Structure of the CcbJ Methyltransferase from Streptomyces caelestis

Experimental Data Snapshot

  • Resolution: 2.70 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 

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This is version 1.2 of the entry. See complete history


Structure and possible mechanism of the CcbJ methyltransferase from Streptomyces caelestis.

Bauer, J.Ondrovicova, G.Najmanova, L.Pevala, V.Kamenik, Z.Kostan, J.Janata, J.Kutejova, E.

(2014) Acta Crystallogr D Biol Crystallogr 70: 943-957

  • DOI: https://doi.org/10.1107/S139900471303397X
  • Primary Citation of Related Structures:  
    4HGY, 4HGZ, 4HH4

  • PubMed Abstract: 

    The S-adenosyl-L-methionine (SAM)-dependent methyltransferase CcbJ from Streptomyces caelestis catalyzes one of the final steps in the biosynthesis of the antibiotic celesticetin, methylation of the N atom of its proline moiety, which greatly enhances the activity of the antibiotic. Since several celesticetin variants exist, this enzyme may be able to act on a variety of substrates. The structures of CcbJ determined by MAD phasing at 3.0 Å resolution, its native form at 2.7 Å resolution and its complex with S-adenosyl-L-homocysteine (SAH) at 2.9 Å resolution are reported here. Based on these structures, three point mutants, Y9F, Y17F and F117G, were prepared in order to study its behaviour as well as docking simulations of both CcbJ-SAM-substrate and CcbJ-SAH-product complexes. The structures show that CcbJ is a class I SAM-dependent methyltransferase with a wide active site, thereby suggesting that it may accommodate a number of different substrates. The mutation results show that the Y9F and F117G mutants are almost non-functional, while the Y17F mutant has almost half of the wild-type activity. In combination with the docking studies, these results suggest that Tyr9 and Phe117 are likely to help to position the substrate for the methyl-transfer reaction and that Tyr9 may also facilitate the reaction by removing an H(+) ion. Tyr17, on the other hand, seems to operate by helping to stabilize the SAM cofactor.

  • Organizational Affiliation

    Institute of Molecular Biology, Slovak Academy of Sciences, 851 45 Bratislava, Slovakia.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D, E
A, B, C, D, E, F
276Streptomyces caelestisMutation(s): 0 
Gene Names: ccbJ
Find proteins for E9JES0 (Streptomyces caelestis)
Explore E9JES0 
Go to UniProtKB:  E9JES0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE9JES0
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on SO4

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth A]
J [auth B]
P [auth E]
G [auth A],
H [auth A],
I [auth A],
J [auth B],
P [auth E],
Q [auth E],
S [auth F],
T [auth F]
O4 S
Query on EDO

Download Ideal Coordinates CCD File 
K [auth B],
M [auth C],
O [auth D],
R [auth E]
C2 H6 O2
Query on LI

Download Ideal Coordinates CCD File 
L [auth C],
N [auth D]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.70 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 168.02α = 90
b = 244.55β = 90
c = 117.85γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-10-30
    Type: Initial release
  • Version 1.1: 2014-04-16
    Changes: Database references
  • Version 1.2: 2020-02-26
    Changes: Data collection, Database references