7C1K

Crystal structure of the starter condensation domain of rhizomide synthetase RzmA mutant R148A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.238 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Engineering and elucidation of the lipoinitiation process in nonribosomal peptide biosynthesis.

Zhong, L.Diao, X.Zhang, N.Li, F.Zhou, H.Chen, H.Bai, X.Ren, X.Zhang, Y.Wu, D.Bian, X.

(2021) Nat Commun 12: 296-296

  • DOI: https://doi.org/10.1038/s41467-020-20548-8
  • Primary Citation of Related Structures:  
    7C1H, 7C1K, 7C1L, 7C1P, 7C1R, 7C1S, 7C1U

  • PubMed Abstract: 

    Nonribosomal peptide synthetases containing starter condensation domains direct the biosynthesis of nonribosomal lipopeptides, which generally exhibit wide bioactivities. The acyl chain has strong impacts on bioactivity and toxicity, but the lack of an in-depth understanding of starter condensation domain-mediated lipoinitiation limits the bioengineering of NRPSs to obtain novel derivatives with desired acyl chains. Here, we show that the acyl chains of the lipopeptides rhizomide, holrhizin, and glidobactin were modified by engineering the starter condensation domain, suggesting a workable approach to change the acyl chain. Based on the structure of the mutated starter condensation domain of rhizomide biosynthetic enzyme RzmA in complex with octanoyl-CoA and related point mutation experiments, we identify a set of residues responsible for the selectivity of substrate acyl chains and extend the acyl chains from acetyl to palmitoyl. Furthermore, we illustrate three possible conformational states of starter condensation domains during the reaction cycle of the lipoinitiation process. Our studies provide further insights into the mechanism of lipoinitiation and the engineering of nonribosomal peptide synthetases.


  • Organizational Affiliation

    Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Non-ribosomal peptide synthetase modules
A, B, C, D
434Mycetohabitans rhizoxinica HKI 454Mutation(s): 1 
Gene Names: RBRH_01504
EC: 6.3.2
UniProt
Find proteins for E5ATN9 (Mycetohabitans rhizoxinica (strain DSM 19002 / CIP 109453 / HKI 454))
Explore E5ATN9 
Go to UniProtKB:  E5ATN9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE5ATN9
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.238 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.965α = 113.22
b = 89.701β = 90.09
c = 98.345γ = 89.92
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-25
    Type: Initial release
  • Version 1.1: 2021-01-27
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Database references, Refinement description