(1~{H}-1,2,3,4-tetrazol-5-yl)propyl]sulfanylmethyl]oxolane-3,4-diol
C14 H20 N10 O3 S
PRVMDGXUVZTDPT-XLZJSAHRSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 60.562α = 90.00
b = 104.180β = 105.20
c = 62.986γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHENIXrefinement
PHENIXphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesU01 GM098248
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesR37 AI52188

Revision History 

  • Version 1.0: 2015-12-23
    Type: Initial release
  • Version 1.1: 2016-07-13
    Type: Database references
  • Version 1.2: 2016-09-28
    Type: Database references
  • Version 1.3: 2017-09-20
    Type: Author supporting evidence, Derived calculations