Crystal structure of saAcmM involved in actinomycin biosynthesis

Experimental Data Snapshot

  • Resolution: 2.23 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 

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This is version 1.3 of the entry. See complete history


Ketonization of Proline Residues in the Peptide Chains of Actinomycins by a 4-Oxoproline Synthase.

Semsary, S.Crnovcic, I.Driller, R.Vater, J.Loll, B.Keller, U.

(2018) Chembiochem 19: 706-715

  • DOI: https://doi.org/10.1002/cbic.201700666
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    X-type actinomycins (Acms) contain 4-hydroxyproline (Acm X 0 ) or 4-oxoproline (Acm X 2 ) in their β-pentapeptide lactone rings, whereas their α ring contains proline. We demonstrate that these Acms are formed through asymmetric condensation of Acm half molecules (Acm halves) containing proline with 4-hydroxyproline- or 4-oxoproline-containing Acm halves. In turn, we show-using an artificial Acm half analogue (PPL 1) with proline in its peptide chain-their conversion into the 4-hydroxyproline- and 4-oxoproline-containing Acm halves, PPL 0 and PPL 2, in mycelial suspensions of Streptomyces antibioticus. Two responsible genes of the Acm X biosynthetic gene cluster of S. antibioticus, saacmM and saacmN, encoding a cytochrome P450 monooxygenase (Cyp) and a ferredoxin were identified. After coexpression in Escherichia coli, their gene products converted PPL 1 into PPL 0 and PPL 2 in vivo as well as in situ in permeabilized cell of the transformed E. coli strain in conjunction with the host-encoded ferredoxin reductase in a NADH (NADPH)-dependent manner. saAcmM has high sequence similarity to the Cyp107Z (Ema) family of Cyps, which can convert avermectin B1 into its keto derivative, 4''-oxoavermectin B1. Determination of the structure of saAcmM reveals high similarity to the Ema structure but with significant differences in residues decorating their active sites, which defines saAcmM and its orthologues as a distinct new family of peptidylprolineketonizing Cyp.

  • Organizational Affiliation

    Institut für Chemie, Biologische Chemie, Technische Universität Berlin, Müller-Breslau-Strasse 10, 10623, Berlin, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
saAcmM435Streptomyces antibioticusMutation(s): 0 
Find proteins for A0A1S9NIH4 (Streptomyces antibioticus)
Explore A0A1S9NIH4 
Go to UniProtKB:  A0A1S9NIH4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1S9NIH4
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.23 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 
  • Space Group: C 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.254α = 90
b = 129.539β = 90
c = 111.611γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-01-24
    Type: Initial release
  • Version 1.1: 2018-04-18
    Changes: Data collection, Database references
  • Version 1.2: 2019-10-16
    Changes: Data collection
  • Version 1.3: 2024-01-17
    Changes: Data collection, Database references, Refinement description