9J56 | pdb_00009j56

Functional Investigation of the SAM-Dependent Methyltransferases Rdmb in Anthracycline Biosynthesis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.259 (Depositor), 0.263 (DCC) 
  • R-Value Work: 
    0.214 (Depositor), 0.228 (DCC) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Functional investigation of the SAM-dependent methyltransferase RdmB in anthracycline biosynthesis.

Sang, M.Yang, Q.Guo, J.Feng, P.Ma, W.Zhang, W.

(2025) Synth Syst Biotechnol 10: 102-109

  • DOI: https://doi.org/10.1016/j.synbio.2024.09.002
  • Primary Citation Related Structures: 
    9J56

  • PubMed Abstract: 

    A novel sub-class of S -adenosyl-l-methionine (SAM)-dependent methyltransferases catalyze atypical chemical transformations in the biosynthesis of anthracyclines. Exemplified by RdmB from Streptomyces purpurascens, it was found with 10-decarboxylative hydroxylation activity on anthracyclines. We herein investigated the catalytic activities of RdmB and discovered a previously unknown 4- O -methylation activity. The site-directed mutagenesis studies proved that the residue at position R307 and N260 are vital for the decarboxylative hydroxylation and 4- O -methylation, respectively, which define two distinct catalytic centers in RdmB. Furthermore, the multifunctionality of RdmB activity was found as cofactor-dependent and stepwise. Our findings expand the versatility and importance of methyltransferases and should aid studies to enrich the structural diversity and bioactivities of anthracyclines.


  • Organizational Affiliation
    • State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China.

Macromolecule Content 

  • Total Structure Weight: 81.47 kDa 
  • Atom Count: 5,270 
  • Modeled Residue Count: 669 
  • Deposited Residue Count: 748 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Aclacinomycin 10-hydroxylase RdmB
A, B
374Streptomyces purpurascensMutation(s): 0 
Gene Names: rdmB
EC: 4.1.1 (PDB Primary Data), 2.1.1 (UniProt)
UniProt
Find proteins for Q54527 (Streptomyces purpurascens)
Explore Q54527 
Go to UniProtKB:  Q54527
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ54527
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.259 (Depositor), 0.263 (DCC) 
  • R-Value Work:  0.214 (Depositor), 0.228 (DCC) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.997α = 90
b = 79.997β = 90
c = 234.203γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-06
    Type: Initial release