7S6B

Crystal structure of modular polyketide synthase apo-Lsd14 from the Lasalocid biosynthesis pathway, trapped in the transacylation step


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Modular polyketide synthase contains two reaction chambers that operate asynchronously.

Bagde, S.R.Mathews, I.I.Fromme, J.C.Kim, C.Y.

(2021) Science 374: 723-729

  • DOI: https://doi.org/10.1126/science.abi8532
  • Primary Citation of Related Structures:  
    7S6B, 7S6C, 7S6D

  • PubMed Abstract: 

    Type I modular polyketide synthases are homodimeric multidomain assembly line enzymes that synthesize a variety of polyketide natural products by performing polyketide chain extension and β-keto group modification reactions. We determined the 2.4-angstrom-resolution x-ray crystal structure and the 3.1-angstrom-resolution cryo–electron microscopy structure of the Lsd14 polyketide synthase, stalled at the transacylation and condensation steps, respectively. These structures revealed how the constituent domains are positioned relative to each other, how they rearrange depending on the step in the reaction cycle, and the specific interactions formed between the domains. Like the evolutionarily related mammalian fatty acid synthase, Lsd14 contains two reaction chambers, but only one chamber in Lsd14 has the full complement of catalytic domains, indicating that only one chamber produces the polyketide product at any given time.


  • Organizational Affiliation

    Department of Chemistry and Biochemistry, The University of Texas at El Paso, El Paso, TX 79968, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Polyketide synthase
A, B
944Streptomyces lasalocidiMutation(s): 0 
Gene Names: lsd14
UniProt
Find proteins for B6ZK67 (Streptomyces lasalocidi)
Explore B6ZK67 
Go to UniProtKB:  B6ZK67
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB6ZK67
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Polyketide synthase
C, D
544Streptomyces lasalocidiMutation(s): 0 
Gene Names: lsd14
UniProt
Find proteins for B6ZK67 (Streptomyces lasalocidi)
Explore B6ZK67 
Go to UniProtKB:  B6ZK67
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB6ZK67
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Polyketide synthase179Streptomyces lasalocidiMutation(s): 0 
Gene Names: lsd14
UniProt
Find proteins for B6ZK67 (Streptomyces lasalocidi)
Explore B6ZK67 
Go to UniProtKB:  B6ZK67
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB6ZK67
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.74α = 99.63
b = 92.85β = 94.93
c = 107.45γ = 106.07
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
autoPROCdata reduction
XDSdata scaling
autoPROCdata scaling
PHENIXphasing
Cootmodel building

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1R01GM138990
Department of Energy (DOE, United States)United StatesDE-AC02-76SF00515
Department of Energy (DOE, United States)United StatesDE-AC02-05CH11231
Department of Energy (DOE, United States)United StatesDE-AC02-06CH11357

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-03
    Type: Initial release
  • Version 1.1: 2021-11-17
    Changes: Database references