3T5Y

Crystal structure of CerJ from Streptomyces tendae - malonic acid covalently linked to the catalytic Cystein C116


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.170 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

A ketosynthase homolog uses malonyl units to form esters in cervimycin biosynthesis.

Bretschneider, T.Zocher, G.Unger, M.Scherlach, K.Stehle, T.Hertweck, C.

(2011) Nat Chem Biol 8: 154-161

  • DOI: https://doi.org/10.1038/nchembio.746
  • Primary Citation of Related Structures:  
    3S3L, 3T5Y, 3T6S, 3T8E

  • PubMed Abstract: 

    Ketosynthases produce the carbon backbones of a vast number of biologically active polyketides by catalyzing Claisen condensations of activated acyl and malonyl building blocks. Here we report that a ketosynthase homolog from Streptomyces tendae, CerJ, unexpectedly forms malonyl esters during the biosynthesis of cervimycin, a glycoside antibiotic against methicillin-resistant Staphylococcus aureus (MRSA). Deletion of cerJ yielded a substantially more active cervimycin variant lacking the malonyl side chain, and in vitro biotransformations revealed that CerJ is capable of transferring malonyl, methylmalonyl and dimethylmalonyl units onto the glycoside. According to phylogenetic analyses and elucidation of the crystal structure, CerJ is functionally and structurally positioned between the ketosynthase catalyzing Claisen condensations and acyl-ACP shuttles, and it features a noncanonical catalytic triad. Site-directed mutagenesis and structures of CerJ in complex with substrates not only allowed us to establish a model for the reaction mechanism but also provided insights into the evolution of this important subclass of the thiolase superfamily.


  • Organizational Affiliation

    Leibniz Institute for Natural Product Research and Infection Biology, Jena, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CerJ357Streptomyces tendaeMutation(s): 0 
UniProt
Find proteins for H2L2M1 (Streptomyces tendae)
Explore H2L2M1 
Go to UniProtKB:  H2L2M1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupH2L2M1
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
CerJ357Streptomyces tendaeMutation(s): 0 
UniProt
Find proteins for H2L2M1 (Streptomyces tendae)
Explore H2L2M1 
Go to UniProtKB:  H2L2M1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupH2L2M1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MCS
Query on MCS
B
L-PEPTIDE LINKINGC6 H9 N O5 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.170 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.04α = 90
b = 106.04β = 90
c = 121.69γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-12-21
    Type: Initial release
  • Version 1.1: 2012-01-11
    Changes: Database references
  • Version 1.2: 2012-02-01
    Changes: Database references
  • Version 1.3: 2017-11-08
    Changes: Refinement description