5EEH

Crystal structure of carminomycin-4-O-methyltransferase DnrK in complex with SAH and 2-chloro-4-nitrophenol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.155 

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Ligand Structure Quality Assessment 


This is version 1.4 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:  
    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) ...

    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

    Center for Pharmaceutical Research and Innovation (CPRI), College of Pharmacy, University of Kentucky , 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Carminomycin 4-O-methyltransferase DnrKA, B, C376Streptomyces 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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAH
Query on SAH

Download Ideal Coordinates CCD File 
D [auth A],
P [auth B],
Z [auth C]
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
P9P
Query on P9P

Download Ideal Coordinates CCD File 
AA [auth C],
BA [auth C],
CA [auth C],
E [auth A],
F [auth A],
AA [auth C],
BA [auth C],
CA [auth C],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
O [auth B],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
U [auth B]
2-chloranyl-4-nitro-phenol
C6 H4 Cl N O3
BOFRXDMCQRTGII-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
DA [auth C],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
DA [auth C],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
V [auth B],
W [auth B],
X [auth B],
Y [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 123.347α = 90
b = 110.678β = 120.24
c = 116.869γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata 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: 2015-12-16
    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