5EEG | pdb_00005eeg

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 
    0.248 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.197 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 
    0.200 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.5 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: https://doi.org/10.1021/acschembio.6b00348
  • Primary Citation Related Structures: 
    5EEG, 5EEH

  • 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 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.

Macromolecule Content 

  • Total Structure Weight: 82.82 kDa 
  • Atom Count: 5,683 
  • Modeled Residue Count: 665 
  • Deposited Residue Count: 752 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Carminomycin 4-O-methyltransferase DnrK
A, B
376Streptomyces peucetiusMutation(s): 0 
Gene Names: dnrK
EC: 2.1.1.292
UniProt
Find proteins for Q06528 (Streptomyces peucetius)
Explore Q06528 
Go to UniProtKB:  Q06528
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ06528
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
S8M

Query on S8M



Download:Ideal Coordinates CCD File
C [auth A],
D [auth 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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free:  0.248 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.197 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 0.200 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.562α = 90
b = 104.18β = 105.2
c = 62.986γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesU01 GM098248
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR37 AI52188

Revision History  (Full details and data files)

  • Version 1.0: 2015-12-23
    Type: Initial release
  • Version 1.1: 2016-07-13
    Changes: Database references
  • Version 1.2: 2016-09-28
    Changes: Database references
  • Version 1.3: 2017-09-20
    Changes: Author supporting evidence, Derived calculations
  • Version 1.4: 2019-12-11
    Changes: Author supporting evidence
  • Version 1.5: 2023-09-27
    Changes: Data collection, Database references, Refinement description