Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 82.94 kDa 
• Atom Count: 5855 
• Modelled Residue Count: 684 
• Deposited Residue Count: 734 
• Unique protein chains: 1

4WXH

Carminomycin-4-O-methyltransferase (DnrK) variant (298Ser insert) in complex with S-adenosyl-L-homocysteine (SAH) and aclacinomycin T

• PDB DOI: 10.2210/pdb4WXH/pdb

• Classification: TRANSFERASE
• Organism(s): Streptomyces peucetius
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-11-13 Released: 2015-07-29 
• Deposition Author(s): Metsa-Ketela, M., Niiranen, L.
• Funding Organization(s): Academy of Finland

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.234 
• R-Value Work: 0.193 
• R-Value Observed: 0.195 

Literature

Divergent evolution of an atypical S-adenosyl-l-methionine-dependent monooxygenase involved in anthracycline biosynthesis.

Grocholski, T., Dinis, P., Niiranen, L., Niemi, J., Metsa-Ketela, M.

(2015) Proc Natl Acad Sci U S A 112: 9866-9871

• PubMed: 26216966 
• DOI: 10.1073/pnas.1501765112
• Primary Citation of Related Structures:  
  4WXH


• PubMed Abstract: 
  

Bacterial secondary metabolic pathways are responsible for the biosynthesis of thousands of bioactive natural products. Many enzymes residing in these pathways have evolved to catalyze unusual chemical transformations, which is facilitated by an evolutionary pressure promoting chemical diversity. Such divergent enzyme evolution has been observed in S-adenosyl-L-methionine (SAM)-dependent methyltransferases involved in the biosynthesis of anthracycline anticancer antibiotics; whereas DnrK from the daunorubicin pathway is a canonical 4-O-methyltransferase, the closely related RdmB (52% sequence identity) from the rhodomycin pathways is an atypical 10-hydroxylase that requires SAM, a thiol reducing agent, and molecular oxygen for activity. Here, we have used extensive chimeragenesis to gain insight into the functional differentiation of RdmB and show that insertion of a single serine residue to DnrK is sufficient for introduction of the monooxygenation activity. The crystal structure of DnrK-Ser in complex with aclacinomycin T and S-adenosyl-L-homocysteine refined to 1.9-Å resolution revealed that the inserted serine S297 resides in an α-helical segment adjacent to the substrate, but in a manner where the side chain points away from the active site. Further experimental work indicated that the shift in activity is mediated by rotation of a preceding phenylalanine F296 toward the active site, which blocks a channel to the surface of the protein that is present in native DnrK. The channel is also closed in RdmB and may be important for monooxygenation in a solvent-free environment. Finally, we postulate that the hydroxylation ability of RdmB originates from a previously undetected 10-decarboxylation activity of DnrK.

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Organizational Affiliation: 

Department of Biochemistry, University of Turku, FIN-20014 Turku, Finland [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carminomycin 4-O-methyltransferase DnrK	A, B	367	Streptomyces peucetius	Mutation(s): 0  Gene Names: dnrK EC: 2.1.1.292
UniProt
Find proteins for Q06528 (Streptomyces peucetius) Explore Q06528  Go to UniProtKB:  Q06528

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3VL	D [auth A], J [auth B]	methyl (1R,2R,4S)-2-ethyl-2,5,7-trihydroxy-6,11-dioxo-4-{[2,3,6-trideoxy-3-(dimethylamino)-alpha-L-lyxo-hexopyranosyl]oxy}-1,2,3,4,6,11-hexahydrotetracene-1-carboxylate C30 H35 N O10 LJZPVWKMAYDYAS-QKKPTTNWSA-N
SAH	C [auth A], I [auth B]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N
DTU	E [auth A]	(2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL C4 H10 O2 S2 VHJLVAABSRFDPM-ZXZARUISSA-N
SO4	F [auth A], G [auth A], H [auth A], K [auth B], L [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.234 
• R-Value Work: 0.193 
• R-Value Observed: 0.195 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.803	α = 90
b = 100.995	β = 102.47
c = 62.398	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
MOLREP	phasing
XDS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2014-11-13 
• Released Date: 2015-07-29 
Deposition Author(s): Metsa-Ketela, M., Niiranen, L.

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Funding Organization	Location	Grant Number
Academy of Finland	Finland	136060

Revision History  

• Version 1.0: 2015-07-29
  Type: Initial release
  
• Version 1.1: 2015-08-12
  Changes: Database references
• Version 1.2: 2015-08-19
  Changes: Database references
• Version 1.3: 2018-02-28
  Changes: Structure summary